Starting phenix.real_space_refine on Wed Aug 5 08:10:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9rv1_54282/08_2026/9rv1_54282.cif Found real_map, /net/cci-nas-00/data/ceres_data/9rv1_54282/08_2026/9rv1_54282.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9rv1_54282/08_2026/9rv1_54282.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9rv1_54282/08_2026/9rv1_54282.map" model { file = "/net/cci-nas-00/data/ceres_data/9rv1_54282/08_2026/9rv1_54282.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9rv1_54282/08_2026/9rv1_54282.cif" } resolution = 2.62 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.020 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: 6 Type Number sf(0) Gaussians P 9 5.49 5 Mg 1 5.21 5 S 54 5.16 5 C 5602 2.51 5 N 1536 2.21 5 O 1630 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8832 Number of models: 1 Model: "" Number of chains: 6 Chain: "1" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 120 Classifications: {'RNA': 6} Modifications used: {'rna3p_pyr': 6} Link IDs: {'rna3p': 5} Chain: "A" Number of atoms: 2342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2342 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 27, 'TRANS': 279} Chain breaks: 1 Chain: "B" Number of atoms: 2826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2826 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 9, 'TRANS': 336} Chain breaks: 4 Chain: "C" Number of atoms: 443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 443 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 1, 'TRANS': 50} Chain: "H" Number of atoms: 3061 Number of conformers: 1 Conformer: "" Number of residues, atoms: 378, 3061 Classifications: {'peptide': 378} Link IDs: {'PTRANS': 14, 'TRANS': 363} Chain breaks: 2 Chain: "H" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 40 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2, 'water': 8} Link IDs: {None: 9} Time building chain proxies: 1.67, per 1000 atoms: 0.19 Number of scatterers: 8832 At special positions: 0 Unit cell: (76.33, 111.352, 123.026, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 54 16.00 P 9 15.00 Mg 1 11.99 O 1630 8.00 N 1536 7.00 C 5602 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 0.52 Conformation dependent library (CDL) restraints added in 409.8 milliseconds 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2068 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 5 sheets defined 62.5% alpha, 6.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'A' and resid 62 through 72 Processing helix chain 'A' and resid 117 through 131 Processing helix chain 'A' and resid 139 through 160 Processing helix chain 'A' and resid 164 through 186 Processing helix chain 'A' and resid 196 through 218 Processing helix chain 'A' and resid 224 through 236 Processing helix chain 'A' and resid 239 through 248 Processing helix chain 'A' and resid 250 through 255 Processing helix chain 'A' and resid 256 through 271 Processing helix chain 'A' and resid 273 through 284 removed outlier: 3.611A pdb=" N THR A 283 " --> pdb=" O ARG A 279 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU A 284 " --> pdb=" O LEU A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 312 removed outlier: 5.576A pdb=" N CYS A 294 " --> pdb=" O CYS A 290 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N HIS A 295 " --> pdb=" O ALA A 291 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N GLY A 297 " --> pdb=" O GLN A 293 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ARG A 306 " --> pdb=" O GLU A 302 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ARG A 309 " --> pdb=" O ALA A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 328 Processing helix chain 'A' and resid 332 through 343 removed outlier: 3.509A pdb=" N HIS A 343 " --> pdb=" O LEU A 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 20 Processing helix chain 'B' and resid 21 through 29 Processing helix chain 'B' and resid 57 through 68 Processing helix chain 'B' and resid 78 through 98 removed outlier: 3.581A pdb=" N ARG B 93 " --> pdb=" O GLN B 89 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA B 94 " --> pdb=" O SER B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 126 removed outlier: 3.518A pdb=" N ASN B 121 " --> pdb=" O VAL B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 155 removed outlier: 3.555A pdb=" N LYS B 140 " --> pdb=" O ASP B 136 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU B 144 " --> pdb=" O LYS B 140 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASP B 155 " --> pdb=" O VAL B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 182 removed outlier: 4.617A pdb=" N PHE B 170 " --> pdb=" O TRP B 166 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LYS B 181 " --> pdb=" O LYS B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 186 No H-bonds generated for 'chain 'B' and resid 184 through 186' Processing helix chain 'B' and resid 187 through 198 removed outlier: 4.380A pdb=" N LEU B 191 " --> pdb=" O LEU B 187 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG B 193 " --> pdb=" O LYS B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 223 Processing helix chain 'B' and resid 225 through 239 Processing helix chain 'B' and resid 244 through 262 removed outlier: 3.757A pdb=" N TYR B 254 " --> pdb=" O MET B 250 " (cutoff:3.500A) Proline residue: B 257 - end of helix Processing helix chain 'B' and resid 267 through 274 removed outlier: 3.571A pdb=" N LEU B 271 " --> pdb=" O THR B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 289 removed outlier: 3.924A pdb=" N GLU B 281 " --> pdb=" O MET B 277 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N VAL B 282 " --> pdb=" O GLN B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 301 Processing helix chain 'B' and resid 301 through 308 Processing helix chain 'B' and resid 310 through 333 removed outlier: 3.821A pdb=" N LYS B 316 " --> pdb=" O LEU B 312 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LEU B 317 " --> pdb=" O ILE B 313 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N LYS B 318 " --> pdb=" O LEU B 314 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N ILE B 319 " --> pdb=" O GLU B 315 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ILE B 320 " --> pdb=" O LYS B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 350 Processing helix chain 'B' and resid 356 through 371 Processing helix chain 'C' and resid 28 through 32 Processing helix chain 'C' and resid 50 through 63 removed outlier: 3.628A pdb=" N HIS C 63 " --> pdb=" O GLU C 59 " (cutoff:3.500A) Processing helix chain 'H' and resid 39 through 43 Processing helix chain 'H' and resid 45 through 49 Processing helix chain 'H' and resid 53 through 63 removed outlier: 3.733A pdb=" N ALA H 59 " --> pdb=" O GLU H 55 " (cutoff:3.500A) Processing helix chain 'H' and resid 69 through 81 Proline residue: H 77 - end of helix removed outlier: 3.749A pdb=" N LEU H 81 " --> pdb=" O PRO H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 94 through 107 removed outlier: 3.553A pdb=" N VAL H 98 " --> pdb=" O GLY H 94 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE H 99 " --> pdb=" O LYS H 95 " (cutoff:3.500A) Processing helix chain 'H' and resid 122 through 137 Processing helix chain 'H' and resid 153 through 163 removed outlier: 3.945A pdb=" N ASP H 157 " --> pdb=" O SER H 153 " (cutoff:3.500A) Processing helix chain 'H' and resid 172 through 182 Processing helix chain 'H' and resid 197 through 204 removed outlier: 3.610A pdb=" N GLN H 204 " --> pdb=" O LYS H 200 " (cutoff:3.500A) Processing helix chain 'H' and resid 204 through 218 Processing helix chain 'H' and resid 235 through 241 removed outlier: 3.583A pdb=" N LYS H 241 " --> pdb=" O PRO H 237 " (cutoff:3.500A) Processing helix chain 'H' and resid 273 through 285 Processing helix chain 'H' and resid 296 through 310 Processing helix chain 'H' and resid 322 through 335 removed outlier: 3.554A pdb=" N LEU H 327 " --> pdb=" O GLN H 323 " (cutoff:3.500A) Processing helix chain 'H' and resid 367 through 376 removed outlier: 3.568A pdb=" N ALA H 376 " --> pdb=" O LEU H 372 " (cutoff:3.500A) Processing helix chain 'H' and resid 393 through 407 removed outlier: 3.513A pdb=" N ASP H 405 " --> pdb=" O ASN H 401 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 317 through 320 Processing sheet with id=AA2, first strand: chain 'B' and resid 265 through 266 removed outlier: 3.539A pdb=" N MET B 265 " --> pdb=" O GLU C 40 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 337 through 339 Processing sheet with id=AA4, first strand: chain 'H' and resid 145 through 148 removed outlier: 6.637A pdb=" N LEU H 117 " --> pdb=" O ILE H 194 " (cutoff:3.500A) removed outlier: 8.121A pdb=" N ASP H 196 " --> pdb=" O LEU H 117 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N MET H 119 " --> pdb=" O ASP H 196 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N LEU H 86 " --> pdb=" O ILE H 249 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 314 through 317 removed outlier: 6.196A pdb=" N ILE H 315 " --> pdb=" O VAL H 342 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N VAL H 290 " --> pdb=" O LEU H 341 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N ALA H 343 " --> pdb=" O VAL H 290 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N ILE H 292 " --> pdb=" O ALA H 343 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N GLN H 289 " --> pdb=" O ILE H 358 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N PHE H 360 " --> pdb=" O GLN H 289 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N VAL H 291 " --> pdb=" O PHE H 360 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ASN H 357 " --> pdb=" O LEU H 386 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N ILE H 388 " --> pdb=" O ASN H 357 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ALA H 359 " --> pdb=" O ILE H 388 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N PHE H 390 " --> pdb=" O ALA H 359 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N ASN H 361 " --> pdb=" O PHE H 390 " (cutoff:3.500A) removed outlier: 9.143A pdb=" N SER H 412 " --> pdb=" O LEU H 262 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N GLN H 264 " --> pdb=" O SER H 412 " (cutoff:3.500A) 467 hydrogen bonds defined for protein. 1380 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: 1.30 Time building geometry restraints manager: 0.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1840 1.33 - 1.45: 2001 1.45 - 1.57: 5065 1.57 - 1.69: 20 1.69 - 1.81: 84 Bond restraints: 9010 Sorted by residual: bond pdb=" C LEU A 249 " pdb=" N PRO A 250 " ideal model delta sigma weight residual 1.331 1.371 -0.040 1.27e-02 6.20e+03 9.85e+00 bond pdb=" CG1 ILE H 168 " pdb=" CD1 ILE H 168 " ideal model delta sigma weight residual 1.513 1.414 0.099 3.90e-02 6.57e+02 6.47e+00 bond pdb=" CB ARG B 323 " pdb=" CG ARG B 323 " ideal model delta sigma weight residual 1.520 1.595 -0.075 3.00e-02 1.11e+03 6.22e+00 bond pdb=" C ILE H 76 " pdb=" N PRO H 77 " ideal model delta sigma weight residual 1.335 1.366 -0.031 1.28e-02 6.10e+03 6.03e+00 bond pdb=" C GLN A 225 " pdb=" N PRO A 226 " ideal model delta sigma weight residual 1.335 1.368 -0.033 1.36e-02 5.41e+03 5.85e+00 ... (remaining 9005 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.97: 10962 1.97 - 3.94: 1027 3.94 - 5.91: 164 5.91 - 7.89: 32 7.89 - 9.86: 8 Bond angle restraints: 12193 Sorted by residual: angle pdb=" C2 U 1 6 " pdb=" N1 U 1 6 " pdb=" C6 U 1 6 " ideal model delta sigma weight residual 121.00 116.90 4.10 6.00e-01 2.78e+00 4.67e+01 angle pdb=" N1 U 1 6 " pdb=" C6 U 1 6 " pdb=" C5 U 1 6 " ideal model delta sigma weight residual 122.70 126.07 -3.37 5.00e-01 4.00e+00 4.55e+01 angle pdb=" O2 U 1 6 " pdb=" C2 U 1 6 " pdb=" N3 U 1 6 " ideal model delta sigma weight residual 122.20 118.21 3.99 7.00e-01 2.04e+00 3.25e+01 angle pdb=" O5' U 1 5 " pdb=" C5' U 1 5 " pdb=" C4' U 1 5 " ideal model delta sigma weight residual 109.40 113.84 -4.44 8.00e-01 1.56e+00 3.08e+01 angle pdb=" N PRO A 257 " pdb=" CA PRO A 257 " pdb=" C PRO A 257 " ideal model delta sigma weight residual 110.70 117.19 -6.49 1.22e+00 6.72e-01 2.83e+01 ... (remaining 12188 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.13: 5329 27.13 - 54.26: 161 54.26 - 81.39: 34 81.39 - 108.52: 6 108.52 - 135.66: 1 Dihedral angle restraints: 5531 sinusoidal: 2358 harmonic: 3173 Sorted by residual: dihedral pdb=" CA ASP A 87 " pdb=" C ASP A 87 " pdb=" N PRO A 88 " pdb=" CA PRO A 88 " ideal model delta harmonic sigma weight residual 180.00 151.83 28.17 0 5.00e+00 4.00e-02 3.17e+01 dihedral pdb=" CA GLY H 320 " pdb=" C GLY H 320 " pdb=" N MET H 321 " pdb=" CA MET H 321 " ideal model delta harmonic sigma weight residual 180.00 153.34 26.66 0 5.00e+00 4.00e-02 2.84e+01 dihedral pdb=" CA ASN H 357 " pdb=" C ASN H 357 " pdb=" N ILE H 358 " pdb=" CA ILE H 358 " ideal model delta harmonic sigma weight residual 180.00 153.99 26.01 0 5.00e+00 4.00e-02 2.71e+01 ... (remaining 5528 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 1005 0.070 - 0.139: 281 0.139 - 0.209: 63 0.209 - 0.278: 7 0.278 - 0.348: 2 Chirality restraints: 1358 Sorted by residual: chirality pdb=" CB THR H 122 " pdb=" CA THR H 122 " pdb=" OG1 THR H 122 " pdb=" CG2 THR H 122 " both_signs ideal model delta sigma weight residual False 2.55 2.20 0.35 2.00e-01 2.50e+01 3.02e+00 chirality pdb=" CB ILE H 60 " pdb=" CA ILE H 60 " pdb=" CG1 ILE H 60 " pdb=" CG2 ILE H 60 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.29 2.00e-01 2.50e+01 2.12e+00 chirality pdb=" CA LEU B 256 " pdb=" N LEU B 256 " pdb=" C LEU B 256 " pdb=" CB LEU B 256 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.56e+00 ... (remaining 1355 not shown) Planarity restraints: 1561 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL C 38 " 0.016 2.00e-02 2.50e+03 3.26e-02 1.06e+01 pdb=" C VAL C 38 " -0.056 2.00e-02 2.50e+03 pdb=" O VAL C 38 " 0.021 2.00e-02 2.50e+03 pdb=" N TRP C 39 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 69 " -0.248 9.50e-02 1.11e+02 1.12e-01 1.05e+01 pdb=" NE ARG A 69 " 0.025 2.00e-02 2.50e+03 pdb=" CZ ARG A 69 " -0.027 2.00e-02 2.50e+03 pdb=" NH1 ARG A 69 " 0.012 2.00e-02 2.50e+03 pdb=" NH2 ARG A 69 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 270 " -0.243 9.50e-02 1.11e+02 1.10e-01 8.88e+00 pdb=" NE ARG A 270 " 0.022 2.00e-02 2.50e+03 pdb=" CZ ARG A 270 " -0.019 2.00e-02 2.50e+03 pdb=" NH1 ARG A 270 " 0.010 2.00e-02 2.50e+03 pdb=" NH2 ARG A 270 " -0.002 2.00e-02 2.50e+03 ... (remaining 1558 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.52: 9 2.52 - 3.12: 6062 3.12 - 3.71: 13091 3.71 - 4.31: 20057 4.31 - 4.90: 32146 Nonbonded interactions: 71365 Sorted by model distance: nonbonded pdb="MG MG H 502 " pdb=" O HOH H 603 " model vdw 1.928 2.170 nonbonded pdb=" OD2 ASP H 196 " pdb=" O HOH H 601 " model vdw 2.044 3.040 nonbonded pdb="MG MG H 502 " pdb=" O HOH H 604 " model vdw 2.085 2.170 nonbonded pdb="MG MG H 502 " pdb=" O HOH H 601 " model vdw 2.157 2.170 nonbonded pdb=" OG1 THR H 96 " pdb=" O HOH H 601 " model vdw 2.304 3.040 ... (remaining 71360 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: 1.120 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: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.320 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 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:6.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 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 : 0.008 0.118 9010 Z= 0.381 Angle : 1.243 9.857 12193 Z= 0.762 Chirality : 0.068 0.348 1358 Planarity : 0.012 0.112 1561 Dihedral : 14.287 135.655 3463 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 0.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.33 (0.22), residues: 1061 helix: -1.05 (0.17), residues: 652 sheet: -0.21 (0.50), residues: 65 loop : -0.25 (0.32), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.029 0.004 ARG A 69 TYR 0.035 0.006 TYR H 39 PHE 0.036 0.004 PHE H 99 TRP 0.015 0.003 TRP C 27 HIS 0.028 0.003 HIS A 298 Details of bonding type rmsd/Z covalent geometry : bond 0.00824 / 0.38 ( 9010) covalent geometry : angle 1.24344 / 0.76 (12193) hydrogen bonds : bond 0.23183 / 18.15 ( 467) hydrogen bonds : angle 7.19222 / 5.63 ( 1380) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 195 time to evaluate : 0.305 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 206 GLU cc_start: 0.7744 (mt-10) cc_final: 0.7538 (mm-30) REVERT: A 333 LEU cc_start: 0.8661 (mt) cc_final: 0.8376 (tt) REVERT: B 349 PHE cc_start: 0.8869 (t80) cc_final: 0.8499 (t80) REVERT: B 354 ASP cc_start: 0.7557 (m-30) cc_final: 0.6791 (t0) REVERT: H 404 GLN cc_start: 0.6056 (tt0) cc_final: 0.5476 (tm130) outliers start: 0 outliers final: 0 residues processed: 195 average time/residue: 0.6285 time to fit residues: 129.2426 Evaluate side-chains 127 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 0.7980 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 20.0000 chunk 65 optimal weight: 0.0270 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.7980 chunk 100 optimal weight: 1.9990 chunk 106 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 overall best weight: 0.6638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN A 293 GLN B 120 ASN ** B 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 295 HIS ** B 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 67 HIS H 192 HIS H 264 GLN H 331 GLN H 361 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.169390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.138874 restraints weight = 12719.009| |-----------------------------------------------------------------------------| r_work (start): 0.3925 rms_B_bonded: 1.91 r_work: 0.3622 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3484 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.2369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 9010 Z= 0.152 Angle : 0.605 6.757 12193 Z= 0.325 Chirality : 0.041 0.140 1358 Planarity : 0.005 0.044 1561 Dihedral : 8.642 107.394 1302 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.82 % Allowed : 11.37 % Favored : 86.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.25), residues: 1061 helix: 0.74 (0.20), residues: 654 sheet: 0.08 (0.55), residues: 70 loop : 0.31 (0.36), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 71 TYR 0.020 0.002 TYR B 232 PHE 0.025 0.002 PHE A 146 TRP 0.007 0.001 TRP B 166 HIS 0.007 0.001 HIS A 298 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.15 ( 9010) covalent geometry : angle 0.60505 / 0.33 (12193) hydrogen bonds : bond 0.04991 / 3.93 ( 467) hydrogen bonds : angle 4.50500 / 3.49 ( 1380) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 148 time to evaluate : 0.242 Fit side-chains revert: symmetry clash REVERT: A 206 GLU cc_start: 0.7729 (mt-10) cc_final: 0.7415 (mm-30) REVERT: A 282 GLN cc_start: 0.7710 (mm110) cc_final: 0.7419 (mt0) REVERT: A 333 LEU cc_start: 0.8249 (mt) cc_final: 0.7515 (mp) REVERT: B 200 LEU cc_start: 0.6369 (mp) cc_final: 0.6020 (mt) REVERT: B 232 TYR cc_start: 0.8236 (m-10) cc_final: 0.7944 (m-10) REVERT: B 242 ARG cc_start: 0.6669 (ttp80) cc_final: 0.6283 (ttp80) REVERT: B 354 ASP cc_start: 0.7649 (m-30) cc_final: 0.6683 (t0) REVERT: C 59 GLU cc_start: 0.8362 (tp30) cc_final: 0.8130 (tt0) REVERT: H 138 LYS cc_start: 0.8478 (ttpp) cc_final: 0.8163 (tttt) REVERT: H 233 LYS cc_start: 0.7782 (OUTLIER) cc_final: 0.7450 (tptp) REVERT: H 404 GLN cc_start: 0.6090 (tt0) cc_final: 0.5399 (tm130) outliers start: 17 outliers final: 6 residues processed: 156 average time/residue: 0.5188 time to fit residues: 85.7929 Evaluate side-chains 130 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 123 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 293 GLN Chi-restraints excluded: chain B residue 77 PHE Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 199 ASN Chi-restraints excluded: chain H residue 233 LYS Chi-restraints excluded: chain H residue 383 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 0 optimal weight: 4.9990 chunk 63 optimal weight: 0.7980 chunk 26 optimal weight: 10.0000 chunk 67 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 chunk 101 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 96 optimal weight: 0.9990 chunk 77 optimal weight: 0.9990 chunk 86 optimal weight: 1.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 248 GLN ** B 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 332 GLN H 337 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.168368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.133903 restraints weight = 12652.034| |-----------------------------------------------------------------------------| r_work (start): 0.3818 rms_B_bonded: 1.77 r_work: 0.3594 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3462 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.2845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 9010 Z= 0.201 Angle : 0.624 7.945 12193 Z= 0.324 Chirality : 0.042 0.165 1358 Planarity : 0.005 0.042 1561 Dihedral : 8.672 110.907 1302 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 3.33 % Allowed : 12.34 % Favored : 84.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.26), residues: 1061 helix: 0.93 (0.20), residues: 647 sheet: -0.32 (0.51), residues: 86 loop : 0.26 (0.36), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 337 TYR 0.017 0.002 TYR B 254 PHE 0.028 0.002 PHE H 99 TRP 0.003 0.001 TRP C 43 HIS 0.007 0.001 HIS B 186 Details of bonding type rmsd/Z covalent geometry : bond 0.00464 / 0.20 ( 9010) covalent geometry : angle 0.62435 / 0.32 (12193) hydrogen bonds : bond 0.04480 / 3.49 ( 467) hydrogen bonds : angle 4.34870 / 3.34 ( 1380) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 132 time to evaluate : 0.263 Fit side-chains revert: symmetry clash REVERT: A 206 GLU cc_start: 0.7797 (mt-10) cc_final: 0.7405 (mm-30) REVERT: A 341 GLN cc_start: 0.8360 (mp10) cc_final: 0.8153 (mp10) REVERT: B 82 LYS cc_start: 0.8574 (ptmm) cc_final: 0.8294 (pptt) REVERT: B 242 ARG cc_start: 0.6630 (ttp80) cc_final: 0.6312 (ttp80) REVERT: B 354 ASP cc_start: 0.7637 (m-30) cc_final: 0.6599 (t0) REVERT: C 59 GLU cc_start: 0.8311 (OUTLIER) cc_final: 0.7990 (tt0) REVERT: H 233 LYS cc_start: 0.7750 (OUTLIER) cc_final: 0.7429 (tptp) REVERT: H 273 GLU cc_start: 0.7760 (OUTLIER) cc_final: 0.6994 (mp0) REVERT: H 339 ARG cc_start: 0.7365 (mmm-85) cc_final: 0.6963 (mmm160) REVERT: H 404 GLN cc_start: 0.6306 (tt0) cc_final: 0.6023 (mt0) outliers start: 31 outliers final: 15 residues processed: 150 average time/residue: 0.5867 time to fit residues: 92.9207 Evaluate side-chains 133 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 115 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 248 GLN Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain B residue 77 PHE Chi-restraints excluded: chain B residue 199 ASN Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 348 LYS Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain C residue 59 GLU Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain H residue 206 ASP Chi-restraints excluded: chain H residue 233 LYS Chi-restraints excluded: chain H residue 273 GLU Chi-restraints excluded: chain H residue 375 VAL Chi-restraints excluded: chain H residue 383 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 41 optimal weight: 3.9990 chunk 72 optimal weight: 0.8980 chunk 42 optimal weight: 7.9990 chunk 51 optimal weight: 0.9990 chunk 25 optimal weight: 10.0000 chunk 10 optimal weight: 4.9990 chunk 22 optimal weight: 0.3980 chunk 45 optimal weight: 0.5980 chunk 20 optimal weight: 3.9990 chunk 70 optimal weight: 5.9990 chunk 77 optimal weight: 0.8980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 366 ASN H 332 GLN H 337 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.169190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.137143 restraints weight = 12849.854| |-----------------------------------------------------------------------------| r_work (start): 0.3893 rms_B_bonded: 2.02 r_work: 0.3596 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3462 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.3118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9010 Z= 0.141 Angle : 0.554 8.714 12193 Z= 0.287 Chirality : 0.039 0.141 1358 Planarity : 0.004 0.040 1561 Dihedral : 8.420 108.001 1302 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 3.65 % Allowed : 12.66 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.26), residues: 1061 helix: 1.19 (0.21), residues: 646 sheet: -0.20 (0.52), residues: 86 loop : 0.23 (0.36), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 126 TYR 0.019 0.002 TYR B 369 PHE 0.025 0.001 PHE A 146 TRP 0.003 0.000 TRP C 43 HIS 0.005 0.001 HIS B 186 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 ( 9010) covalent geometry : angle 0.55426 / 0.29 (12193) hydrogen bonds : bond 0.03859 / 3.00 ( 467) hydrogen bonds : angle 4.13284 / 3.15 ( 1380) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 131 time to evaluate : 0.205 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 206 GLU cc_start: 0.7787 (mt-10) cc_final: 0.7409 (mm-30) REVERT: A 217 ARG cc_start: 0.6655 (OUTLIER) cc_final: 0.4793 (mtm180) REVERT: A 282 GLN cc_start: 0.7884 (mm110) cc_final: 0.7495 (mt0) REVERT: B 82 LYS cc_start: 0.8576 (ptmm) cc_final: 0.8357 (pptt) REVERT: B 242 ARG cc_start: 0.6705 (ttp80) cc_final: 0.6407 (ttp80) REVERT: B 354 ASP cc_start: 0.7620 (m-30) cc_final: 0.6598 (t0) REVERT: C 59 GLU cc_start: 0.8318 (OUTLIER) cc_final: 0.8051 (tt0) REVERT: H 233 LYS cc_start: 0.7784 (OUTLIER) cc_final: 0.7519 (ttmt) REVERT: H 248 GLU cc_start: 0.7396 (OUTLIER) cc_final: 0.7042 (tt0) REVERT: H 339 ARG cc_start: 0.7364 (mmm-85) cc_final: 0.7017 (mmm160) outliers start: 34 outliers final: 10 residues processed: 151 average time/residue: 0.6118 time to fit residues: 97.5976 Evaluate side-chains 134 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 120 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 217 ARG Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain B residue 77 PHE Chi-restraints excluded: chain B residue 199 ASN Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain C residue 59 GLU Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain H residue 206 ASP Chi-restraints excluded: chain H residue 233 LYS Chi-restraints excluded: chain H residue 248 GLU Chi-restraints excluded: chain H residue 375 VAL Chi-restraints excluded: chain H residue 383 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 62 optimal weight: 5.9990 chunk 23 optimal weight: 0.0470 chunk 28 optimal weight: 0.7980 chunk 1 optimal weight: 0.0050 chunk 22 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 66 optimal weight: 9.9990 chunk 98 optimal weight: 0.9980 chunk 17 optimal weight: 5.9990 chunk 30 optimal weight: 10.0000 chunk 43 optimal weight: 0.8980 overall best weight: 0.5492 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 73 HIS H 332 GLN H 337 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.168906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.138514 restraints weight = 13072.072| |-----------------------------------------------------------------------------| r_work (start): 0.3917 rms_B_bonded: 2.19 r_work: 0.3596 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3457 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.3318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9010 Z= 0.123 Angle : 0.533 9.286 12193 Z= 0.274 Chirality : 0.038 0.129 1358 Planarity : 0.004 0.038 1561 Dihedral : 8.256 107.294 1302 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 3.11 % Allowed : 13.52 % Favored : 83.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.26), residues: 1061 helix: 1.39 (0.21), residues: 645 sheet: 0.02 (0.53), residues: 86 loop : 0.24 (0.36), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 284 TYR 0.011 0.001 TYR H 371 PHE 0.027 0.001 PHE A 146 TRP 0.002 0.000 TRP C 39 HIS 0.004 0.001 HIS B 186 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 ( 9010) covalent geometry : angle 0.53289 / 0.27 (12193) hydrogen bonds : bond 0.03499 / 2.72 ( 467) hydrogen bonds : angle 3.97160 / 3.01 ( 1380) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 131 time to evaluate : 0.283 Fit side-chains revert: symmetry clash REVERT: A 206 GLU cc_start: 0.7791 (mt-10) cc_final: 0.7426 (mm-30) REVERT: A 217 ARG cc_start: 0.6663 (OUTLIER) cc_final: 0.4862 (mtm180) REVERT: A 282 GLN cc_start: 0.7932 (mm110) cc_final: 0.7583 (mt0) REVERT: B 82 LYS cc_start: 0.8554 (ptmm) cc_final: 0.8349 (pptt) REVERT: B 200 LEU cc_start: 0.6348 (OUTLIER) cc_final: 0.6019 (mp) REVERT: B 354 ASP cc_start: 0.7592 (m-30) cc_final: 0.6550 (t0) REVERT: C 59 GLU cc_start: 0.8316 (OUTLIER) cc_final: 0.8060 (tt0) REVERT: H 233 LYS cc_start: 0.7770 (OUTLIER) cc_final: 0.7541 (ttmt) REVERT: H 339 ARG cc_start: 0.7413 (mmm-85) cc_final: 0.7097 (mmm160) outliers start: 29 outliers final: 10 residues processed: 149 average time/residue: 0.5763 time to fit residues: 90.9245 Evaluate side-chains 132 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 118 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 217 ARG Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 331 ASP Chi-restraints excluded: chain B residue 199 ASN Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain C residue 59 GLU Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain H residue 233 LYS Chi-restraints excluded: chain H residue 243 MET Chi-restraints excluded: chain H residue 375 VAL Chi-restraints excluded: chain H residue 383 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 0 optimal weight: 4.9990 chunk 68 optimal weight: 6.9990 chunk 44 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 71 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 chunk 63 optimal weight: 0.5980 chunk 40 optimal weight: 0.9980 chunk 77 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 290 ASN H 332 GLN H 337 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.168125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.137513 restraints weight = 13141.176| |-----------------------------------------------------------------------------| r_work (start): 0.3900 rms_B_bonded: 2.16 r_work: 0.3586 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3448 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.3461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 9010 Z= 0.149 Angle : 0.552 7.348 12193 Z= 0.283 Chirality : 0.039 0.147 1358 Planarity : 0.004 0.041 1561 Dihedral : 8.318 107.859 1302 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.58 % Allowed : 14.38 % Favored : 83.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.27 (0.26), residues: 1061 helix: 1.38 (0.20), residues: 654 sheet: -0.03 (0.54), residues: 86 loop : 0.15 (0.36), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 284 TYR 0.020 0.002 TYR B 369 PHE 0.026 0.002 PHE A 146 TRP 0.004 0.001 TRP C 39 HIS 0.004 0.001 HIS B 186 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 ( 9010) covalent geometry : angle 0.55181 / 0.28 (12193) hydrogen bonds : bond 0.03562 / 2.76 ( 467) hydrogen bonds : angle 3.99014 / 3.02 ( 1380) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 122 time to evaluate : 0.356 Fit side-chains revert: symmetry clash REVERT: A 206 GLU cc_start: 0.7823 (mt-10) cc_final: 0.7422 (mm-30) REVERT: A 217 ARG cc_start: 0.6783 (OUTLIER) cc_final: 0.4934 (mtm180) REVERT: A 282 GLN cc_start: 0.7928 (mm110) cc_final: 0.7556 (mt0) REVERT: B 354 ASP cc_start: 0.7565 (m-30) cc_final: 0.6494 (t0) REVERT: C 59 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.8110 (tt0) REVERT: H 248 GLU cc_start: 0.7181 (OUTLIER) cc_final: 0.6950 (tt0) REVERT: H 339 ARG cc_start: 0.7390 (mmm-85) cc_final: 0.7074 (mmm160) outliers start: 24 outliers final: 11 residues processed: 136 average time/residue: 0.6656 time to fit residues: 95.8385 Evaluate side-chains 130 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 116 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 217 ARG Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain B residue 199 ASN Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain C residue 59 GLU Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain H residue 206 ASP Chi-restraints excluded: chain H residue 243 MET Chi-restraints excluded: chain H residue 248 GLU Chi-restraints excluded: chain H residue 375 VAL Chi-restraints excluded: chain H residue 383 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 34 optimal weight: 8.9990 chunk 91 optimal weight: 0.8980 chunk 32 optimal weight: 8.9990 chunk 62 optimal weight: 4.9990 chunk 31 optimal weight: 10.0000 chunk 77 optimal weight: 0.4980 chunk 72 optimal weight: 0.6980 chunk 25 optimal weight: 0.8980 chunk 24 optimal weight: 0.8980 chunk 11 optimal weight: 4.9990 chunk 12 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 86 GLN ** B 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 332 GLN H 337 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.168242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.138389 restraints weight = 13233.012| |-----------------------------------------------------------------------------| r_work (start): 0.3917 rms_B_bonded: 2.37 r_work: 0.3579 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3437 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.3574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 9010 Z= 0.142 Angle : 0.564 8.477 12193 Z= 0.288 Chirality : 0.039 0.140 1358 Planarity : 0.004 0.040 1561 Dihedral : 8.279 107.279 1302 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.58 % Allowed : 14.59 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.36 (0.26), residues: 1061 helix: 1.47 (0.21), residues: 652 sheet: 0.06 (0.56), residues: 86 loop : 0.14 (0.36), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 284 TYR 0.020 0.001 TYR B 369 PHE 0.027 0.002 PHE A 146 TRP 0.002 0.000 TRP C 27 HIS 0.004 0.001 HIS B 186 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 ( 9010) covalent geometry : angle 0.56369 / 0.29 (12193) hydrogen bonds : bond 0.03472 / 2.70 ( 467) hydrogen bonds : angle 3.97267 / 3.01 ( 1380) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 127 time to evaluate : 0.374 Fit side-chains revert: symmetry clash REVERT: A 206 GLU cc_start: 0.7845 (mt-10) cc_final: 0.7467 (mm-30) REVERT: A 217 ARG cc_start: 0.6822 (OUTLIER) cc_final: 0.4974 (mtm180) REVERT: A 282 GLN cc_start: 0.7937 (mm110) cc_final: 0.7572 (mt0) REVERT: B 82 LYS cc_start: 0.8038 (pptt) cc_final: 0.7720 (ptmt) REVERT: B 354 ASP cc_start: 0.7530 (m-30) cc_final: 0.6516 (t0) REVERT: C 59 GLU cc_start: 0.8369 (OUTLIER) cc_final: 0.8131 (tt0) REVERT: H 83 MET cc_start: 0.7983 (mtm) cc_final: 0.7749 (tpt) REVERT: H 339 ARG cc_start: 0.7403 (mmm-85) cc_final: 0.7156 (mtt-85) outliers start: 24 outliers final: 13 residues processed: 141 average time/residue: 0.6129 time to fit residues: 91.2858 Evaluate side-chains 135 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 120 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 217 ARG Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain B residue 146 MET Chi-restraints excluded: chain B residue 199 ASN Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain C residue 59 GLU Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain H residue 206 ASP Chi-restraints excluded: chain H residue 243 MET Chi-restraints excluded: chain H residue 375 VAL Chi-restraints excluded: chain H residue 383 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 0 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 10 optimal weight: 7.9990 chunk 58 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 chunk 79 optimal weight: 0.6980 chunk 82 optimal weight: 0.9980 chunk 3 optimal weight: 0.7980 chunk 32 optimal weight: 7.9990 chunk 8 optimal weight: 6.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 298 HIS ** B 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 121 HIS H 332 GLN H 337 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.167811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.137410 restraints weight = 13111.933| |-----------------------------------------------------------------------------| r_work (start): 0.3901 rms_B_bonded: 2.27 r_work: 0.3567 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3427 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.3627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 9010 Z= 0.169 Angle : 0.589 8.055 12193 Z= 0.301 Chirality : 0.041 0.152 1358 Planarity : 0.004 0.051 1561 Dihedral : 8.378 107.679 1302 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.47 % Allowed : 14.91 % Favored : 82.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.26), residues: 1061 helix: 1.41 (0.21), residues: 653 sheet: -0.08 (0.55), residues: 86 loop : 0.03 (0.36), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 71 TYR 0.012 0.002 TYR B 214 PHE 0.029 0.002 PHE A 146 TRP 0.003 0.001 TRP B 166 HIS 0.004 0.001 HIS B 186 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.17 ( 9010) covalent geometry : angle 0.58910 / 0.30 (12193) hydrogen bonds : bond 0.03603 / 2.80 ( 467) hydrogen bonds : angle 4.00918 / 3.05 ( 1380) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 127 time to evaluate : 0.337 Fit side-chains revert: symmetry clash REVERT: A 206 GLU cc_start: 0.7840 (mt-10) cc_final: 0.7476 (mm-30) REVERT: A 217 ARG cc_start: 0.6853 (OUTLIER) cc_final: 0.5039 (mtm180) REVERT: A 282 GLN cc_start: 0.7943 (mm110) cc_final: 0.7588 (mt0) REVERT: B 77 PHE cc_start: 0.5334 (OUTLIER) cc_final: 0.4978 (t80) REVERT: B 354 ASP cc_start: 0.7521 (m-30) cc_final: 0.6505 (t0) REVERT: C 43 TRP cc_start: 0.8075 (p-90) cc_final: 0.7744 (p-90) REVERT: C 59 GLU cc_start: 0.8385 (OUTLIER) cc_final: 0.8143 (tt0) REVERT: H 83 MET cc_start: 0.8057 (mtm) cc_final: 0.7841 (tpt) REVERT: H 233 LYS cc_start: 0.7811 (OUTLIER) cc_final: 0.7469 (tptp) REVERT: H 339 ARG cc_start: 0.7371 (mmm-85) cc_final: 0.7079 (mtp-110) outliers start: 23 outliers final: 13 residues processed: 140 average time/residue: 0.5986 time to fit residues: 88.7464 Evaluate side-chains 135 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 118 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 217 ARG Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain B residue 77 PHE Chi-restraints excluded: chain B residue 199 ASN Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain C residue 59 GLU Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain H residue 206 ASP Chi-restraints excluded: chain H residue 233 LYS Chi-restraints excluded: chain H residue 243 MET Chi-restraints excluded: chain H residue 375 VAL Chi-restraints excluded: chain H residue 383 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 85 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 88 optimal weight: 0.0570 chunk 35 optimal weight: 3.9990 chunk 76 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 14 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 97 optimal weight: 0.9990 overall best weight: 0.8104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 332 GLN H 337 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.168320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.138361 restraints weight = 13104.879| |-----------------------------------------------------------------------------| r_work (start): 0.3922 rms_B_bonded: 2.38 r_work: 0.3582 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3439 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.3712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 9010 Z= 0.147 Angle : 0.584 8.402 12193 Z= 0.299 Chirality : 0.040 0.140 1358 Planarity : 0.004 0.055 1561 Dihedral : 8.320 107.163 1302 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.15 % Allowed : 16.09 % Favored : 81.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.28 (0.26), residues: 1061 helix: 1.43 (0.21), residues: 653 sheet: -0.03 (0.56), residues: 86 loop : 0.06 (0.36), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 71 TYR 0.011 0.001 TYR B 214 PHE 0.029 0.002 PHE A 146 TRP 0.003 0.001 TRP C 27 HIS 0.004 0.001 HIS B 186 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 ( 9010) covalent geometry : angle 0.58409 / 0.30 (12193) hydrogen bonds : bond 0.03448 / 2.68 ( 467) hydrogen bonds : angle 3.98078 / 3.02 ( 1380) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 130 time to evaluate : 0.354 Fit side-chains revert: symmetry clash REVERT: A 206 GLU cc_start: 0.7825 (mt-10) cc_final: 0.7454 (mm-30) REVERT: A 217 ARG cc_start: 0.6836 (OUTLIER) cc_final: 0.5078 (mtm180) REVERT: A 282 GLN cc_start: 0.7929 (mm110) cc_final: 0.7608 (mt0) REVERT: B 77 PHE cc_start: 0.5542 (OUTLIER) cc_final: 0.5120 (t80) REVERT: B 82 LYS cc_start: 0.8008 (pptt) cc_final: 0.7636 (ptmt) REVERT: B 354 ASP cc_start: 0.7520 (m-30) cc_final: 0.6484 (t0) REVERT: C 43 TRP cc_start: 0.8094 (p-90) cc_final: 0.7745 (p-90) REVERT: C 59 GLU cc_start: 0.8383 (OUTLIER) cc_final: 0.8152 (tt0) REVERT: H 233 LYS cc_start: 0.7758 (OUTLIER) cc_final: 0.7420 (tptp) REVERT: H 339 ARG cc_start: 0.7354 (mmm-85) cc_final: 0.7057 (mtm180) outliers start: 20 outliers final: 12 residues processed: 141 average time/residue: 0.6996 time to fit residues: 104.2169 Evaluate side-chains 138 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 122 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 217 ARG Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain B residue 77 PHE Chi-restraints excluded: chain B residue 146 MET Chi-restraints excluded: chain B residue 199 ASN Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain C residue 59 GLU Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain H residue 206 ASP Chi-restraints excluded: chain H residue 233 LYS Chi-restraints excluded: chain H residue 243 MET Chi-restraints excluded: chain H residue 375 VAL Chi-restraints excluded: chain H residue 383 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 43 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 7 optimal weight: 0.0570 chunk 12 optimal weight: 0.8980 chunk 4 optimal weight: 10.0000 chunk 15 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 64 optimal weight: 8.9990 chunk 69 optimal weight: 9.9990 chunk 90 optimal weight: 0.0000 chunk 9 optimal weight: 4.9990 overall best weight: 0.7904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 332 GLN H 337 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.168331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.133691 restraints weight = 13064.410| |-----------------------------------------------------------------------------| r_work (start): 0.3814 rms_B_bonded: 1.76 r_work: 0.3631 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3506 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.3781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 9010 Z= 0.145 Angle : 0.586 8.366 12193 Z= 0.299 Chirality : 0.040 0.155 1358 Planarity : 0.004 0.059 1561 Dihedral : 8.303 107.125 1302 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.82 % Allowed : 16.52 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.26), residues: 1061 helix: 1.42 (0.21), residues: 654 sheet: -0.06 (0.56), residues: 86 loop : -0.02 (0.36), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 71 TYR 0.020 0.001 TYR B 369 PHE 0.029 0.002 PHE A 146 TRP 0.003 0.001 TRP C 39 HIS 0.004 0.001 HIS B 186 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.14 ( 9010) covalent geometry : angle 0.58562 / 0.30 (12193) hydrogen bonds : bond 0.03426 / 2.66 ( 467) hydrogen bonds : angle 3.96517 / 3.00 ( 1380) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 130 time to evaluate : 0.355 Fit side-chains REVERT: A 206 GLU cc_start: 0.7798 (mt-10) cc_final: 0.7410 (mm-30) REVERT: A 217 ARG cc_start: 0.6765 (OUTLIER) cc_final: 0.5032 (mtm180) REVERT: A 282 GLN cc_start: 0.7897 (mm110) cc_final: 0.7536 (mt0) REVERT: B 77 PHE cc_start: 0.5616 (OUTLIER) cc_final: 0.5110 (t80) REVERT: B 82 LYS cc_start: 0.7962 (pptt) cc_final: 0.7612 (ptmt) REVERT: B 354 ASP cc_start: 0.7429 (m-30) cc_final: 0.6427 (t0) REVERT: C 43 TRP cc_start: 0.8038 (p-90) cc_final: 0.7760 (p-90) REVERT: C 59 GLU cc_start: 0.8320 (OUTLIER) cc_final: 0.8090 (tt0) REVERT: H 233 LYS cc_start: 0.7697 (OUTLIER) cc_final: 0.7327 (tptp) REVERT: H 339 ARG cc_start: 0.7297 (mmm-85) cc_final: 0.6992 (mtm180) outliers start: 17 outliers final: 13 residues processed: 139 average time/residue: 0.7098 time to fit residues: 104.0255 Evaluate side-chains 144 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 127 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 217 ARG Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain B residue 77 PHE Chi-restraints excluded: chain B residue 199 ASN Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain C residue 59 GLU Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain H residue 206 ASP Chi-restraints excluded: chain H residue 233 LYS Chi-restraints excluded: chain H residue 243 MET Chi-restraints excluded: chain H residue 375 VAL Chi-restraints excluded: chain H residue 383 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 43 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 36 optimal weight: 0.0970 chunk 32 optimal weight: 6.9990 chunk 97 optimal weight: 0.3980 chunk 85 optimal weight: 0.8980 chunk 69 optimal weight: 10.0000 chunk 9 optimal weight: 6.9990 chunk 70 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 88 optimal weight: 0.8980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 332 GLN H 337 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.168811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.134400 restraints weight = 12909.397| |-----------------------------------------------------------------------------| r_work (start): 0.3827 rms_B_bonded: 1.71 r_work: 0.3644 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3520 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.3833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9010 Z= 0.136 Angle : 0.605 13.850 12193 Z= 0.307 Chirality : 0.040 0.175 1358 Planarity : 0.004 0.060 1561 Dihedral : 8.261 106.856 1302 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.04 % Allowed : 16.42 % Favored : 81.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.31 (0.26), residues: 1061 helix: 1.45 (0.21), residues: 653 sheet: -0.02 (0.56), residues: 86 loop : 0.09 (0.37), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 71 TYR 0.010 0.001 TYR B 214 PHE 0.029 0.002 PHE A 146 TRP 0.003 0.000 TRP C 39 HIS 0.004 0.001 HIS B 186 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 ( 9010) covalent geometry : angle 0.60467 / 0.31 (12193) hydrogen bonds : bond 0.03334 / 2.59 ( 467) hydrogen bonds : angle 3.95742 / 2.99 ( 1380) =============================================================================== Job complete usr+sys time: 3884.30 seconds wall clock time: 66 minutes 34.58 seconds (3994.58 seconds total)