Starting phenix.real_space_refine on Wed Mar 4 00:37:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7dty_30860/03_2026/7dty_30860.cif Found real_map, /net/cci-nas-00/data/ceres_data/7dty_30860/03_2026/7dty_30860.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7dty_30860/03_2026/7dty_30860.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7dty_30860/03_2026/7dty_30860.map" model { file = "/net/cci-nas-00/data/ceres_data/7dty_30860/03_2026/7dty_30860.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7dty_30860/03_2026/7dty_30860.cif" } resolution = 2.98 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 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= 0.020 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: 4 Type Number sf(0) Gaussians S 56 5.16 5 C 6005 2.51 5 N 1649 2.21 5 O 1697 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9407 Number of models: 1 Model: "" Number of chains: 7 Chain: "R" Number of atoms: 3034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 3034 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 12, 'TRANS': 354} Chain breaks: 2 Chain: "P" Number of atoms: 249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 249 Classifications: {'peptide': 30} Link IDs: {'TRANS': 29} Chain: "A" Number of atoms: 1921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1921 Classifications: {'peptide': 232} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 225} Chain breaks: 2 Chain: "B" Number of atoms: 2616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2616 Classifications: {'peptide': 341} Link IDs: {'PTRANS': 5, 'TRANS': 335} Chain: "G" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "N" Number of atoms: 983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 983 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "R" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 168 Unusual residues: {'CLR': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Time building chain proxies: 2.44, per 1000 atoms: 0.26 Number of scatterers: 9407 At special positions: 0 Unit cell: (97.461, 95.319, 155.295, 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 56 16.00 O 1697 8.00 N 1649 7.00 C 6005 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS R 46 " - pdb=" SG CYS R 70 " distance=2.05 Simple disulfide: pdb=" SG CYS R 61 " - pdb=" SG CYS R 103 " distance=2.03 Simple disulfide: pdb=" SG CYS R 84 " - pdb=" SG CYS R 118 " distance=2.03 Simple disulfide: pdb=" SG CYS R 216 " - pdb=" SG CYS R 286 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " 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: 0.74 Conformation dependent library (CDL) restraints added in 364.4 milliseconds 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2172 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 11 sheets defined 44.1% alpha, 19.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'R' and resid 31 through 49 Processing helix chain 'R' and resid 115 through 119 removed outlier: 3.572A pdb=" N CYS R 118 " --> pdb=" O HIS R 115 " (cutoff:3.500A) Processing helix chain 'R' and resid 124 through 162 removed outlier: 3.633A pdb=" N LEU R 128 " --> pdb=" O ASN R 124 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ASP R 129 " --> pdb=" O GLU R 125 " (cutoff:3.500A) Processing helix chain 'R' and resid 167 through 194 Processing helix chain 'R' and resid 196 through 201 Processing helix chain 'R' and resid 211 through 246 Processing helix chain 'R' and resid 255 through 281 removed outlier: 3.702A pdb=" N TYR R 259 " --> pdb=" O HIS R 255 " (cutoff:3.500A) Proline residue: R 267 - end of helix Proline residue: R 273 - end of helix Processing helix chain 'R' and resid 292 through 328 removed outlier: 3.802A pdb=" N TRP R 296 " --> pdb=" O VAL R 292 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ILE R 298 " --> pdb=" O ALA R 294 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ILE R 299 " --> pdb=" O ILE R 295 " (cutoff:3.500A) Proline residue: R 302 - end of helix removed outlier: 3.655A pdb=" N THR R 306 " --> pdb=" O PRO R 302 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ARG R 328 " --> pdb=" O LYS R 324 " (cutoff:3.500A) Processing helix chain 'R' and resid 331 through 351 removed outlier: 4.039A pdb=" N ARG R 336 " --> pdb=" O CYS R 332 " (cutoff:3.500A) Proline residue: R 348 - end of helix Processing helix chain 'R' and resid 352 through 357 removed outlier: 4.054A pdb=" N VAL R 356 " --> pdb=" O VAL R 352 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N PHE R 357 " --> pdb=" O HIS R 353 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 352 through 357' Processing helix chain 'R' and resid 367 through 394 removed outlier: 3.678A pdb=" N PHE R 371 " --> pdb=" O GLY R 367 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ILE R 378 " --> pdb=" O LEU R 374 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N GLY R 385 " --> pdb=" O SER R 381 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N PHE R 386 " --> pdb=" O SER R 382 " (cutoff:3.500A) Processing helix chain 'R' and resid 396 through 415 Processing helix chain 'P' and resid 2 through 29 Processing helix chain 'A' and resid 10 through 40 removed outlier: 4.205A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N THR A 40 " --> pdb=" O VAL A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 60 Processing helix chain 'A' and resid 233 through 239 removed outlier: 3.713A pdb=" N GLN A 236 " --> pdb=" O LYS A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 279 Processing helix chain 'A' and resid 280 through 284 removed outlier: 3.585A pdb=" N ARG A 283 " --> pdb=" O LYS A 280 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ASP A 284 " --> pdb=" O TRP A 281 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 280 through 284' Processing helix chain 'A' and resid 293 through 303 Processing helix chain 'A' and resid 307 through 312 Processing helix chain 'A' and resid 313 through 316 Processing helix chain 'A' and resid 331 through 353 removed outlier: 4.255A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N GLY A 353 " --> pdb=" O SER A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'B' and resid 4 through 26 removed outlier: 3.762A pdb=" N GLU B 10 " --> pdb=" O GLN B 6 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 7 through 24 removed outlier: 3.591A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.519A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.688A pdb=" N ASN N 31 " --> pdb=" O THR N 28 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 28 through 32' Processing helix chain 'N' and resid 62 through 65 removed outlier: 3.551A pdb=" N LYS N 65 " --> pdb=" O GLY N 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 62 through 65' Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.941A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'R' and resid 78 through 83 Processing sheet with id=AA2, first strand: chain 'A' and resid 207 through 213 removed outlier: 3.926A pdb=" N VAL A 224 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 45 through 51 removed outlier: 6.962A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.818A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 3.537A 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: 6.567A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.489A 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: 4.385A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.432A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.472A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.910A 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: 3.541A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'N' and resid 10 through 11 removed outlier: 6.154A pdb=" N GLY N 10 " --> pdb=" O THR N 125 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N SER N 59 " --> pdb=" O ASP N 50 " (cutoff:3.500A) 487 hydrogen bonds defined for protein. 1413 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: 1.22 Time building geometry restraints manager: 0.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 3069 1.35 - 1.48: 2396 1.48 - 1.61: 4081 1.61 - 1.74: 0 1.74 - 1.86: 76 Bond restraints: 9622 Sorted by residual: bond pdb=" C ALA R 266 " pdb=" N PRO R 267 " ideal model delta sigma weight residual 1.335 1.359 -0.023 1.36e-02 5.41e+03 2.90e+00 bond pdb=" CB CYS R 46 " pdb=" SG CYS R 46 " ideal model delta sigma weight residual 1.808 1.864 -0.056 3.30e-02 9.18e+02 2.88e+00 bond pdb=" C5 CLR R 603 " pdb=" C6 CLR R 603 " ideal model delta sigma weight residual 1.332 1.300 0.032 2.00e-02 2.50e+03 2.53e+00 bond pdb=" C5 CLR R 602 " pdb=" C6 CLR R 602 " ideal model delta sigma weight residual 1.332 1.300 0.032 2.00e-02 2.50e+03 2.52e+00 bond pdb=" C5 CLR R 601 " pdb=" C6 CLR R 601 " ideal model delta sigma weight residual 1.332 1.301 0.031 2.00e-02 2.50e+03 2.45e+00 ... (remaining 9617 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.55: 12397 1.55 - 3.09: 526 3.09 - 4.64: 107 4.64 - 6.18: 18 6.18 - 7.73: 14 Bond angle restraints: 13062 Sorted by residual: angle pdb=" CA TYR R 141 " pdb=" CB TYR R 141 " pdb=" CG TYR R 141 " ideal model delta sigma weight residual 113.90 120.25 -6.35 1.80e+00 3.09e-01 1.24e+01 angle pdb=" C HIS R 166 " pdb=" N CYS R 167 " pdb=" CA CYS R 167 " ideal model delta sigma weight residual 121.62 128.01 -6.39 1.83e+00 2.99e-01 1.22e+01 angle pdb=" C LEU R 269 " pdb=" N PHE R 270 " pdb=" CA PHE R 270 " ideal model delta sigma weight residual 122.26 116.29 5.97 1.73e+00 3.34e-01 1.19e+01 angle pdb=" C ALA P 2 " pdb=" N GLU P 3 " pdb=" CA GLU P 3 " ideal model delta sigma weight residual 120.54 124.87 -4.33 1.35e+00 5.49e-01 1.03e+01 angle pdb=" C LEU R 161 " pdb=" N PHE R 162 " pdb=" CA PHE R 162 " ideal model delta sigma weight residual 122.30 118.08 4.22 1.35e+00 5.49e-01 9.77e+00 ... (remaining 13057 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.07: 5767 15.07 - 30.14: 190 30.14 - 45.21: 49 45.21 - 60.28: 1 60.28 - 75.35: 3 Dihedral angle restraints: 6010 sinusoidal: 2649 harmonic: 3361 Sorted by residual: dihedral pdb=" CB CYS R 216 " pdb=" SG CYS R 216 " pdb=" SG CYS R 286 " pdb=" CB CYS R 286 " ideal model delta sinusoidal sigma weight residual 93.00 138.25 -45.25 1 1.00e+01 1.00e-02 2.84e+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 180.00 159.05 20.95 0 5.00e+00 4.00e-02 1.76e+01 dihedral pdb=" CA LEU R 247 " pdb=" C LEU R 247 " pdb=" N VAL R 248 " pdb=" CA VAL R 248 " ideal model delta harmonic sigma weight residual -180.00 -159.41 -20.59 0 5.00e+00 4.00e-02 1.70e+01 ... (remaining 6007 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 1270 0.082 - 0.165: 150 0.165 - 0.247: 22 0.247 - 0.330: 6 0.330 - 0.412: 6 Chirality restraints: 1454 Sorted by residual: chirality pdb=" C14 CLR R 606 " pdb=" C13 CLR R 606 " pdb=" C15 CLR R 606 " pdb=" C8 CLR R 606 " both_signs ideal model delta sigma weight residual False -2.32 -2.73 0.41 2.00e-01 2.50e+01 4.25e+00 chirality pdb=" C14 CLR R 605 " pdb=" C13 CLR R 605 " pdb=" C15 CLR R 605 " pdb=" C8 CLR R 605 " both_signs ideal model delta sigma weight residual False -2.32 -2.73 0.41 2.00e-01 2.50e+01 4.19e+00 chirality pdb=" C14 CLR R 602 " pdb=" C13 CLR R 602 " pdb=" C15 CLR R 602 " pdb=" C8 CLR R 602 " both_signs ideal model delta sigma weight residual False -2.32 -2.71 0.40 2.00e-01 2.50e+01 3.95e+00 ... (remaining 1451 not shown) Planarity restraints: 1638 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN P 20 " 0.017 2.00e-02 2.50e+03 3.46e-02 1.20e+01 pdb=" C GLN P 20 " -0.060 2.00e-02 2.50e+03 pdb=" O GLN P 20 " 0.022 2.00e-02 2.50e+03 pdb=" N ASP P 21 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU R 262 " 0.016 2.00e-02 2.50e+03 3.23e-02 1.05e+01 pdb=" C LEU R 262 " -0.056 2.00e-02 2.50e+03 pdb=" O LEU R 262 " 0.021 2.00e-02 2.50e+03 pdb=" N GLY R 263 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN P 24 " -0.014 2.00e-02 2.50e+03 2.90e-02 8.41e+00 pdb=" C ASN P 24 " 0.050 2.00e-02 2.50e+03 pdb=" O ASN P 24 " -0.019 2.00e-02 2.50e+03 pdb=" N TRP P 25 " -0.017 2.00e-02 2.50e+03 ... (remaining 1635 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1674 2.78 - 3.31: 8430 3.31 - 3.84: 15214 3.84 - 4.37: 17401 4.37 - 4.90: 30989 Nonbonded interactions: 73708 Sorted by model distance: nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.249 3.040 nonbonded pdb=" O ARG A 42 " pdb=" OG1 THR A 242 " model vdw 2.303 3.040 nonbonded pdb=" O ASN A 239 " pdb=" OG1 THR A 285 " model vdw 2.312 3.040 nonbonded pdb=" OH TYR A 318 " pdb=" OD2 ASP A 343 " model vdw 2.327 3.040 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.329 3.040 ... (remaining 73703 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: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 10.120 Find NCS groups from input model: 0.050 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:6.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 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 0.062 9628 Z= 0.202 Angle : 0.781 10.203 13074 Z= 0.430 Chirality : 0.062 0.412 1454 Planarity : 0.006 0.065 1638 Dihedral : 8.413 75.348 3820 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % 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 (0.21), residues: 1136 helix: -0.34 (0.20), residues: 447 sheet: -0.46 (0.33), residues: 236 loop : -1.50 (0.25), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 183 TYR 0.024 0.002 TYR P 1 PHE 0.024 0.002 PHE B 199 TRP 0.030 0.003 TRP A 281 HIS 0.017 0.002 HIS R 409 Details of bonding type rmsd covalent geometry : bond 0.00379 ( 9622) covalent geometry : angle 0.77531 (13062) SS BOND : bond 0.00783 ( 6) SS BOND : angle 3.27388 ( 12) hydrogen bonds : bond 0.10052 ( 487) hydrogen bonds : angle 5.47412 ( 1413) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 300 time to evaluate : 0.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 189 SER cc_start: 0.8431 (m) cc_final: 0.8157 (t) REVERT: R 357 PHE cc_start: 0.8966 (m-80) cc_final: 0.8679 (m-80) REVERT: R 396 ASN cc_start: 0.8852 (t0) cc_final: 0.7981 (t0) REVERT: P 10 TYR cc_start: 0.8463 (t80) cc_final: 0.8167 (t80) REVERT: A 12 GLN cc_start: 0.8015 (mm-40) cc_final: 0.7782 (pp30) REVERT: B 36 ASN cc_start: 0.8791 (m-40) cc_final: 0.8560 (p0) REVERT: B 127 LYS cc_start: 0.8338 (tttt) cc_final: 0.8035 (ttmm) REVERT: B 155 ASN cc_start: 0.8388 (m-40) cc_final: 0.7911 (t0) REVERT: B 158 VAL cc_start: 0.9254 (t) cc_final: 0.9039 (p) REVERT: B 172 GLU cc_start: 0.8702 (tp30) cc_final: 0.8478 (tp30) REVERT: B 217 MET cc_start: 0.7851 (ptt) cc_final: 0.7623 (ptm) REVERT: G 29 LYS cc_start: 0.9195 (mmtt) cc_final: 0.8187 (mmmt) REVERT: G 52 THR cc_start: 0.8381 (m) cc_final: 0.8041 (p) REVERT: G 57 SER cc_start: 0.9533 (p) cc_final: 0.9255 (p) REVERT: N 11 LEU cc_start: 0.8903 (tp) cc_final: 0.8321 (tp) REVERT: N 31 ASN cc_start: 0.8716 (m-40) cc_final: 0.8465 (m-40) REVERT: N 69 THR cc_start: 0.8828 (m) cc_final: 0.8340 (p) REVERT: N 73 ASP cc_start: 0.8032 (t0) cc_final: 0.7568 (t0) REVERT: N 103 PHE cc_start: 0.9137 (m-80) cc_final: 0.8650 (m-80) REVERT: N 125 THR cc_start: 0.8830 (m) cc_final: 0.8409 (p) outliers start: 0 outliers final: 0 residues processed: 300 average time/residue: 0.5962 time to fit residues: 190.7107 Evaluate side-chains 173 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 173 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 9.9990 chunk 53 optimal weight: 7.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.1980 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 6.9990 chunk 106 optimal weight: 0.8980 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 93 HIS R 224 GLN R 242 HIS A 19 GLN A 23 ASN ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 ASN B 91 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.118739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.079231 restraints weight = 17230.198| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 3.23 r_work: 0.2956 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.2990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 9628 Z= 0.210 Angle : 0.620 7.161 13074 Z= 0.326 Chirality : 0.043 0.139 1454 Planarity : 0.005 0.041 1638 Dihedral : 5.112 39.483 1668 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 4.15 % Allowed : 13.17 % Favored : 82.67 % 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: 0.17 (0.23), residues: 1136 helix: 1.47 (0.23), residues: 449 sheet: -0.23 (0.32), residues: 232 loop : -1.05 (0.27), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 197 TYR 0.022 0.002 TYR R 335 PHE 0.015 0.002 PHE B 199 TRP 0.024 0.002 TRP A 281 HIS 0.009 0.002 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00486 ( 9622) covalent geometry : angle 0.61858 (13062) SS BOND : bond 0.00439 ( 6) SS BOND : angle 1.66969 ( 12) hydrogen bonds : bond 0.04429 ( 487) hydrogen bonds : angle 4.50076 ( 1413) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 181 time to evaluate : 0.478 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 298 ILE cc_start: 0.8453 (OUTLIER) cc_final: 0.8190 (tt) REVERT: R 357 PHE cc_start: 0.9182 (m-80) cc_final: 0.8708 (m-80) REVERT: P 10 TYR cc_start: 0.8781 (t80) cc_final: 0.8408 (t80) REVERT: P 18 HIS cc_start: 0.8471 (t-170) cc_final: 0.8208 (t-170) REVERT: P 25 TRP cc_start: 0.8413 (t60) cc_final: 0.8052 (t60) REVERT: A 27 GLU cc_start: 0.8874 (mm-30) cc_final: 0.8459 (mm-30) REVERT: A 365 CYS cc_start: 0.7667 (m) cc_final: 0.6837 (p) REVERT: B 36 ASN cc_start: 0.9195 (m-40) cc_final: 0.8822 (p0) REVERT: B 127 LYS cc_start: 0.8567 (tttt) cc_final: 0.8179 (ttmm) REVERT: B 155 ASN cc_start: 0.8752 (m-40) cc_final: 0.8095 (t0) REVERT: B 158 VAL cc_start: 0.9360 (t) cc_final: 0.9094 (p) REVERT: B 172 GLU cc_start: 0.9079 (tp30) cc_final: 0.8704 (tp30) REVERT: B 197 ARG cc_start: 0.8649 (tpp-160) cc_final: 0.8216 (mmm160) REVERT: B 215 GLU cc_start: 0.8108 (OUTLIER) cc_final: 0.7704 (pt0) REVERT: B 217 MET cc_start: 0.9042 (ptt) cc_final: 0.8528 (ppp) REVERT: B 254 ASP cc_start: 0.8167 (t0) cc_final: 0.7825 (t0) REVERT: G 29 LYS cc_start: 0.9165 (mmtt) cc_final: 0.8844 (mmtm) REVERT: G 52 THR cc_start: 0.8440 (m) cc_final: 0.8012 (p) REVERT: N 11 LEU cc_start: 0.8991 (tp) cc_final: 0.8453 (tp) REVERT: N 69 THR cc_start: 0.8925 (m) cc_final: 0.8341 (p) REVERT: N 73 ASP cc_start: 0.8235 (t0) cc_final: 0.7631 (t0) REVERT: N 78 THR cc_start: 0.8335 (m) cc_final: 0.7962 (t) REVERT: N 105 ARG cc_start: 0.8659 (mtm-85) cc_final: 0.7945 (mtp85) REVERT: N 114 THR cc_start: 0.8909 (OUTLIER) cc_final: 0.8687 (p) REVERT: N 125 THR cc_start: 0.9020 (m) cc_final: 0.8587 (p) outliers start: 41 outliers final: 13 residues processed: 204 average time/residue: 0.5948 time to fit residues: 129.6392 Evaluate side-chains 154 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 138 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 143 VAL Chi-restraints excluded: chain R residue 160 SER Chi-restraints excluded: chain R residue 165 LEU Chi-restraints excluded: chain R residue 245 LEU Chi-restraints excluded: chain R residue 298 ILE Chi-restraints excluded: chain R residue 327 THR Chi-restraints excluded: chain R residue 347 VAL Chi-restraints excluded: chain R residue 374 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 280 LYS Chi-restraints excluded: chain G residue 36 ASP Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain N residue 114 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 86 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 61 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 99 optimal weight: 0.8980 chunk 51 optimal weight: 0.7980 chunk 67 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 chunk 15 optimal weight: 6.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.118405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.078987 restraints weight = 17149.233| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 3.21 r_work: 0.3001 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.3532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 9628 Z= 0.143 Angle : 0.573 11.042 13074 Z= 0.299 Chirality : 0.041 0.154 1454 Planarity : 0.004 0.050 1638 Dihedral : 4.858 50.620 1668 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 3.04 % Allowed : 15.40 % Favored : 81.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % 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: 0.83 (0.24), residues: 1136 helix: 2.20 (0.23), residues: 449 sheet: -0.19 (0.32), residues: 238 loop : -0.72 (0.29), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG N 105 TYR 0.019 0.002 TYR N 60 PHE 0.019 0.001 PHE B 292 TRP 0.015 0.001 TRP R 233 HIS 0.008 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00328 ( 9622) covalent geometry : angle 0.56748 (13062) SS BOND : bond 0.00203 ( 6) SS BOND : angle 2.71150 ( 12) hydrogen bonds : bond 0.03963 ( 487) hydrogen bonds : angle 4.26696 ( 1413) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 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: 30 poor density : 155 time to evaluate : 0.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 298 ILE cc_start: 0.8568 (OUTLIER) cc_final: 0.8290 (tt) REVERT: R 344 LEU cc_start: 0.8106 (OUTLIER) cc_final: 0.7872 (mm) REVERT: R 376 PHE cc_start: 0.8802 (t80) cc_final: 0.8557 (t80) REVERT: R 397 LYS cc_start: 0.8694 (mppt) cc_final: 0.8355 (mppt) REVERT: P 18 HIS cc_start: 0.8582 (t-170) cc_final: 0.8340 (t-170) REVERT: A 27 GLU cc_start: 0.8916 (mm-30) cc_final: 0.8423 (mm-30) REVERT: A 365 CYS cc_start: 0.7634 (m) cc_final: 0.6809 (p) REVERT: B 155 ASN cc_start: 0.8749 (m-40) cc_final: 0.8136 (t0) REVERT: B 158 VAL cc_start: 0.9321 (t) cc_final: 0.9083 (p) REVERT: B 172 GLU cc_start: 0.8907 (tp30) cc_final: 0.8616 (tp30) REVERT: B 217 MET cc_start: 0.8990 (ptt) cc_final: 0.8627 (ptm) REVERT: B 254 ASP cc_start: 0.8289 (t0) cc_final: 0.7889 (t0) REVERT: G 29 LYS cc_start: 0.9158 (mmtt) cc_final: 0.8896 (mmtm) REVERT: G 46 LYS cc_start: 0.9153 (mtmm) cc_final: 0.8830 (mppt) REVERT: G 52 THR cc_start: 0.8634 (m) cc_final: 0.8267 (p) REVERT: N 73 ASP cc_start: 0.8247 (t0) cc_final: 0.7711 (t0) REVERT: N 114 THR cc_start: 0.8943 (OUTLIER) cc_final: 0.8669 (p) outliers start: 30 outliers final: 4 residues processed: 173 average time/residue: 0.6187 time to fit residues: 114.0940 Evaluate side-chains 146 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 139 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 143 VAL Chi-restraints excluded: chain R residue 160 SER Chi-restraints excluded: chain R residue 298 ILE Chi-restraints excluded: chain R residue 344 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain N residue 114 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 31 optimal weight: 0.8980 chunk 18 optimal weight: 0.8980 chunk 34 optimal weight: 4.9990 chunk 72 optimal weight: 0.7980 chunk 74 optimal weight: 1.9990 chunk 53 optimal weight: 6.9990 chunk 8 optimal weight: 6.9990 chunk 51 optimal weight: 0.9980 chunk 23 optimal weight: 4.9990 chunk 90 optimal weight: 0.7980 chunk 56 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN ** B 88 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 = 0.3774 r_free = 0.3774 target = 0.117998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.078455 restraints weight = 17286.009| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 3.22 r_work: 0.2993 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.3837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9628 Z= 0.138 Angle : 0.554 8.371 13074 Z= 0.290 Chirality : 0.040 0.139 1454 Planarity : 0.004 0.036 1638 Dihedral : 4.678 51.365 1668 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 3.04 % Allowed : 15.60 % Favored : 81.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % 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: 1.03 (0.25), residues: 1136 helix: 2.38 (0.24), residues: 455 sheet: -0.15 (0.32), residues: 239 loop : -0.61 (0.29), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 13 TYR 0.020 0.001 TYR N 60 PHE 0.014 0.001 PHE A 212 TRP 0.032 0.001 TRP P 25 HIS 0.007 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 9622) covalent geometry : angle 0.55010 (13062) SS BOND : bond 0.00402 ( 6) SS BOND : angle 2.22012 ( 12) hydrogen bonds : bond 0.03819 ( 487) hydrogen bonds : angle 4.15287 ( 1413) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 149 time to evaluate : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 203 ASP cc_start: 0.8564 (m-30) cc_final: 0.8060 (t70) REVERT: R 279 TYR cc_start: 0.8189 (t80) cc_final: 0.7708 (t80) REVERT: R 298 ILE cc_start: 0.8574 (OUTLIER) cc_final: 0.8308 (tt) REVERT: R 344 LEU cc_start: 0.8145 (OUTLIER) cc_final: 0.7892 (mm) REVERT: R 345 PHE cc_start: 0.8568 (OUTLIER) cc_final: 0.8281 (t80) REVERT: R 376 PHE cc_start: 0.8894 (t80) cc_final: 0.8645 (t80) REVERT: R 398 GLU cc_start: 0.8525 (tm-30) cc_final: 0.8214 (tm-30) REVERT: P 10 TYR cc_start: 0.8957 (t80) cc_final: 0.8744 (t80) REVERT: P 14 MET cc_start: 0.8998 (mmm) cc_final: 0.8793 (tpt) REVERT: P 18 HIS cc_start: 0.8605 (t-170) cc_final: 0.8359 (t-170) REVERT: A 27 GLU cc_start: 0.8915 (mm-30) cc_final: 0.8424 (mm-30) REVERT: A 365 CYS cc_start: 0.7661 (m) cc_final: 0.7417 (t) REVERT: B 12 GLU cc_start: 0.9251 (tp30) cc_final: 0.8969 (tp30) REVERT: B 15 LYS cc_start: 0.9271 (tptt) cc_final: 0.8849 (tmmt) REVERT: B 23 LYS cc_start: 0.9481 (mmmt) cc_final: 0.9172 (tptp) REVERT: B 155 ASN cc_start: 0.8745 (m-40) cc_final: 0.8108 (t0) REVERT: B 158 VAL cc_start: 0.9325 (t) cc_final: 0.9084 (p) REVERT: B 172 GLU cc_start: 0.8949 (tp30) cc_final: 0.8701 (tp30) REVERT: B 217 MET cc_start: 0.8921 (ptt) cc_final: 0.8562 (ppp) REVERT: B 254 ASP cc_start: 0.8293 (t0) cc_final: 0.7884 (t0) REVERT: G 13 ARG cc_start: 0.8896 (ptm-80) cc_final: 0.8411 (tmm160) REVERT: G 14 LYS cc_start: 0.9587 (tppp) cc_final: 0.9302 (tppp) REVERT: G 29 LYS cc_start: 0.9132 (mmtt) cc_final: 0.8880 (mmtm) REVERT: G 46 LYS cc_start: 0.9140 (mtmm) cc_final: 0.8849 (mppt) REVERT: G 52 THR cc_start: 0.8690 (m) cc_final: 0.8355 (p) REVERT: N 35 ASN cc_start: 0.9013 (OUTLIER) cc_final: 0.8742 (p0) REVERT: N 73 ASP cc_start: 0.8205 (t0) cc_final: 0.7687 (t0) REVERT: N 87 LYS cc_start: 0.9005 (mtmm) cc_final: 0.8790 (mtmm) REVERT: N 114 THR cc_start: 0.9007 (OUTLIER) cc_final: 0.8717 (p) outliers start: 30 outliers final: 9 residues processed: 168 average time/residue: 0.5821 time to fit residues: 104.6337 Evaluate side-chains 148 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 134 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 143 VAL Chi-restraints excluded: chain R residue 160 SER Chi-restraints excluded: chain R residue 174 ILE Chi-restraints excluded: chain R residue 245 LEU Chi-restraints excluded: chain R residue 298 ILE Chi-restraints excluded: chain R residue 344 LEU Chi-restraints excluded: chain R residue 345 PHE Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 36 ASP Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 114 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 110 optimal weight: 0.6980 chunk 102 optimal weight: 0.0050 chunk 45 optimal weight: 3.9990 chunk 42 optimal weight: 0.6980 chunk 74 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 94 optimal weight: 4.9990 chunk 15 optimal weight: 20.0000 chunk 18 optimal weight: 0.8980 overall best weight: 0.8596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 230 ASN A 23 ASN ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN B 88 ASN B 239 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.118206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.079257 restraints weight = 17315.091| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 3.18 r_work: 0.2967 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.4056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9628 Z= 0.140 Angle : 0.550 7.569 13074 Z= 0.289 Chirality : 0.040 0.140 1454 Planarity : 0.004 0.046 1638 Dihedral : 4.590 54.136 1668 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.84 % Allowed : 16.92 % Favored : 80.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % 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: 1.16 (0.25), residues: 1136 helix: 2.48 (0.24), residues: 455 sheet: -0.14 (0.32), residues: 241 loop : -0.51 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG N 105 TYR 0.020 0.001 TYR N 60 PHE 0.014 0.001 PHE R 270 TRP 0.019 0.001 TRP P 25 HIS 0.006 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 9622) covalent geometry : angle 0.54640 (13062) SS BOND : bond 0.00384 ( 6) SS BOND : angle 2.01962 ( 12) hydrogen bonds : bond 0.03767 ( 487) hydrogen bonds : angle 4.06317 ( 1413) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 135 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 203 ASP cc_start: 0.8635 (m-30) cc_final: 0.8096 (t70) REVERT: R 279 TYR cc_start: 0.8214 (t80) cc_final: 0.7743 (t80) REVERT: R 298 ILE cc_start: 0.8606 (OUTLIER) cc_final: 0.8319 (tt) REVERT: R 344 LEU cc_start: 0.8208 (OUTLIER) cc_final: 0.7942 (mm) REVERT: R 345 PHE cc_start: 0.8654 (OUTLIER) cc_final: 0.8381 (t80) REVERT: R 376 PHE cc_start: 0.8829 (t80) cc_final: 0.8586 (t80) REVERT: R 397 LYS cc_start: 0.8508 (mppt) cc_final: 0.8275 (mppt) REVERT: R 398 GLU cc_start: 0.8480 (tm-30) cc_final: 0.8256 (tm-30) REVERT: P 10 TYR cc_start: 0.8977 (t80) cc_final: 0.8736 (t80) REVERT: P 18 HIS cc_start: 0.8589 (t-170) cc_final: 0.8328 (t-170) REVERT: A 27 GLU cc_start: 0.8930 (mm-30) cc_final: 0.8437 (mm-30) REVERT: A 365 CYS cc_start: 0.7697 (m) cc_final: 0.7442 (t) REVERT: B 12 GLU cc_start: 0.9255 (tp30) cc_final: 0.8856 (tp30) REVERT: B 15 LYS cc_start: 0.9242 (tptt) cc_final: 0.8847 (tmmt) REVERT: B 23 LYS cc_start: 0.9446 (mmmt) cc_final: 0.9156 (tptp) REVERT: B 155 ASN cc_start: 0.8763 (m-40) cc_final: 0.8144 (t0) REVERT: B 158 VAL cc_start: 0.9297 (t) cc_final: 0.9066 (p) REVERT: B 172 GLU cc_start: 0.9012 (tp30) cc_final: 0.8686 (tp30) REVERT: B 217 MET cc_start: 0.8941 (ptt) cc_final: 0.8616 (ppp) REVERT: B 254 ASP cc_start: 0.8309 (t0) cc_final: 0.7949 (t0) REVERT: G 29 LYS cc_start: 0.9101 (mmtt) cc_final: 0.8840 (mmtm) REVERT: G 46 LYS cc_start: 0.9125 (mtmm) cc_final: 0.8855 (mppt) REVERT: G 52 THR cc_start: 0.8846 (m) cc_final: 0.8565 (p) REVERT: N 11 LEU cc_start: 0.9325 (mm) cc_final: 0.9105 (mm) REVERT: N 35 ASN cc_start: 0.9002 (OUTLIER) cc_final: 0.8699 (p0) REVERT: N 73 ASP cc_start: 0.8237 (t0) cc_final: 0.7724 (t0) REVERT: N 114 THR cc_start: 0.9046 (OUTLIER) cc_final: 0.8809 (p) outliers start: 28 outliers final: 10 residues processed: 153 average time/residue: 0.5939 time to fit residues: 97.0843 Evaluate side-chains 146 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 131 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 143 VAL Chi-restraints excluded: chain R residue 160 SER Chi-restraints excluded: chain R residue 174 ILE Chi-restraints excluded: chain R residue 298 ILE Chi-restraints excluded: chain R residue 344 LEU Chi-restraints excluded: chain R residue 345 PHE Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 114 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 90 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 1 optimal weight: 0.1980 chunk 0 optimal weight: 8.9990 chunk 76 optimal weight: 1.9990 chunk 104 optimal weight: 3.9990 chunk 8 optimal weight: 6.9990 chunk 28 optimal weight: 3.9990 chunk 66 optimal weight: 0.0570 chunk 44 optimal weight: 6.9990 chunk 77 optimal weight: 0.8980 overall best weight: 1.2302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.115732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.076016 restraints weight = 17191.835| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 3.19 r_work: 0.2931 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.4380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 9628 Z= 0.172 Angle : 0.571 7.315 13074 Z= 0.300 Chirality : 0.041 0.144 1454 Planarity : 0.004 0.050 1638 Dihedral : 4.608 57.870 1668 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 3.24 % Allowed : 16.92 % Favored : 79.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % 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: 1.19 (0.25), residues: 1136 helix: 2.48 (0.24), residues: 457 sheet: -0.15 (0.31), residues: 244 loop : -0.45 (0.30), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG N 105 TYR 0.022 0.002 TYR N 60 PHE 0.014 0.001 PHE R 180 TRP 0.015 0.001 TRP P 25 HIS 0.006 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00402 ( 9622) covalent geometry : angle 0.56764 (13062) SS BOND : bond 0.00115 ( 6) SS BOND : angle 2.21343 ( 12) hydrogen bonds : bond 0.03900 ( 487) hydrogen bonds : angle 4.07211 ( 1413) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 139 time to evaluate : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 203 ASP cc_start: 0.8589 (m-30) cc_final: 0.7997 (t70) REVERT: R 237 GLU cc_start: 0.8835 (tp30) cc_final: 0.8558 (mm-30) REVERT: R 279 TYR cc_start: 0.8206 (t80) cc_final: 0.7753 (t80) REVERT: R 344 LEU cc_start: 0.8225 (OUTLIER) cc_final: 0.7966 (mm) REVERT: R 376 PHE cc_start: 0.8905 (t80) cc_final: 0.8650 (t80) REVERT: R 378 ILE cc_start: 0.8786 (OUTLIER) cc_final: 0.8462 (tt) REVERT: R 397 LYS cc_start: 0.8590 (mppt) cc_final: 0.8332 (mppt) REVERT: R 398 GLU cc_start: 0.8456 (tm-30) cc_final: 0.8238 (tm-30) REVERT: P 18 HIS cc_start: 0.8613 (t-170) cc_final: 0.7659 (t70) REVERT: P 21 ASP cc_start: 0.9246 (m-30) cc_final: 0.8979 (p0) REVERT: A 27 GLU cc_start: 0.8945 (mm-30) cc_final: 0.8478 (mm-30) REVERT: A 33 ASP cc_start: 0.8788 (t70) cc_final: 0.8336 (m-30) REVERT: A 365 CYS cc_start: 0.7751 (m) cc_final: 0.7471 (t) REVERT: B 12 GLU cc_start: 0.9184 (tp30) cc_final: 0.8898 (tp30) REVERT: B 15 LYS cc_start: 0.9178 (tptt) cc_final: 0.8909 (tptp) REVERT: B 23 LYS cc_start: 0.9442 (mmmt) cc_final: 0.9178 (tptp) REVERT: B 155 ASN cc_start: 0.8782 (m-40) cc_final: 0.8194 (t0) REVERT: B 172 GLU cc_start: 0.8996 (tp30) cc_final: 0.8743 (tp30) REVERT: B 217 MET cc_start: 0.8988 (ptt) cc_final: 0.8781 (ppp) REVERT: B 254 ASP cc_start: 0.8335 (t0) cc_final: 0.7975 (t0) REVERT: G 13 ARG cc_start: 0.9022 (ptm-80) cc_final: 0.8574 (tmm160) REVERT: G 14 LYS cc_start: 0.9610 (tppp) cc_final: 0.9368 (tppp) REVERT: G 29 LYS cc_start: 0.9129 (mmtt) cc_final: 0.8834 (mmtm) REVERT: G 46 LYS cc_start: 0.9131 (mtmm) cc_final: 0.8882 (mppt) REVERT: G 52 THR cc_start: 0.8895 (m) cc_final: 0.8633 (p) REVERT: N 73 ASP cc_start: 0.8303 (t0) cc_final: 0.7766 (t0) REVERT: N 114 THR cc_start: 0.9086 (OUTLIER) cc_final: 0.8721 (p) outliers start: 32 outliers final: 12 residues processed: 161 average time/residue: 0.5753 time to fit residues: 99.0289 Evaluate side-chains 149 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 134 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 143 VAL Chi-restraints excluded: chain R residue 160 SER Chi-restraints excluded: chain R residue 245 LEU Chi-restraints excluded: chain R residue 298 ILE Chi-restraints excluded: chain R residue 344 LEU Chi-restraints excluded: chain R residue 378 ILE Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 114 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 37 optimal weight: 2.9990 chunk 69 optimal weight: 0.5980 chunk 88 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 105 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 109 optimal weight: 0.9980 chunk 98 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 chunk 12 optimal weight: 0.8980 chunk 74 optimal weight: 0.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 91 HIS ** A 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 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 = 0.3778 r_free = 0.3778 target = 0.117333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.078417 restraints weight = 17178.380| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 3.16 r_work: 0.2971 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.4484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9628 Z= 0.142 Angle : 0.555 8.084 13074 Z= 0.291 Chirality : 0.040 0.136 1454 Planarity : 0.004 0.049 1638 Dihedral : 4.509 58.489 1668 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.84 % Allowed : 18.14 % Favored : 79.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % 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 (0.25), residues: 1136 helix: 2.55 (0.24), residues: 457 sheet: -0.13 (0.32), residues: 251 loop : -0.32 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 278 TYR 0.022 0.001 TYR N 60 PHE 0.015 0.001 PHE R 270 TRP 0.014 0.001 TRP B 169 HIS 0.005 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 9622) covalent geometry : angle 0.55270 (13062) SS BOND : bond 0.00106 ( 6) SS BOND : angle 1.86240 ( 12) hydrogen bonds : bond 0.03726 ( 487) hydrogen bonds : angle 4.01798 ( 1413) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 137 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 181 MET cc_start: 0.8724 (tpp) cc_final: 0.8452 (mmp) REVERT: R 203 ASP cc_start: 0.8604 (m-30) cc_final: 0.8016 (t70) REVERT: R 237 GLU cc_start: 0.8831 (tp30) cc_final: 0.8553 (mm-30) REVERT: R 279 TYR cc_start: 0.8221 (t80) cc_final: 0.7770 (t80) REVERT: R 298 ILE cc_start: 0.8670 (OUTLIER) cc_final: 0.8421 (tt) REVERT: R 344 LEU cc_start: 0.8280 (OUTLIER) cc_final: 0.8015 (mm) REVERT: R 376 PHE cc_start: 0.8912 (t80) cc_final: 0.8674 (t80) REVERT: R 397 LYS cc_start: 0.8654 (mppt) cc_final: 0.8354 (mppt) REVERT: R 398 GLU cc_start: 0.8686 (tm-30) cc_final: 0.8469 (tm-30) REVERT: P 18 HIS cc_start: 0.8614 (t-170) cc_final: 0.7631 (t70) REVERT: P 21 ASP cc_start: 0.9250 (m-30) cc_final: 0.8990 (p0) REVERT: A 27 GLU cc_start: 0.8936 (mm-30) cc_final: 0.8456 (mm-30) REVERT: A 33 ASP cc_start: 0.8679 (t70) cc_final: 0.8280 (m-30) REVERT: A 365 CYS cc_start: 0.7657 (m) cc_final: 0.7407 (t) REVERT: B 12 GLU cc_start: 0.9147 (tp30) cc_final: 0.8867 (tp30) REVERT: B 23 LYS cc_start: 0.9458 (mmmt) cc_final: 0.9191 (tptp) REVERT: B 155 ASN cc_start: 0.8766 (m-40) cc_final: 0.8202 (t0) REVERT: B 158 VAL cc_start: 0.9302 (t) cc_final: 0.9088 (p) REVERT: B 172 GLU cc_start: 0.8999 (tp30) cc_final: 0.8745 (tp30) REVERT: B 217 MET cc_start: 0.8949 (ptt) cc_final: 0.8718 (ppp) REVERT: B 254 ASP cc_start: 0.8299 (t0) cc_final: 0.7825 (t0) REVERT: G 13 ARG cc_start: 0.9004 (ptm-80) cc_final: 0.8661 (tmm160) REVERT: G 14 LYS cc_start: 0.9590 (tppp) cc_final: 0.9324 (tppp) REVERT: G 29 LYS cc_start: 0.9123 (mmtt) cc_final: 0.8847 (mmtm) REVERT: G 46 LYS cc_start: 0.9108 (mtmm) cc_final: 0.8871 (mppt) REVERT: G 52 THR cc_start: 0.8921 (m) cc_final: 0.8700 (p) REVERT: N 35 ASN cc_start: 0.8817 (OUTLIER) cc_final: 0.8596 (p0) REVERT: N 73 ASP cc_start: 0.8258 (t0) cc_final: 0.7721 (t0) REVERT: N 77 ASN cc_start: 0.8833 (OUTLIER) cc_final: 0.8494 (t0) REVERT: N 114 THR cc_start: 0.9068 (OUTLIER) cc_final: 0.8787 (p) outliers start: 28 outliers final: 13 residues processed: 154 average time/residue: 0.5724 time to fit residues: 94.4203 Evaluate side-chains 147 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 129 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 143 VAL Chi-restraints excluded: chain R residue 153 LEU Chi-restraints excluded: chain R residue 160 SER Chi-restraints excluded: chain R residue 174 ILE Chi-restraints excluded: chain R residue 298 ILE Chi-restraints excluded: chain R residue 305 MET Chi-restraints excluded: chain R residue 344 LEU Chi-restraints excluded: chain R residue 352 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain G residue 36 ASP Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 77 ASN Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 114 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 111 optimal weight: 0.6980 chunk 102 optimal weight: 0.1980 chunk 54 optimal weight: 0.4980 chunk 47 optimal weight: 0.6980 chunk 112 optimal weight: 0.7980 chunk 24 optimal weight: 0.7980 chunk 95 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 chunk 60 optimal weight: 0.8980 chunk 59 optimal weight: 6.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.117151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.078047 restraints weight = 17260.537| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 3.19 r_work: 0.2965 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.4571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9628 Z= 0.125 Angle : 0.549 8.186 13074 Z= 0.287 Chirality : 0.040 0.135 1454 Planarity : 0.004 0.043 1638 Dihedral : 4.400 56.561 1668 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.33 % Allowed : 19.05 % Favored : 78.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % 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: 1.35 (0.26), residues: 1136 helix: 2.65 (0.24), residues: 457 sheet: -0.22 (0.32), residues: 249 loop : -0.31 (0.31), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG N 105 TYR 0.022 0.001 TYR N 60 PHE 0.015 0.001 PHE R 270 TRP 0.015 0.001 TRP B 169 HIS 0.005 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 9622) covalent geometry : angle 0.54672 (13062) SS BOND : bond 0.00085 ( 6) SS BOND : angle 1.76455 ( 12) hydrogen bonds : bond 0.03626 ( 487) hydrogen bonds : angle 3.94659 ( 1413) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 140 time to evaluate : 0.425 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 237 GLU cc_start: 0.8794 (tp30) cc_final: 0.8531 (mm-30) REVERT: R 279 TYR cc_start: 0.8221 (t80) cc_final: 0.7766 (t80) REVERT: R 298 ILE cc_start: 0.8613 (OUTLIER) cc_final: 0.8355 (tt) REVERT: R 376 PHE cc_start: 0.8874 (t80) cc_final: 0.8651 (t80) REVERT: R 397 LYS cc_start: 0.8620 (mppt) cc_final: 0.8307 (mppt) REVERT: R 398 GLU cc_start: 0.8706 (tm-30) cc_final: 0.8442 (tm-30) REVERT: P 18 HIS cc_start: 0.8569 (t-170) cc_final: 0.7529 (t70) REVERT: P 21 ASP cc_start: 0.9255 (m-30) cc_final: 0.8999 (p0) REVERT: A 27 GLU cc_start: 0.8921 (mm-30) cc_final: 0.8436 (mm-30) REVERT: A 33 ASP cc_start: 0.8715 (t70) cc_final: 0.8269 (m-30) REVERT: A 365 CYS cc_start: 0.7617 (m) cc_final: 0.7359 (t) REVERT: B 12 GLU cc_start: 0.9178 (tp30) cc_final: 0.8873 (tp30) REVERT: B 23 LYS cc_start: 0.9470 (mmmt) cc_final: 0.9169 (tptp) REVERT: B 155 ASN cc_start: 0.8780 (m-40) cc_final: 0.8192 (t0) REVERT: B 158 VAL cc_start: 0.9254 (t) cc_final: 0.9039 (p) REVERT: B 172 GLU cc_start: 0.8997 (tp30) cc_final: 0.8761 (tp30) REVERT: B 217 MET cc_start: 0.8975 (ptt) cc_final: 0.8728 (ppp) REVERT: B 254 ASP cc_start: 0.8248 (t0) cc_final: 0.7775 (t0) REVERT: G 13 ARG cc_start: 0.8980 (ptm-80) cc_final: 0.8664 (tmm160) REVERT: G 14 LYS cc_start: 0.9563 (tppp) cc_final: 0.9277 (tppt) REVERT: G 29 LYS cc_start: 0.9127 (mmtt) cc_final: 0.8854 (mmtm) REVERT: G 46 LYS cc_start: 0.9120 (mtmm) cc_final: 0.8863 (mppt) REVERT: N 73 ASP cc_start: 0.8250 (t0) cc_final: 0.7709 (t0) REVERT: N 103 PHE cc_start: 0.9367 (m-80) cc_final: 0.8896 (m-80) REVERT: N 114 THR cc_start: 0.9074 (OUTLIER) cc_final: 0.8801 (p) outliers start: 23 outliers final: 14 residues processed: 153 average time/residue: 0.5531 time to fit residues: 90.8802 Evaluate side-chains 144 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 128 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 143 VAL Chi-restraints excluded: chain R residue 153 LEU Chi-restraints excluded: chain R residue 160 SER Chi-restraints excluded: chain R residue 298 ILE Chi-restraints excluded: chain R residue 305 MET Chi-restraints excluded: chain R residue 352 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain G residue 36 ASP Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 114 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 106 optimal weight: 0.0050 chunk 82 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 65 optimal weight: 0.0870 chunk 101 optimal weight: 3.9990 chunk 44 optimal weight: 6.9990 chunk 71 optimal weight: 0.9980 chunk 90 optimal weight: 0.5980 chunk 79 optimal weight: 3.9990 chunk 102 optimal weight: 0.0270 chunk 57 optimal weight: 0.9990 overall best weight: 0.2830 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.119303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.081285 restraints weight = 17063.422| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 3.13 r_work: 0.3004 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.4632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9628 Z= 0.111 Angle : 0.549 8.969 13074 Z= 0.286 Chirality : 0.039 0.166 1454 Planarity : 0.003 0.038 1638 Dihedral : 4.281 56.040 1668 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.93 % Allowed : 19.15 % Favored : 78.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % 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: 1.41 (0.26), residues: 1136 helix: 2.73 (0.24), residues: 456 sheet: -0.22 (0.32), residues: 249 loop : -0.26 (0.31), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG N 105 TYR 0.021 0.001 TYR N 60 PHE 0.016 0.001 PHE R 270 TRP 0.016 0.001 TRP B 169 HIS 0.005 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00253 ( 9622) covalent geometry : angle 0.54777 (13062) SS BOND : bond 0.00138 ( 6) SS BOND : angle 1.53023 ( 12) hydrogen bonds : bond 0.03454 ( 487) hydrogen bonds : angle 3.89159 ( 1413) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 136 time to evaluate : 0.347 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 279 TYR cc_start: 0.8192 (t80) cc_final: 0.7769 (t80) REVERT: R 298 ILE cc_start: 0.8564 (OUTLIER) cc_final: 0.8293 (tt) REVERT: R 397 LYS cc_start: 0.8617 (mppt) cc_final: 0.8292 (mppt) REVERT: R 398 GLU cc_start: 0.8716 (tm-30) cc_final: 0.8451 (tm-30) REVERT: P 18 HIS cc_start: 0.8512 (t-170) cc_final: 0.7539 (t70) REVERT: P 21 ASP cc_start: 0.9231 (m-30) cc_final: 0.8995 (p0) REVERT: A 27 GLU cc_start: 0.8905 (mm-30) cc_final: 0.8402 (mm-30) REVERT: A 33 ASP cc_start: 0.8681 (t70) cc_final: 0.8095 (m-30) REVERT: A 365 CYS cc_start: 0.7538 (m) cc_final: 0.7306 (t) REVERT: B 12 GLU cc_start: 0.9137 (tp30) cc_final: 0.8743 (tp30) REVERT: B 23 LYS cc_start: 0.9464 (mmmt) cc_final: 0.9164 (tptp) REVERT: B 155 ASN cc_start: 0.8776 (m-40) cc_final: 0.8221 (t0) REVERT: B 158 VAL cc_start: 0.9224 (t) cc_final: 0.9014 (p) REVERT: B 215 GLU cc_start: 0.8150 (tt0) cc_final: 0.7641 (tm-30) REVERT: B 254 ASP cc_start: 0.8293 (t0) cc_final: 0.7796 (t0) REVERT: G 13 ARG cc_start: 0.8965 (ptm-80) cc_final: 0.8630 (tmm160) REVERT: G 14 LYS cc_start: 0.9568 (tppp) cc_final: 0.9234 (tppt) REVERT: G 29 LYS cc_start: 0.9092 (mmtt) cc_final: 0.8829 (mmtm) REVERT: G 46 LYS cc_start: 0.9085 (mtmm) cc_final: 0.8846 (mppt) REVERT: N 73 ASP cc_start: 0.8205 (t0) cc_final: 0.7676 (t0) REVERT: N 103 PHE cc_start: 0.9345 (m-80) cc_final: 0.8914 (m-80) REVERT: N 114 THR cc_start: 0.9044 (OUTLIER) cc_final: 0.8837 (p) outliers start: 19 outliers final: 14 residues processed: 144 average time/residue: 0.5559 time to fit residues: 85.5013 Evaluate side-chains 146 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 130 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 143 VAL Chi-restraints excluded: chain R residue 160 SER Chi-restraints excluded: chain R residue 298 ILE Chi-restraints excluded: chain R residue 305 MET Chi-restraints excluded: chain R residue 352 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 36 ASP Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 114 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 64 optimal weight: 8.9990 chunk 84 optimal weight: 0.8980 chunk 49 optimal weight: 0.7980 chunk 93 optimal weight: 4.9990 chunk 102 optimal weight: 0.0070 chunk 63 optimal weight: 6.9990 chunk 71 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 68 optimal weight: 0.0670 chunk 39 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 overall best weight: 0.5136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.118137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.079060 restraints weight = 17048.186| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 3.17 r_work: 0.2992 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.4730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9628 Z= 0.122 Angle : 0.572 8.911 13074 Z= 0.296 Chirality : 0.040 0.170 1454 Planarity : 0.004 0.038 1638 Dihedral : 4.291 56.334 1668 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.93 % Allowed : 19.66 % Favored : 78.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % 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: 1136 helix: 2.70 (0.24), residues: 458 sheet: -0.30 (0.32), residues: 250 loop : -0.30 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG N 105 TYR 0.019 0.001 TYR N 60 PHE 0.015 0.001 PHE R 270 TRP 0.019 0.001 TRP P 25 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 9622) covalent geometry : angle 0.57067 (13062) SS BOND : bond 0.00066 ( 6) SS BOND : angle 1.49753 ( 12) hydrogen bonds : bond 0.03502 ( 487) hydrogen bonds : angle 3.90552 ( 1413) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 135 time to evaluate : 0.293 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 279 TYR cc_start: 0.8200 (t80) cc_final: 0.7782 (t80) REVERT: R 298 ILE cc_start: 0.8596 (OUTLIER) cc_final: 0.8335 (tt) REVERT: R 397 LYS cc_start: 0.8649 (mppt) cc_final: 0.8318 (mppt) REVERT: R 398 GLU cc_start: 0.8725 (tm-30) cc_final: 0.8462 (tm-30) REVERT: P 18 HIS cc_start: 0.8546 (t-170) cc_final: 0.7581 (t70) REVERT: P 21 ASP cc_start: 0.9217 (m-30) cc_final: 0.8965 (p0) REVERT: A 27 GLU cc_start: 0.8897 (mm-30) cc_final: 0.8410 (mm-30) REVERT: A 33 ASP cc_start: 0.8683 (t70) cc_final: 0.8250 (m-30) REVERT: A 365 CYS cc_start: 0.7535 (m) cc_final: 0.7311 (t) REVERT: B 12 GLU cc_start: 0.9076 (tp30) cc_final: 0.8735 (tp30) REVERT: B 23 LYS cc_start: 0.9451 (mmmt) cc_final: 0.9066 (tptp) REVERT: B 155 ASN cc_start: 0.8770 (m-40) cc_final: 0.8240 (t0) REVERT: B 158 VAL cc_start: 0.9245 (t) cc_final: 0.9029 (p) REVERT: B 215 GLU cc_start: 0.7888 (tt0) cc_final: 0.7564 (tm-30) REVERT: B 254 ASP cc_start: 0.8209 (t0) cc_final: 0.7786 (t0) REVERT: G 13 ARG cc_start: 0.8939 (ptm-80) cc_final: 0.8605 (tmm160) REVERT: G 14 LYS cc_start: 0.9548 (tppp) cc_final: 0.9210 (tppt) REVERT: G 29 LYS cc_start: 0.9090 (mmtt) cc_final: 0.8824 (mmtm) REVERT: G 46 LYS cc_start: 0.9092 (mtmm) cc_final: 0.8860 (mppt) REVERT: N 73 ASP cc_start: 0.8185 (t0) cc_final: 0.7637 (t0) REVERT: N 103 PHE cc_start: 0.9322 (m-80) cc_final: 0.8894 (m-80) REVERT: N 114 THR cc_start: 0.9070 (OUTLIER) cc_final: 0.8866 (p) outliers start: 19 outliers final: 13 residues processed: 144 average time/residue: 0.6219 time to fit residues: 95.4553 Evaluate side-chains 145 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 130 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 143 VAL Chi-restraints excluded: chain R residue 153 LEU Chi-restraints excluded: chain R residue 160 SER Chi-restraints excluded: chain R residue 298 ILE Chi-restraints excluded: chain R residue 305 MET Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain G residue 36 ASP Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 114 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 25 optimal weight: 0.8980 chunk 31 optimal weight: 7.9990 chunk 79 optimal weight: 3.9990 chunk 98 optimal weight: 4.9990 chunk 84 optimal weight: 0.5980 chunk 76 optimal weight: 0.6980 chunk 30 optimal weight: 0.0870 chunk 11 optimal weight: 1.9990 chunk 6 optimal weight: 7.9990 chunk 97 optimal weight: 8.9990 chunk 78 optimal weight: 0.9990 overall best weight: 0.6560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.117736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.078657 restraints weight = 17084.669| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 3.17 r_work: 0.3000 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.4800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9628 Z= 0.132 Angle : 0.605 9.597 13074 Z= 0.310 Chirality : 0.040 0.169 1454 Planarity : 0.004 0.063 1638 Dihedral : 4.308 56.011 1668 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.62 % Allowed : 20.47 % Favored : 77.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % 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: 1.26 (0.25), residues: 1136 helix: 2.58 (0.24), residues: 464 sheet: -0.27 (0.32), residues: 250 loop : -0.40 (0.30), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG B 134 TYR 0.020 0.001 TYR N 60 PHE 0.016 0.001 PHE R 376 TRP 0.020 0.001 TRP P 25 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 9622) covalent geometry : angle 0.60363 (13062) SS BOND : bond 0.00087 ( 6) SS BOND : angle 1.58699 ( 12) hydrogen bonds : bond 0.03533 ( 487) hydrogen bonds : angle 3.93585 ( 1413) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3456.88 seconds wall clock time: 59 minutes 33.75 seconds (3573.75 seconds total)