Starting phenix.real_space_refine on Fri Mar 14 05:14:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7dty_30860/03_2025/7dty_30860.cif Found real_map, /net/cci-nas-00/data/ceres_data/7dty_30860/03_2025/7dty_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_2025/7dty_30860.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7dty_30860/03_2025/7dty_30860.map" model { file = "/net/cci-nas-00/data/ceres_data/7dty_30860/03_2025/7dty_30860.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7dty_30860/03_2025/7dty_30860.cif" } resolution = 2.98 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.020 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 5.60, per 1000 atoms: 0.60 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: 2.38 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 0.90 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: 2.66 Time building geometry restraints manager: 2.78 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: 1.230 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: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 23.550 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.710 ------------------------------------------------------------------------------- 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 9622 Z= 0.249 Angle : 0.775 7.728 13062 Z= 0.427 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (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 TRP 0.030 0.003 TRP A 281 HIS 0.017 0.002 HIS R 409 PHE 0.024 0.002 PHE B 199 TYR 0.024 0.002 TYR P 1 ARG 0.006 0.000 ARG R 183 *********************** 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 : 1.055 Fit side-chains revert: symmetry clash 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: 0.8149 (t80) REVERT: A 12 GLN cc_start: 0.8015 (mm-40) cc_final: 0.7726 (pp30) REVERT: B 36 ASN cc_start: 0.8792 (m-40) cc_final: 0.8563 (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: 0.7906 (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: 0.8477 (tp30) REVERT: B 217 MET cc_start: 0.7850 (ptt) cc_final: 0.7620 (ptm) 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: 0.8457 (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: 0.7569 (t0) REVERT: N 103 PHE cc_start: 0.9137 (m-80) cc_final: 0.8641 (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: 1.2131 time to fit residues: 390.3331 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 : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 95 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 47 optimal weight: 0.5980 chunk 29 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 88 optimal weight: 6.9990 chunk 34 optimal weight: 0.9990 chunk 53 optimal weight: 4.9990 chunk 65 optimal weight: 0.8980 chunk 102 optimal weight: 3.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 93 HIS R 102 GLN R 224 GLN R 242 HIS ** P 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.120233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.080760 restraints weight = 17018.268| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 3.24 r_work: 0.2989 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.2951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9622 Z= 0.249 Angle : 0.593 6.693 13062 Z= 0.312 Chirality : 0.042 0.136 1454 Planarity : 0.004 0.039 1638 Dihedral : 5.011 41.064 1668 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 3.75 % Allowed : 13.48 % Favored : 82.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.24), residues: 1136 helix: 1.55 (0.23), residues: 449 sheet: -0.27 (0.32), residues: 233 loop : -1.01 (0.27), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 281 HIS 0.008 0.001 HIS A 357 PHE 0.014 0.002 PHE B 199 TYR 0.022 0.002 TYR R 335 ARG 0.009 0.001 ARG B 197 *********************** 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 224 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 187 time to evaluate : 0.974 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 102 GLN cc_start: 0.6311 (OUTLIER) cc_final: 0.5977 (pm20) REVERT: R 357 PHE cc_start: 0.9154 (m-80) cc_final: 0.8708 (m-80) REVERT: P 10 TYR cc_start: 0.8689 (t80) cc_final: 0.8415 (t80) REVERT: P 18 HIS cc_start: 0.8453 (t-170) cc_final: 0.8223 (t-170) REVERT: P 25 TRP cc_start: 0.8387 (t60) cc_final: 0.8018 (t60) REVERT: A 27 GLU cc_start: 0.8879 (mm-30) cc_final: 0.8434 (mm-30) REVERT: A 365 CYS cc_start: 0.7601 (m) cc_final: 0.6792 (p) REVERT: B 36 ASN cc_start: 0.9199 (m-40) cc_final: 0.8794 (p0) REVERT: B 78 LYS cc_start: 0.8537 (OUTLIER) cc_final: 0.8274 (mptt) REVERT: B 127 LYS cc_start: 0.8511 (tttt) cc_final: 0.8106 (ttmm) REVERT: B 155 ASN cc_start: 0.8715 (m-40) cc_final: 0.8068 (t0) REVERT: B 158 VAL cc_start: 0.9291 (t) cc_final: 0.9006 (p) REVERT: B 172 GLU cc_start: 0.9056 (tp30) cc_final: 0.8623 (tp30) REVERT: B 197 ARG cc_start: 0.8617 (tpp-160) cc_final: 0.8177 (mmm160) REVERT: B 215 GLU cc_start: 0.8063 (OUTLIER) cc_final: 0.7682 (pt0) REVERT: B 217 MET cc_start: 0.9062 (ptt) cc_final: 0.8540 (ppp) REVERT: B 292 PHE cc_start: 0.9142 (m-10) cc_final: 0.8884 (m-80) REVERT: G 29 LYS cc_start: 0.9151 (mmtt) cc_final: 0.8884 (mmtm) REVERT: G 52 THR cc_start: 0.8393 (m) cc_final: 0.7981 (p) REVERT: N 11 LEU cc_start: 0.8986 (tp) cc_final: 0.8422 (tp) REVERT: N 69 THR cc_start: 0.8809 (m) cc_final: 0.8267 (p) REVERT: N 73 ASP cc_start: 0.8194 (t0) cc_final: 0.7613 (t0) REVERT: N 105 ARG cc_start: 0.8645 (mtm-85) cc_final: 0.7916 (mtp85) REVERT: N 125 THR cc_start: 0.8992 (m) cc_final: 0.8550 (p) outliers start: 37 outliers final: 11 residues processed: 205 average time/residue: 1.1513 time to fit residues: 252.9959 Evaluate side-chains 158 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 144 time to evaluate : 1.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 102 GLN 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 191 ASP Chi-restraints excluded: chain R residue 245 LEU Chi-restraints excluded: chain R residue 327 THR Chi-restraints excluded: chain B residue 78 LYS 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 280 LYS Chi-restraints excluded: chain G residue 36 ASP Chi-restraints excluded: chain G residue 41 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 95 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 99 optimal weight: 4.9990 chunk 2 optimal weight: 30.0000 chunk 90 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 20 optimal weight: 0.1980 chunk 37 optimal weight: 0.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 102 GLN ** P 20 GLN ** 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.117492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.077724 restraints weight = 17249.411| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 3.21 r_work: 0.2981 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.3523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9622 Z= 0.258 Angle : 0.588 11.027 13062 Z= 0.307 Chirality : 0.042 0.146 1454 Planarity : 0.004 0.054 1638 Dihedral : 4.864 47.763 1668 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 3.34 % Allowed : 15.30 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.25), residues: 1136 helix: 2.23 (0.23), residues: 449 sheet: -0.23 (0.32), residues: 238 loop : -0.70 (0.28), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 281 HIS 0.007 0.001 HIS A 220 PHE 0.015 0.001 PHE A 212 TYR 0.019 0.002 TYR R 335 ARG 0.005 0.001 ARG A 228 *********************** 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: 33 poor density : 152 time to evaluate : 1.097 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 102 GLN cc_start: 0.6068 (OUTLIER) cc_final: 0.5751 (pm20) REVERT: R 298 ILE cc_start: 0.8593 (OUTLIER) cc_final: 0.8318 (tt) REVERT: R 344 LEU cc_start: 0.8115 (OUTLIER) cc_final: 0.7881 (mm) REVERT: R 376 PHE cc_start: 0.8830 (t80) cc_final: 0.8627 (t80) REVERT: P 10 TYR cc_start: 0.8886 (t80) cc_final: 0.8642 (t80) REVERT: P 18 HIS cc_start: 0.8575 (t-170) cc_final: 0.8314 (t-170) REVERT: A 27 GLU cc_start: 0.8906 (mm-30) cc_final: 0.8430 (mm-30) REVERT: A 365 CYS cc_start: 0.7667 (m) cc_final: 0.6837 (p) REVERT: B 155 ASN cc_start: 0.8790 (m-40) cc_final: 0.8182 (t0) REVERT: B 172 GLU cc_start: 0.8900 (tp30) cc_final: 0.8523 (tp30) REVERT: B 215 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7808 (pt0) REVERT: B 217 MET cc_start: 0.8988 (ptt) cc_final: 0.8593 (ppp) REVERT: B 254 ASP cc_start: 0.8269 (t0) cc_final: 0.7871 (t0) REVERT: G 13 ARG cc_start: 0.8970 (ptm-80) cc_final: 0.8523 (tmm160) REVERT: G 14 LYS cc_start: 0.9587 (tppp) cc_final: 0.9301 (tppt) REVERT: G 29 LYS cc_start: 0.9166 (mmtt) cc_final: 0.8924 (mmtm) REVERT: G 46 LYS cc_start: 0.9152 (mtmm) cc_final: 0.8834 (mppt) REVERT: G 52 THR cc_start: 0.8646 (m) cc_final: 0.8271 (p) REVERT: N 73 ASP cc_start: 0.8229 (t0) cc_final: 0.7683 (t0) REVERT: N 105 ARG cc_start: 0.8689 (mtm-85) cc_final: 0.8124 (mtp85) outliers start: 33 outliers final: 9 residues processed: 172 average time/residue: 1.1701 time to fit residues: 215.7121 Evaluate side-chains 148 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 135 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 102 GLN 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 387 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 336 LEU Chi-restraints excluded: chain G residue 36 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 42 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 21 optimal weight: 0.4980 chunk 64 optimal weight: 6.9990 chunk 92 optimal weight: 0.8980 chunk 59 optimal weight: 6.9990 chunk 19 optimal weight: 0.8980 chunk 89 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 71 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 102 GLN P 20 GLN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.117653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.078148 restraints weight = 17094.590| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 3.19 r_work: 0.2993 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.3798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9622 Z= 0.211 Angle : 0.565 8.105 13062 Z= 0.294 Chirality : 0.040 0.142 1454 Planarity : 0.004 0.044 1638 Dihedral : 4.699 50.228 1668 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 2.84 % Allowed : 16.21 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.25), residues: 1136 helix: 2.38 (0.24), residues: 455 sheet: -0.16 (0.32), residues: 238 loop : -0.63 (0.29), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP P 25 HIS 0.007 0.001 HIS A 220 PHE 0.014 0.001 PHE R 270 TYR 0.020 0.002 TYR N 60 ARG 0.005 0.000 ARG A 228 *********************** 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 176 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 148 time to evaluate : 1.086 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 102 GLN cc_start: 0.5404 (OUTLIER) cc_final: 0.5027 (pm20) REVERT: R 153 LEU cc_start: 0.9092 (OUTLIER) cc_final: 0.8880 (tm) REVERT: R 203 ASP cc_start: 0.8486 (m-30) cc_final: 0.7946 (t70) REVERT: R 279 TYR cc_start: 0.8190 (t80) cc_final: 0.7689 (t80) REVERT: R 298 ILE cc_start: 0.8590 (OUTLIER) cc_final: 0.8322 (tt) REVERT: R 344 LEU cc_start: 0.8137 (OUTLIER) cc_final: 0.7877 (mm) REVERT: R 345 PHE cc_start: 0.8563 (OUTLIER) cc_final: 0.8269 (t80) REVERT: R 376 PHE cc_start: 0.8913 (t80) cc_final: 0.8673 (t80) REVERT: R 398 GLU cc_start: 0.8239 (mp0) cc_final: 0.7899 (mp0) REVERT: P 10 TYR cc_start: 0.8885 (t80) cc_final: 0.8680 (t80) REVERT: P 18 HIS cc_start: 0.8556 (t-170) cc_final: 0.8296 (t-170) REVERT: A 27 GLU cc_start: 0.8901 (mm-30) cc_final: 0.8426 (mm-30) REVERT: A 365 CYS cc_start: 0.7652 (m) cc_final: 0.7416 (t) REVERT: B 12 GLU cc_start: 0.9241 (tp30) cc_final: 0.8969 (tp30) REVERT: B 13 GLN cc_start: 0.9004 (pp30) cc_final: 0.8715 (pp30) REVERT: B 15 LYS cc_start: 0.9268 (tptt) cc_final: 0.8851 (tmmt) REVERT: B 23 LYS cc_start: 0.9482 (mmmt) cc_final: 0.9156 (tptp) REVERT: B 155 ASN cc_start: 0.8787 (m-40) cc_final: 0.8192 (t0) REVERT: B 158 VAL cc_start: 0.9268 (t) cc_final: 0.8993 (p) REVERT: B 172 GLU cc_start: 0.8872 (tp30) cc_final: 0.8503 (tp30) REVERT: B 217 MET cc_start: 0.9003 (ptt) cc_final: 0.8658 (ptm) REVERT: B 254 ASP cc_start: 0.8272 (t0) cc_final: 0.7877 (t0) REVERT: G 13 ARG cc_start: 0.8944 (ptm-80) cc_final: 0.8721 (ptm-80) REVERT: G 14 LYS cc_start: 0.9620 (tppp) cc_final: 0.9398 (tppp) REVERT: G 29 LYS cc_start: 0.9090 (mmtt) cc_final: 0.8837 (mmtm) REVERT: G 46 LYS cc_start: 0.9150 (mtmm) cc_final: 0.8849 (mppt) REVERT: G 52 THR cc_start: 0.8676 (m) cc_final: 0.8330 (p) REVERT: N 35 ASN cc_start: 0.8864 (OUTLIER) cc_final: 0.8624 (p0) REVERT: N 73 ASP cc_start: 0.8235 (t0) cc_final: 0.7726 (t0) REVERT: N 87 LYS cc_start: 0.9028 (mtmm) cc_final: 0.8825 (mtmm) outliers start: 28 outliers final: 6 residues processed: 166 average time/residue: 1.3192 time to fit residues: 234.8973 Evaluate side-chains 152 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 140 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 102 GLN 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 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 N residue 35 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 42 optimal weight: 3.9990 chunk 57 optimal weight: 0.9990 chunk 54 optimal weight: 4.9990 chunk 86 optimal weight: 3.9990 chunk 74 optimal weight: 0.7980 chunk 106 optimal weight: 0.9990 chunk 56 optimal weight: 0.9990 chunk 78 optimal weight: 0.5980 chunk 108 optimal weight: 2.9990 chunk 64 optimal weight: 7.9990 chunk 31 optimal weight: 0.0040 overall best weight: 0.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 102 GLN 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 = 0.3776 r_free = 0.3776 target = 0.118032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.078517 restraints weight = 17144.392| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 3.20 r_work: 0.2998 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.3922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9622 Z= 0.191 Angle : 0.547 7.966 13062 Z= 0.287 Chirality : 0.040 0.136 1454 Planarity : 0.004 0.047 1638 Dihedral : 4.594 52.046 1668 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.84 % Allowed : 16.51 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.25), residues: 1136 helix: 2.51 (0.24), residues: 455 sheet: -0.13 (0.32), residues: 239 loop : -0.55 (0.29), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP P 25 HIS 0.006 0.001 HIS A 220 PHE 0.014 0.001 PHE R 270 TYR 0.020 0.001 TYR N 60 ARG 0.005 0.000 ARG N 105 *********************** 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 168 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 140 time to evaluate : 1.097 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 102 GLN cc_start: 0.5785 (OUTLIER) cc_final: 0.5232 (pm20) REVERT: R 203 ASP cc_start: 0.8544 (m-30) cc_final: 0.8018 (t70) REVERT: R 279 TYR cc_start: 0.8195 (t80) cc_final: 0.7717 (t80) REVERT: R 298 ILE cc_start: 0.8567 (OUTLIER) cc_final: 0.8310 (tt) REVERT: R 344 LEU cc_start: 0.8181 (OUTLIER) cc_final: 0.7932 (mm) REVERT: R 345 PHE cc_start: 0.8585 (OUTLIER) cc_final: 0.8299 (t80) REVERT: R 398 GLU cc_start: 0.8248 (mp0) cc_final: 0.7921 (mp0) REVERT: P 18 HIS cc_start: 0.8539 (t-170) cc_final: 0.8295 (t-170) REVERT: A 27 GLU cc_start: 0.8916 (mm-30) cc_final: 0.8416 (mm-30) REVERT: A 347 ARG cc_start: 0.8782 (OUTLIER) cc_final: 0.8557 (ptp-110) REVERT: A 365 CYS cc_start: 0.7664 (m) cc_final: 0.7421 (t) REVERT: B 12 GLU cc_start: 0.9288 (tp30) cc_final: 0.8944 (tp30) REVERT: B 15 LYS cc_start: 0.9252 (tptt) cc_final: 0.8843 (tmmt) REVERT: B 23 LYS cc_start: 0.9461 (mmmt) cc_final: 0.9159 (tptp) REVERT: B 155 ASN cc_start: 0.8786 (m-40) cc_final: 0.8197 (t0) REVERT: B 158 VAL cc_start: 0.9221 (t) cc_final: 0.8951 (p) REVERT: B 172 GLU cc_start: 0.8845 (tp30) cc_final: 0.8513 (tp30) REVERT: B 217 MET cc_start: 0.8924 (ptt) cc_final: 0.8625 (ppp) REVERT: B 254 ASP cc_start: 0.8274 (t0) cc_final: 0.7870 (t0) REVERT: G 13 ARG cc_start: 0.8881 (ptm-80) cc_final: 0.8577 (ptm-80) REVERT: G 14 LYS cc_start: 0.9618 (tppp) cc_final: 0.9313 (tppt) REVERT: G 29 LYS cc_start: 0.9094 (mmtt) cc_final: 0.8839 (mmtm) REVERT: G 46 LYS cc_start: 0.9124 (mtmm) cc_final: 0.8838 (mppt) REVERT: G 52 THR cc_start: 0.8769 (m) cc_final: 0.8474 (p) REVERT: N 11 LEU cc_start: 0.9295 (mm) cc_final: 0.9071 (mm) REVERT: N 35 ASN cc_start: 0.8875 (OUTLIER) cc_final: 0.8604 (p0) REVERT: N 73 ASP cc_start: 0.8208 (t0) cc_final: 0.7708 (t0) outliers start: 28 outliers final: 12 residues processed: 155 average time/residue: 1.2155 time to fit residues: 202.1329 Evaluate side-chains 151 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 133 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 102 GLN Chi-restraints excluded: chain R residue 143 VAL Chi-restraints excluded: chain R residue 153 LEU Chi-restraints excluded: chain R residue 154 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 344 LEU Chi-restraints excluded: chain R residue 345 PHE Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 347 ARG 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 99 optimal weight: 4.9990 chunk 53 optimal weight: 5.9990 chunk 78 optimal weight: 0.7980 chunk 3 optimal weight: 8.9990 chunk 87 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 45 optimal weight: 0.8980 chunk 5 optimal weight: 9.9990 chunk 41 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 102 GLN R 230 ASN ** A 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 220 HIS ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.113769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.073111 restraints weight = 17404.982| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 3.21 r_work: 0.2888 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.4420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 9622 Z= 0.395 Angle : 0.622 8.406 13062 Z= 0.326 Chirality : 0.043 0.150 1454 Planarity : 0.004 0.051 1638 Dihedral : 4.862 56.987 1668 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 3.55 % Allowed : 16.11 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.25), residues: 1136 helix: 2.30 (0.24), residues: 463 sheet: -0.18 (0.32), residues: 245 loop : -0.50 (0.30), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP P 25 HIS 0.007 0.002 HIS A 357 PHE 0.016 0.002 PHE R 376 TYR 0.022 0.002 TYR N 60 ARG 0.006 0.000 ARG N 105 *********************** 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 180 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 145 time to evaluate : 0.984 Fit side-chains revert: symmetry clash REVERT: R 102 GLN cc_start: 0.5360 (OUTLIER) cc_final: 0.5002 (pm20) REVERT: R 203 ASP cc_start: 0.8639 (m-30) cc_final: 0.8057 (t70) REVERT: R 279 TYR cc_start: 0.8322 (t80) cc_final: 0.7807 (t80) REVERT: R 378 ILE cc_start: 0.8765 (OUTLIER) cc_final: 0.8432 (tt) REVERT: P 18 HIS cc_start: 0.8545 (t-170) cc_final: 0.7473 (t70) REVERT: P 21 ASP cc_start: 0.9264 (m-30) cc_final: 0.8944 (p0) REVERT: A 27 GLU cc_start: 0.8962 (mm-30) cc_final: 0.8552 (mm-30) REVERT: A 33 ASP cc_start: 0.8802 (t70) cc_final: 0.8420 (m-30) REVERT: A 365 CYS cc_start: 0.7919 (m) cc_final: 0.7631 (t) REVERT: B 12 GLU cc_start: 0.9330 (tp30) cc_final: 0.9088 (tp30) REVERT: B 23 LYS cc_start: 0.9465 (mmmt) cc_final: 0.9201 (tptp) REVERT: B 45 MET cc_start: 0.9326 (mtm) cc_final: 0.9114 (mtm) REVERT: B 155 ASN cc_start: 0.8856 (m-40) cc_final: 0.8339 (t0) REVERT: B 172 GLU cc_start: 0.8961 (tp30) cc_final: 0.8667 (tp30) REVERT: B 217 MET cc_start: 0.8974 (ptt) cc_final: 0.8613 (ppp) REVERT: B 254 ASP cc_start: 0.8397 (t0) cc_final: 0.8105 (t0) REVERT: G 13 ARG cc_start: 0.8961 (ptm-80) cc_final: 0.8635 (ptm-80) REVERT: G 14 LYS cc_start: 0.9606 (tppp) cc_final: 0.9296 (tppt) REVERT: G 29 LYS cc_start: 0.9144 (mmtt) cc_final: 0.8855 (mmtm) REVERT: G 46 LYS cc_start: 0.9161 (OUTLIER) cc_final: 0.8916 (mppt) REVERT: G 52 THR cc_start: 0.8825 (m) cc_final: 0.8491 (p) REVERT: N 11 LEU cc_start: 0.9254 (mm) cc_final: 0.8819 (mm) REVERT: N 35 ASN cc_start: 0.8880 (OUTLIER) cc_final: 0.8627 (p0) REVERT: N 73 ASP cc_start: 0.8332 (t0) cc_final: 0.7736 (t0) REVERT: N 76 LYS cc_start: 0.9480 (tppp) cc_final: 0.9235 (tppp) REVERT: N 78 THR cc_start: 0.8729 (m) cc_final: 0.8405 (t) REVERT: N 114 THR cc_start: 0.9067 (p) cc_final: 0.8738 (t) REVERT: N 125 THR cc_start: 0.9081 (m) cc_final: 0.8751 (p) outliers start: 35 outliers final: 12 residues processed: 169 average time/residue: 1.1181 time to fit residues: 203.1609 Evaluate side-chains 149 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 133 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 102 GLN 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 245 LEU Chi-restraints excluded: chain R residue 298 ILE Chi-restraints excluded: chain R residue 347 VAL Chi-restraints excluded: chain R residue 378 ILE 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 275 SER Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 83 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 48 optimal weight: 0.6980 chunk 99 optimal weight: 0.8980 chunk 40 optimal weight: 0.9990 chunk 71 optimal weight: 0.6980 chunk 78 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 101 optimal weight: 2.9990 chunk 7 optimal weight: 5.9990 chunk 72 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.116518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.077406 restraints weight = 17308.664| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 3.17 r_work: 0.2936 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.4458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 9622 Z= 0.216 Angle : 0.582 8.286 13062 Z= 0.304 Chirality : 0.041 0.163 1454 Planarity : 0.004 0.051 1638 Dihedral : 4.705 59.355 1668 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.53 % Allowed : 18.14 % Favored : 79.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.25), residues: 1136 helix: 2.44 (0.24), residues: 456 sheet: -0.09 (0.32), residues: 248 loop : -0.39 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 169 HIS 0.006 0.001 HIS A 220 PHE 0.014 0.001 PHE R 270 TYR 0.021 0.001 TYR N 60 ARG 0.009 0.000 ARG A 333 *********************** 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 167 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 142 time to evaluate : 0.864 Fit side-chains revert: symmetry clash REVERT: R 203 ASP cc_start: 0.8651 (m-30) cc_final: 0.8047 (t70) REVERT: R 279 TYR cc_start: 0.8276 (t80) cc_final: 0.7771 (t80) REVERT: R 344 LEU cc_start: 0.8257 (OUTLIER) cc_final: 0.7997 (mm) REVERT: P 18 HIS cc_start: 0.8550 (t-170) cc_final: 0.7500 (t70) REVERT: P 21 ASP cc_start: 0.9240 (m-30) cc_final: 0.8965 (p0) REVERT: A 27 GLU cc_start: 0.8926 (mm-30) cc_final: 0.8464 (mm-30) REVERT: A 33 ASP cc_start: 0.8692 (t70) cc_final: 0.8312 (m-30) REVERT: A 365 CYS cc_start: 0.7751 (m) cc_final: 0.7466 (t) REVERT: B 12 GLU cc_start: 0.9241 (tp30) cc_final: 0.8839 (tp30) REVERT: B 15 LYS cc_start: 0.9247 (tptt) cc_final: 0.8778 (tmmt) REVERT: B 23 LYS cc_start: 0.9449 (mmmt) cc_final: 0.9205 (tptp) REVERT: B 45 MET cc_start: 0.9317 (mtm) cc_final: 0.9114 (mtm) REVERT: B 155 ASN cc_start: 0.8801 (m-40) cc_final: 0.8285 (t0) REVERT: B 172 GLU cc_start: 0.8872 (tp30) cc_final: 0.8565 (tp30) REVERT: B 217 MET cc_start: 0.9017 (ptt) cc_final: 0.8714 (ppp) REVERT: B 254 ASP cc_start: 0.8329 (t0) cc_final: 0.8050 (t0) REVERT: G 13 ARG cc_start: 0.8929 (ptm-80) cc_final: 0.8602 (ptm-80) REVERT: G 14 LYS cc_start: 0.9614 (tppp) cc_final: 0.9296 (tppt) REVERT: G 29 LYS cc_start: 0.9148 (mmtt) cc_final: 0.8857 (mmtm) REVERT: G 46 LYS cc_start: 0.9123 (mtmm) cc_final: 0.8882 (mppt) REVERT: G 52 THR cc_start: 0.8917 (m) cc_final: 0.8647 (p) REVERT: N 11 LEU cc_start: 0.9264 (mm) cc_final: 0.8840 (mm) REVERT: N 35 ASN cc_start: 0.8836 (OUTLIER) cc_final: 0.8566 (p0) REVERT: N 73 ASP cc_start: 0.8256 (t0) cc_final: 0.7661 (t0) REVERT: N 76 LYS cc_start: 0.9452 (tppp) cc_final: 0.9144 (tppp) REVERT: N 77 ASN cc_start: 0.8895 (OUTLIER) cc_final: 0.8541 (t0) REVERT: N 78 THR cc_start: 0.8674 (m) cc_final: 0.8169 (p) REVERT: N 114 THR cc_start: 0.9060 (p) cc_final: 0.8746 (t) REVERT: N 125 THR cc_start: 0.9081 (m) cc_final: 0.8746 (p) outliers start: 25 outliers final: 13 residues processed: 158 average time/residue: 1.1405 time to fit residues: 193.6023 Evaluate side-chains 155 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 139 time to evaluate : 0.972 ------------------------------------------------------------------------------- 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 344 LEU Chi-restraints excluded: chain A residue 347 ARG 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 60 optimal weight: 3.9990 chunk 69 optimal weight: 0.8980 chunk 5 optimal weight: 0.8980 chunk 110 optimal weight: 0.9980 chunk 109 optimal weight: 2.9990 chunk 96 optimal weight: 7.9990 chunk 98 optimal weight: 5.9990 chunk 82 optimal weight: 1.9990 chunk 4 optimal weight: 8.9990 chunk 112 optimal weight: 0.9980 chunk 90 optimal weight: 1.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 35 ASN ** 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 = 0.3757 r_free = 0.3757 target = 0.115761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.076853 restraints weight = 17372.848| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 3.15 r_work: 0.2937 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.4581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9622 Z= 0.259 Angle : 0.594 8.398 13062 Z= 0.311 Chirality : 0.041 0.143 1454 Planarity : 0.004 0.045 1638 Dihedral : 4.632 56.669 1668 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.63 % Allowed : 18.24 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.26), residues: 1136 helix: 2.44 (0.24), residues: 459 sheet: -0.13 (0.32), residues: 246 loop : -0.34 (0.31), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 233 HIS 0.006 0.001 HIS A 220 PHE 0.014 0.001 PHE R 270 TYR 0.022 0.002 TYR N 60 ARG 0.006 0.000 ARG N 105 *********************** 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 162 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 136 time to evaluate : 1.109 Fit side-chains revert: symmetry clash REVERT: R 203 ASP cc_start: 0.8648 (m-30) cc_final: 0.8057 (t70) REVERT: R 279 TYR cc_start: 0.8191 (t80) cc_final: 0.7772 (t80) REVERT: P 18 HIS cc_start: 0.8573 (t-170) cc_final: 0.7597 (t70) REVERT: P 21 ASP cc_start: 0.9251 (m-30) cc_final: 0.8983 (p0) REVERT: A 27 GLU cc_start: 0.8932 (mm-30) cc_final: 0.8480 (mm-30) REVERT: A 33 ASP cc_start: 0.8730 (t70) cc_final: 0.8364 (m-30) REVERT: A 365 CYS cc_start: 0.7756 (m) cc_final: 0.7466 (t) REVERT: B 12 GLU cc_start: 0.9188 (tp30) cc_final: 0.8963 (tp30) REVERT: B 23 LYS cc_start: 0.9458 (mmmt) cc_final: 0.9203 (tptp) REVERT: B 45 MET cc_start: 0.9332 (mtm) cc_final: 0.9125 (mtm) REVERT: B 155 ASN cc_start: 0.8798 (m-40) cc_final: 0.8305 (t0) REVERT: B 172 GLU cc_start: 0.8925 (tp30) cc_final: 0.8662 (tp30) REVERT: B 217 MET cc_start: 0.8971 (ptt) cc_final: 0.8711 (ppp) REVERT: B 254 ASP cc_start: 0.8307 (t0) cc_final: 0.7861 (t0) REVERT: G 13 ARG cc_start: 0.8951 (ptm-80) cc_final: 0.8641 (ptm-80) REVERT: G 14 LYS cc_start: 0.9609 (tppp) cc_final: 0.9294 (tppt) REVERT: G 29 LYS cc_start: 0.9131 (mmtt) cc_final: 0.8850 (mmtm) REVERT: G 46 LYS cc_start: 0.9136 (mtmm) cc_final: 0.8889 (mppt) REVERT: G 52 THR cc_start: 0.8961 (m) cc_final: 0.8720 (p) REVERT: N 73 ASP cc_start: 0.8285 (t0) cc_final: 0.7696 (t0) REVERT: N 76 LYS cc_start: 0.9429 (tppp) cc_final: 0.9195 (tppp) REVERT: N 78 THR cc_start: 0.8686 (m) cc_final: 0.8373 (t) REVERT: N 114 THR cc_start: 0.9072 (p) cc_final: 0.8761 (t) outliers start: 26 outliers final: 17 residues processed: 151 average time/residue: 1.3132 time to fit residues: 212.9241 Evaluate side-chains 152 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 135 time to evaluate : 1.016 ------------------------------------------------------------------------------- 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 157 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 A residue 248 VAL Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 347 ARG 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 G residue 36 ASP Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 83 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 38 optimal weight: 0.9990 chunk 52 optimal weight: 9.9990 chunk 57 optimal weight: 0.9990 chunk 29 optimal weight: 0.0030 chunk 53 optimal weight: 6.9990 chunk 90 optimal weight: 0.8980 chunk 79 optimal weight: 5.9990 chunk 55 optimal weight: 5.9990 chunk 69 optimal weight: 0.5980 chunk 8 optimal weight: 6.9990 chunk 84 optimal weight: 0.0870 overall best weight: 0.5170 ------------------------------------------------------------------------------- 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 = 0.3785 r_free = 0.3785 target = 0.117707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.078933 restraints weight = 17131.249| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 3.15 r_work: 0.2964 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.4614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9622 Z= 0.185 Angle : 0.579 9.027 13062 Z= 0.303 Chirality : 0.040 0.180 1454 Planarity : 0.004 0.039 1638 Dihedral : 4.447 55.004 1668 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.13 % Allowed : 18.95 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.26), residues: 1136 helix: 2.54 (0.24), residues: 459 sheet: -0.17 (0.32), residues: 250 loop : -0.29 (0.31), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 169 HIS 0.006 0.001 HIS A 220 PHE 0.015 0.001 PHE R 270 TYR 0.023 0.001 TYR N 60 ARG 0.006 0.000 ARG N 105 *********************** 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 163 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 142 time to evaluate : 1.009 Fit side-chains revert: symmetry clash REVERT: R 279 TYR cc_start: 0.8185 (t80) cc_final: 0.7762 (t80) REVERT: R 298 ILE cc_start: 0.8624 (OUTLIER) cc_final: 0.8377 (tt) REVERT: R 398 GLU cc_start: 0.8614 (tm-30) cc_final: 0.8376 (tm-30) REVERT: P 18 HIS cc_start: 0.8487 (t-170) cc_final: 0.7504 (t70) REVERT: P 21 ASP cc_start: 0.9254 (m-30) cc_final: 0.8982 (p0) REVERT: A 27 GLU cc_start: 0.8914 (mm-30) cc_final: 0.8446 (mm-30) REVERT: A 33 ASP cc_start: 0.8726 (t70) cc_final: 0.8343 (m-30) REVERT: A 365 CYS cc_start: 0.7659 (m) cc_final: 0.7381 (t) REVERT: B 12 GLU cc_start: 0.9116 (tp30) cc_final: 0.8825 (tp30) REVERT: B 23 LYS cc_start: 0.9469 (mmmt) cc_final: 0.9220 (tptp) REVERT: B 45 MET cc_start: 0.9301 (mtm) cc_final: 0.9091 (mtm) REVERT: B 155 ASN cc_start: 0.8765 (m-40) cc_final: 0.8253 (t0) REVERT: B 158 VAL cc_start: 0.9188 (t) cc_final: 0.8941 (p) REVERT: B 172 GLU cc_start: 0.8936 (tp30) cc_final: 0.8665 (tp30) REVERT: B 217 MET cc_start: 0.8960 (ptt) cc_final: 0.8726 (ppp) REVERT: G 13 ARG cc_start: 0.8971 (ptm-80) cc_final: 0.8606 (tmm160) REVERT: G 14 LYS cc_start: 0.9591 (tppp) cc_final: 0.9150 (tppt) REVERT: G 17 GLU cc_start: 0.8867 (tm-30) cc_final: 0.8603 (tm-30) REVERT: G 29 LYS cc_start: 0.9140 (mmtt) cc_final: 0.8872 (mmtm) REVERT: G 46 LYS cc_start: 0.9081 (mtmm) cc_final: 0.8832 (mppt) REVERT: G 48 ASP cc_start: 0.8474 (t0) cc_final: 0.8241 (t0) REVERT: N 3 GLN cc_start: 0.8027 (pt0) cc_final: 0.7813 (tt0) REVERT: N 69 THR cc_start: 0.9093 (m) cc_final: 0.8650 (p) REVERT: N 73 ASP cc_start: 0.8241 (t0) cc_final: 0.7655 (t0) REVERT: N 76 LYS cc_start: 0.9391 (tppp) cc_final: 0.9080 (tppp) REVERT: N 78 THR cc_start: 0.8585 (m) cc_final: 0.8074 (p) REVERT: N 87 LYS cc_start: 0.8901 (mtpm) cc_final: 0.8698 (mtpp) REVERT: N 103 PHE cc_start: 0.9329 (m-80) cc_final: 0.8914 (m-80) REVERT: N 114 THR cc_start: 0.9074 (p) cc_final: 0.8781 (t) outliers start: 21 outliers final: 12 residues processed: 152 average time/residue: 1.2150 time to fit residues: 200.1596 Evaluate side-chains 150 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 137 time to evaluate : 0.986 ------------------------------------------------------------------------------- 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 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 G residue 36 ASP Chi-restraints excluded: chain N residue 35 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 85 optimal weight: 3.9990 chunk 88 optimal weight: 0.2980 chunk 60 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 89 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 73 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 83 optimal weight: 6.9990 chunk 43 optimal weight: 1.9990 chunk 15 optimal weight: 20.0000 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 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** N 123 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.116046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.076579 restraints weight = 17398.145| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 3.20 r_work: 0.2945 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.4707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9622 Z= 0.219 Angle : 0.594 9.285 13062 Z= 0.310 Chirality : 0.040 0.150 1454 Planarity : 0.004 0.039 1638 Dihedral : 4.457 54.921 1668 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.32 % Allowed : 19.76 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.26), residues: 1136 helix: 2.56 (0.24), residues: 460 sheet: -0.21 (0.32), residues: 252 loop : -0.36 (0.31), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP R 233 HIS 0.006 0.001 HIS A 220 PHE 0.015 0.001 PHE R 270 TYR 0.023 0.001 TYR N 60 ARG 0.006 0.000 ARG N 105 ********************** 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: 13 poor density : 141 time to evaluate : 1.232 Fit side-chains revert: symmetry clash REVERT: R 279 TYR cc_start: 0.8194 (t80) cc_final: 0.7783 (t80) REVERT: R 298 ILE cc_start: 0.8679 (OUTLIER) cc_final: 0.8437 (tt) REVERT: P 18 HIS cc_start: 0.8492 (t-170) cc_final: 0.7511 (t70) REVERT: P 21 ASP cc_start: 0.9253 (m-30) cc_final: 0.8986 (p0) REVERT: A 27 GLU cc_start: 0.8945 (mm-30) cc_final: 0.8516 (mm-30) REVERT: A 33 ASP cc_start: 0.8717 (t70) cc_final: 0.8345 (m-30) REVERT: A 365 CYS cc_start: 0.7668 (m) cc_final: 0.7391 (t) REVERT: B 12 GLU cc_start: 0.9108 (tp30) cc_final: 0.8814 (tp30) REVERT: B 23 LYS cc_start: 0.9478 (mmmt) cc_final: 0.9185 (tptp) REVERT: B 45 MET cc_start: 0.9314 (mtm) cc_final: 0.9108 (mtm) REVERT: B 155 ASN cc_start: 0.8785 (m-40) cc_final: 0.8289 (t0) REVERT: B 172 GLU cc_start: 0.8975 (tp30) cc_final: 0.8695 (tp30) REVERT: B 217 MET cc_start: 0.8958 (ptt) cc_final: 0.8715 (ppp) REVERT: G 13 ARG cc_start: 0.8941 (ptm-80) cc_final: 0.8571 (tmm160) REVERT: G 14 LYS cc_start: 0.9583 (tppp) cc_final: 0.9147 (tppt) REVERT: G 17 GLU cc_start: 0.8838 (tm-30) cc_final: 0.8572 (tm-30) REVERT: G 46 LYS cc_start: 0.9097 (mtmm) cc_final: 0.8853 (mppt) REVERT: N 3 GLN cc_start: 0.8041 (pt0) cc_final: 0.7827 (tt0) REVERT: N 69 THR cc_start: 0.9095 (m) cc_final: 0.8619 (p) REVERT: N 73 ASP cc_start: 0.8243 (t0) cc_final: 0.7627 (t0) REVERT: N 76 LYS cc_start: 0.9378 (tppp) cc_final: 0.9069 (tppp) REVERT: N 78 THR cc_start: 0.8635 (m) cc_final: 0.8104 (p) REVERT: N 103 PHE cc_start: 0.9322 (m-80) cc_final: 0.8893 (m-80) REVERT: N 114 THR cc_start: 0.9109 (p) cc_final: 0.8820 (t) outliers start: 13 outliers final: 12 residues processed: 147 average time/residue: 1.2323 time to fit residues: 194.8766 Evaluate side-chains 149 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 136 time to evaluate : 0.977 ------------------------------------------------------------------------------- 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 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 G residue 36 ASP Chi-restraints excluded: chain N residue 35 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 34 optimal weight: 0.8980 chunk 27 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 109 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 86 optimal weight: 4.9990 chunk 47 optimal weight: 0.9990 chunk 85 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 67 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.115770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.076106 restraints weight = 17292.707| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 3.20 r_work: 0.2954 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.4816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9622 Z= 0.231 Angle : 0.608 9.793 13062 Z= 0.316 Chirality : 0.040 0.137 1454 Planarity : 0.004 0.056 1638 Dihedral : 4.445 54.462 1668 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.72 % Allowed : 19.96 % Favored : 78.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.26), residues: 1136 helix: 2.59 (0.24), residues: 460 sheet: -0.19 (0.32), residues: 249 loop : -0.39 (0.31), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 233 HIS 0.006 0.001 HIS A 220 PHE 0.015 0.001 PHE R 270 TYR 0.023 0.001 TYR N 60 ARG 0.018 0.000 ARG B 134 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7095.57 seconds wall clock time: 124 minutes 43.86 seconds (7483.86 seconds total)