Starting phenix.real_space_refine on Wed Mar 4 10:23:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6vwg_21415/03_2026/6vwg_21415_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vwg_21415/03_2026/6vwg_21415.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6vwg_21415/03_2026/6vwg_21415.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vwg_21415/03_2026/6vwg_21415.map" model { file = "/net/cci-nas-00/data/ceres_data/6vwg_21415/03_2026/6vwg_21415_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vwg_21415/03_2026/6vwg_21415_trim.cif" } resolution = 3.21 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.040 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: 5 Type Number sf(0) Gaussians S 52 5.16 5 C 4078 2.51 5 N 1115 2.21 5 O 1224 1.98 5 H 6282 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 65 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12751 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 6916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 6916 Classifications: {'peptide': 439} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 422} Chain breaks: 3 Chain: "B" Number of atoms: 4980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 4980 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 11, 'TRANS': 295} Chain breaks: 2 Chain: "I" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 799 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 1, 'TRANS': 52} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.16, per 1000 atoms: 0.17 Number of scatterers: 12751 At special positions: 0 Unit cell: (76.32, 108.12, 104.94, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 52 16.00 O 1224 8.00 N 1115 7.00 C 4078 6.00 H 6282 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 3 " - pdb=" SG CYS A 22 " distance=2.03 Simple disulfide: pdb=" SG CYS A 120 " - pdb=" SG CYS A 148 " distance=2.02 Simple disulfide: pdb=" SG CYS A 152 " - pdb=" SG CYS A 175 " distance=2.03 Simple disulfide: pdb=" SG CYS A 162 " - pdb=" SG CYS A 181 " distance=2.03 Simple disulfide: pdb=" SG CYS A 185 " - pdb=" SG CYS A 194 " distance=2.03 Simple disulfide: pdb=" SG CYS A 189 " - pdb=" SG CYS A 200 " distance=2.04 Simple disulfide: pdb=" SG CYS A 201 " - pdb=" SG CYS A 209 " distance=2.03 Simple disulfide: pdb=" SG CYS A 205 " - pdb=" SG CYS A 218 " distance=2.04 Simple disulfide: pdb=" SG CYS A 221 " - pdb=" SG CYS A 230 " distance=2.03 Simple disulfide: pdb=" SG CYS A 234 " - pdb=" SG CYS A 246 " distance=2.03 Simple disulfide: pdb=" SG CYS A 252 " - pdb=" SG CYS A 273 " distance=2.03 Simple disulfide: pdb=" SG CYS A 277 " - pdb=" SG CYS A 291 " distance=2.03 Simple disulfide: pdb=" SG CYS A 302 " - pdb=" SG CYS A 323 " distance=2.03 Simple disulfide: pdb=" SG CYS B 302 " - pdb=" SG CYS B 323 " distance=2.02 Simple disulfide: pdb=" SG CYS B 425 " - pdb=" SG CYS B 458 " distance=2.03 Simple disulfide: pdb=" SG CYS I 9 " - pdb=" SG CYS I 47 " distance=2.03 Simple disulfide: pdb=" SG CYS I 21 " - pdb=" SG CYS I 60 " distance=2.03 Simple disulfide: pdb=" SG CYS I 46 " - pdb=" SG CYS I 51 " 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 Links applied NAG-ASN " NAG A1001 " - " ASN A 21 " " NAG A1002 " - " ASN A 387 " " NAG A1003 " - " ASN A 105 " " NAG B1001 " - " ASN B 504 " Time building additional restraints: 0.83 Conformation dependent library (CDL) restraints added in 373.8 milliseconds 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1498 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 13 sheets defined 23.2% alpha, 15.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 12 through 20 removed outlier: 3.596A pdb=" N LYS A 17 " --> pdb=" O GLN A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 70 removed outlier: 4.255A pdb=" N LEU A 69 " --> pdb=" O SER A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 131 removed outlier: 4.007A pdb=" N ILE A 130 " --> pdb=" O ASP A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 137 Processing helix chain 'A' and resid 144 through 149 removed outlier: 4.344A pdb=" N GLY A 149 " --> pdb=" O PRO A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 190 Processing helix chain 'A' and resid 195 through 199 removed outlier: 4.053A pdb=" N GLU A 199 " --> pdb=" O GLU A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 216 No H-bonds generated for 'chain 'A' and resid 214 through 216' Processing helix chain 'A' and resid 248 through 255 Processing helix chain 'A' and resid 313 through 319 removed outlier: 3.849A pdb=" N MET A 319 " --> pdb=" O THR A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 348 removed outlier: 4.991A pdb=" N GLU A 345 " --> pdb=" O ALA A 341 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ASN A 346 " --> pdb=" O SER A 342 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N PHE A 347 " --> pdb=" O GLU A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 407 removed outlier: 3.510A pdb=" N HIS A 406 " --> pdb=" O ASP A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 431 removed outlier: 3.813A pdb=" N ILE A 429 " --> pdb=" O CYS A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 437 removed outlier: 3.582A pdb=" N VAL A 435 " --> pdb=" O ARG A 431 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N GLY A 437 " --> pdb=" O GLU A 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 321 removed outlier: 3.836A pdb=" N GLN B 318 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N MET B 319 " --> pdb=" O SER B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 348 removed outlier: 3.728A pdb=" N GLU B 343 " --> pdb=" O ASN B 339 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ASN B 346 " --> pdb=" O SER B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 428 Processing helix chain 'B' and resid 429 through 436 Processing helix chain 'B' and resid 486 through 488 No H-bonds generated for 'chain 'B' and resid 486 through 488' Processing helix chain 'B' and resid 558 through 563 removed outlier: 4.026A pdb=" N ASP B 562 " --> pdb=" O VAL B 559 " (cutoff:3.500A) Processing helix chain 'B' and resid 677 through 701 removed outlier: 4.186A pdb=" N LYS B 683 " --> pdb=" O LYS B 679 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N PHE B 692 " --> pdb=" O TYR B 688 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE B 701 " --> pdb=" O HIS B 697 " (cutoff:3.500A) Processing helix chain 'I' and resid 10 through 22 removed outlier: 3.592A pdb=" N VAL I 14 " --> pdb=" O GLY I 10 " (cutoff:3.500A) Processing helix chain 'I' and resid 23 through 25 No H-bonds generated for 'chain 'I' and resid 23 through 25' Processing helix chain 'I' and resid 41 through 47 Processing helix chain 'I' and resid 52 through 57 removed outlier: 3.543A pdb=" N GLU I 57 " --> pdb=" O LEU I 53 " (cutoff:3.500A) Processing helix chain 'I' and resid 58 through 60 No H-bonds generated for 'chain 'I' and resid 58 through 60' Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 3 Processing sheet with id=AA2, first strand: chain 'A' and resid 7 through 9 removed outlier: 6.756A pdb=" N ILE A 7 " --> pdb=" O HIS A 30 " (cutoff:3.500A) removed outlier: 8.148A pdb=" N LEU A 32 " --> pdb=" O ILE A 7 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N ILE A 9 " --> pdb=" O LEU A 32 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N LEU A 29 " --> pdb=" O LEU A 56 " (cutoff:3.500A) removed outlier: 8.057A pdb=" N PHE A 58 " --> pdb=" O LEU A 29 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ILE A 31 " --> pdb=" O PHE A 58 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N LEU A 55 " --> pdb=" O VAL A 88 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N PHE A 90 " --> pdb=" O LEU A 55 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N LEU A 57 " --> pdb=" O PHE A 90 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N ARG A 112 " --> pdb=" O ALA A 86 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N VAL A 88 " --> pdb=" O ARG A 112 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N GLU A 114 " --> pdb=" O VAL A 88 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N PHE A 90 " --> pdb=" O GLU A 114 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 164 through 167 Processing sheet with id=AA4, first strand: chain 'A' and resid 206 through 209 removed outlier: 3.811A pdb=" N ALA A 220 " --> pdb=" O LEU A 206 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N SER A 208 " --> pdb=" O CYS A 218 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N CYS A 218 " --> pdb=" O SER A 208 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 224 through 226 Processing sheet with id=AA6, first strand: chain 'A' and resid 239 through 241 removed outlier: 4.175A pdb=" N ARG A 245 " --> pdb=" O PHE A 241 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 267 through 269 Processing sheet with id=AA8, first strand: chain 'A' and resid 308 through 311 removed outlier: 6.399A pdb=" N LEU A 330 " --> pdb=" O LYS A 359 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N ARG A 361 " --> pdb=" O LEU A 330 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N ILE A 332 " --> pdb=" O ARG A 361 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N VAL A 358 " --> pdb=" O TYR A 391 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N LEU A 393 " --> pdb=" O VAL A 358 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N ILE A 360 " --> pdb=" O LEU A 393 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N TYR A 388 " --> pdb=" O LYS A 415 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N TYR A 417 " --> pdb=" O TYR A 388 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N PHE A 390 " --> pdb=" O TYR A 417 " (cutoff:3.500A) removed outlier: 8.408A pdb=" N ALA A 419 " --> pdb=" O PHE A 390 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N VAL A 392 " --> pdb=" O ALA A 419 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 325 through 326 Processing sheet with id=AB1, first strand: chain 'B' and resid 308 through 311 removed outlier: 3.589A pdb=" N LEU B 331 " --> pdb=" O LYS B 309 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N LEU B 330 " --> pdb=" O LYS B 359 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N ARG B 361 " --> pdb=" O LEU B 330 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N ILE B 332 " --> pdb=" O ARG B 361 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N VAL B 358 " --> pdb=" O TYR B 391 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N LEU B 393 " --> pdb=" O VAL B 358 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N ILE B 360 " --> pdb=" O LEU B 393 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N TYR B 417 " --> pdb=" O SER B 389 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N TYR B 391 " --> pdb=" O TYR B 417 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N ALA B 419 " --> pdb=" O TYR B 391 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N LEU B 393 " --> pdb=" O ALA B 419 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 325 through 326 Processing sheet with id=AB3, first strand: chain 'B' and resid 465 through 470 Processing sheet with id=AB4, first strand: chain 'B' and resid 520 through 524 removed outlier: 3.514A pdb=" N SER B 492 " --> pdb=" O VAL B 554 " (cutoff:3.500A) 127 hydrogen bonds defined for protein. 297 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.51 Time building geometry restraints manager: 1.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 6281 1.03 - 1.23: 3 1.23 - 1.42: 2776 1.42 - 1.62: 3750 1.62 - 1.82: 67 Bond restraints: 12877 Sorted by residual: bond pdb=" C1 NAG A1002 " pdb=" O5 NAG A1002 " ideal model delta sigma weight residual 1.406 1.454 -0.048 2.00e-02 2.50e+03 5.84e+00 bond pdb=" N SER I 5 " pdb=" CA SER I 5 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.05e+00 bond pdb=" C1 NAG A1001 " pdb=" O5 NAG A1001 " ideal model delta sigma weight residual 1.406 1.440 -0.034 2.00e-02 2.50e+03 2.83e+00 bond pdb=" C1 NAG B1001 " pdb=" O5 NAG B1001 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.27e+00 bond pdb=" N SER I 5 " pdb=" H SER I 5 " ideal model delta sigma weight residual 0.860 0.888 -0.028 2.00e-02 2.50e+03 2.02e+00 ... (remaining 12872 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.64: 22160 1.64 - 3.27: 949 3.27 - 4.91: 72 4.91 - 6.54: 4 6.54 - 8.18: 1 Bond angle restraints: 23186 Sorted by residual: angle pdb=" N GLU A 305 " pdb=" CA GLU A 305 " pdb=" C GLU A 305 " ideal model delta sigma weight residual 110.80 102.62 8.18 2.13e+00 2.20e-01 1.47e+01 angle pdb=" N PHE A 45 " pdb=" CA PHE A 45 " pdb=" C PHE A 45 " ideal model delta sigma weight residual 108.39 114.26 -5.87 2.10e+00 2.27e-01 7.82e+00 angle pdb=" N ARG A 336 " pdb=" CA ARG A 336 " pdb=" C ARG A 336 " ideal model delta sigma weight residual 108.32 112.89 -4.57 1.64e+00 3.72e-01 7.78e+00 angle pdb=" N GLU A 304 " pdb=" CA GLU A 304 " pdb=" C GLU A 304 " ideal model delta sigma weight residual 110.50 114.29 -3.79 1.41e+00 5.03e-01 7.23e+00 angle pdb=" N PHE B 420 " pdb=" CA PHE B 420 " pdb=" C PHE B 420 " ideal model delta sigma weight residual 110.80 116.39 -5.59 2.13e+00 2.20e-01 6.89e+00 ... (remaining 23181 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 5504 17.90 - 35.80: 424 35.80 - 53.70: 142 53.70 - 71.59: 70 71.59 - 89.49: 9 Dihedral angle restraints: 6149 sinusoidal: 3404 harmonic: 2745 Sorted by residual: dihedral pdb=" CB CYS A 189 " pdb=" SG CYS A 189 " pdb=" SG CYS A 200 " pdb=" CB CYS A 200 " ideal model delta sinusoidal sigma weight residual 93.00 155.18 -62.18 1 1.00e+01 1.00e-02 5.12e+01 dihedral pdb=" CB CYS A 234 " pdb=" SG CYS A 234 " pdb=" SG CYS A 246 " pdb=" CB CYS A 246 " ideal model delta sinusoidal sigma weight residual -86.00 -142.75 56.75 1 1.00e+01 1.00e-02 4.34e+01 dihedral pdb=" CA GLU A 305 " pdb=" C GLU A 305 " pdb=" N LYS A 306 " pdb=" CA LYS A 306 " ideal model delta harmonic sigma weight residual 180.00 150.30 29.70 0 5.00e+00 4.00e-02 3.53e+01 ... (remaining 6146 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 533 0.037 - 0.075: 307 0.075 - 0.112: 130 0.112 - 0.149: 17 0.149 - 0.187: 4 Chirality restraints: 991 Sorted by residual: chirality pdb=" CA ARG A 104 " pdb=" N ARG A 104 " pdb=" C ARG A 104 " pdb=" CB ARG A 104 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.70e-01 chirality pdb=" CA HIS A 362 " pdb=" N HIS A 362 " pdb=" C HIS A 362 " pdb=" CB HIS A 362 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.34e-01 chirality pdb=" C2 NAG A1002 " pdb=" C1 NAG A1002 " pdb=" C3 NAG A1002 " pdb=" N2 NAG A1002 " both_signs ideal model delta sigma weight residual False -2.49 -2.34 -0.15 2.00e-01 2.50e+01 5.75e-01 ... (remaining 988 not shown) Planarity restraints: 1909 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 174 " 0.016 9.50e-02 1.11e+02 4.99e-02 5.54e+01 pdb=" NE ARG A 174 " 0.055 2.00e-02 2.50e+03 pdb=" CZ ARG A 174 " -0.048 2.00e-02 2.50e+03 pdb=" NH1 ARG A 174 " -0.091 2.00e-02 2.50e+03 pdb=" NH2 ARG A 174 " -0.006 2.00e-02 2.50e+03 pdb="HH11 ARG A 174 " -0.004 2.00e-02 2.50e+03 pdb="HH12 ARG A 174 " 0.092 2.00e-02 2.50e+03 pdb="HH21 ARG A 174 " 0.000 2.00e-02 2.50e+03 pdb="HH22 ARG A 174 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 112 " -0.123 9.50e-02 1.11e+02 5.74e-02 3.83e+01 pdb=" NE ARG A 112 " 0.020 2.00e-02 2.50e+03 pdb=" CZ ARG A 112 " -0.076 2.00e-02 2.50e+03 pdb=" NH1 ARG A 112 " 0.073 2.00e-02 2.50e+03 pdb=" NH2 ARG A 112 " 0.046 2.00e-02 2.50e+03 pdb="HH11 ARG A 112 " -0.016 2.00e-02 2.50e+03 pdb="HH12 ARG A 112 " -0.018 2.00e-02 2.50e+03 pdb="HH21 ARG A 112 " -0.001 2.00e-02 2.50e+03 pdb="HH22 ARG A 112 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN B 680 " -0.036 2.00e-02 2.50e+03 4.39e-02 2.89e+01 pdb=" CD GLN B 680 " 0.031 2.00e-02 2.50e+03 pdb=" OE1 GLN B 680 " 0.001 2.00e-02 2.50e+03 pdb=" NE2 GLN B 680 " 0.070 2.00e-02 2.50e+03 pdb="HE21 GLN B 680 " 0.002 2.00e-02 2.50e+03 pdb="HE22 GLN B 680 " -0.067 2.00e-02 2.50e+03 ... (remaining 1906 not shown) Histogram of nonbonded interaction distances: 1.53 - 2.15: 549 2.15 - 2.76: 24376 2.76 - 3.37: 34633 3.37 - 3.99: 44831 3.99 - 4.60: 71369 Nonbonded interactions: 175758 Sorted by model distance: nonbonded pdb=" OE2 GLU B 433 " pdb="HE21 GLN B 442 " model vdw 1.535 2.450 nonbonded pdb=" O GLY A 437 " pdb=" HG1 THR A 438 " model vdw 1.560 2.450 nonbonded pdb=" O LEU B 424 " pdb="HD22 ASN B 452 " model vdw 1.565 2.450 nonbonded pdb=" HZ1 LYS B 498 " pdb=" OD2 ASP B 509 " model vdw 1.566 2.450 nonbonded pdb=" HG SER B 363 " pdb=" OD1 ASN B 395 " model vdw 1.567 2.450 ... (remaining 175753 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.160 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: 0.080 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 12.000 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7147 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 : 0.007 0.060 6617 Z= 0.272 Angle : 0.908 9.716 8956 Z= 0.513 Chirality : 0.051 0.187 991 Planarity : 0.006 0.068 1140 Dihedral : 14.650 89.492 2524 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.38 % Favored : 88.62 % Rotamer: Outliers : 1.26 % Allowed : 5.20 % Favored : 93.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.78 (0.28), residues: 782 helix: -3.47 (0.35), residues: 103 sheet: -0.92 (0.52), residues: 111 loop : -1.84 (0.25), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.092 0.011 ARG A 112 TYR 0.027 0.006 TYR B 496 PHE 0.021 0.003 PHE A 418 TRP 0.035 0.007 TRP A 244 HIS 0.009 0.003 HIS B 480 Details of bonding type rmsd covalent geometry : bond 0.00676 ( 6595) covalent geometry : angle 0.89010 ( 8908) SS BOND : bond 0.00407 ( 18) SS BOND : angle 1.64289 ( 36) hydrogen bonds : bond 0.18937 ( 127) hydrogen bonds : angle 9.37350 ( 297) link_NAG-ASN : bond 0.00221 ( 4) link_NAG-ASN : angle 4.43053 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 137 time to evaluate : 0.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 215 ASP cc_start: 0.6290 (m-30) cc_final: 0.6085 (m-30) REVERT: A 319 MET cc_start: 0.7834 (mtp) cc_final: 0.7619 (mtm) REVERT: A 367 VAL cc_start: 0.7894 (m) cc_final: 0.7678 (m) REVERT: A 400 GLN cc_start: 0.7603 (OUTLIER) cc_final: 0.7395 (pm20) REVERT: B 327 LYS cc_start: 0.8480 (mttt) cc_final: 0.8211 (mtpt) REVERT: B 486 ASP cc_start: 0.6532 (p0) cc_final: 0.6096 (p0) REVERT: B 489 ASP cc_start: 0.7735 (m-30) cc_final: 0.7264 (m-30) REVERT: B 574 ILE cc_start: 0.7628 (mt) cc_final: 0.7404 (tp) outliers start: 9 outliers final: 4 residues processed: 145 average time/residue: 0.2171 time to fit residues: 39.5071 Evaluate side-chains 76 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 71 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 400 GLN Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain B residue 511 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 49 optimal weight: 0.9990 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 0.8980 chunk 74 optimal weight: 0.0980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN A 333 ASN B 396 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.132204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.113755 restraints weight = 32424.200| |-----------------------------------------------------------------------------| r_work (start): 0.3761 rms_B_bonded: 2.62 r_work: 0.3653 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 moved from start: 0.2375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6617 Z= 0.156 Angle : 0.703 6.660 8956 Z= 0.380 Chirality : 0.044 0.150 991 Planarity : 0.004 0.035 1140 Dihedral : 9.465 62.328 972 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 1.54 % Allowed : 11.10 % Favored : 87.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.39 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.46 (0.29), residues: 782 helix: -2.71 (0.43), residues: 104 sheet: -0.91 (0.50), residues: 119 loop : -1.67 (0.26), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 41 TYR 0.031 0.002 TYR A 224 PHE 0.014 0.001 PHE B 326 TRP 0.008 0.001 TRP A 176 HIS 0.004 0.001 HIS B 406 Details of bonding type rmsd covalent geometry : bond 0.00357 ( 6595) covalent geometry : angle 0.68696 ( 8908) SS BOND : bond 0.00373 ( 18) SS BOND : angle 2.01917 ( 36) hydrogen bonds : bond 0.05159 ( 127) hydrogen bonds : angle 6.73852 ( 297) link_NAG-ASN : bond 0.00282 ( 4) link_NAG-ASN : angle 2.46280 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 83 time to evaluate : 0.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 LYS cc_start: 0.7658 (mttt) cc_final: 0.7397 (ttmm) REVERT: A 215 ASP cc_start: 0.6744 (m-30) cc_final: 0.6450 (m-30) REVERT: A 319 MET cc_start: 0.8585 (mtp) cc_final: 0.8133 (mtm) REVERT: A 425 CYS cc_start: 0.8328 (t) cc_final: 0.7935 (m) REVERT: B 327 LYS cc_start: 0.8647 (mttt) cc_final: 0.8408 (mtpt) REVERT: B 552 LYS cc_start: 0.8349 (tttt) cc_final: 0.8080 (tttp) REVERT: B 574 ILE cc_start: 0.8082 (mt) cc_final: 0.7762 (tp) REVERT: I 40 ARG cc_start: 0.6621 (ptt-90) cc_final: 0.5934 (pmt-80) outliers start: 11 outliers final: 8 residues processed: 94 average time/residue: 0.2016 time to fit residues: 24.5353 Evaluate side-chains 84 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 76 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 333 ASN Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 511 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 54 optimal weight: 0.9980 chunk 21 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 49 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 44 optimal weight: 0.2980 chunk 23 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 396 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.129046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.109706 restraints weight = 32650.372| |-----------------------------------------------------------------------------| r_work (start): 0.3726 rms_B_bonded: 2.75 r_work: 0.3614 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7318 moved from start: 0.2974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 6617 Z= 0.165 Angle : 0.629 5.959 8956 Z= 0.339 Chirality : 0.043 0.162 991 Planarity : 0.004 0.034 1140 Dihedral : 8.565 62.935 969 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.18 % Favored : 91.82 % Rotamer: Outliers : 1.69 % Allowed : 12.08 % Favored : 86.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.34 (0.29), residues: 782 helix: -2.27 (0.47), residues: 98 sheet: -1.27 (0.49), residues: 114 loop : -1.58 (0.26), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 441 TYR 0.023 0.002 TYR A 224 PHE 0.014 0.001 PHE B 326 TRP 0.008 0.001 TRP A 176 HIS 0.005 0.001 HIS B 406 Details of bonding type rmsd covalent geometry : bond 0.00375 ( 6595) covalent geometry : angle 0.62019 ( 8908) SS BOND : bond 0.00372 ( 18) SS BOND : angle 1.36660 ( 36) hydrogen bonds : bond 0.04298 ( 127) hydrogen bonds : angle 6.20468 ( 297) link_NAG-ASN : bond 0.00227 ( 4) link_NAG-ASN : angle 1.96494 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 83 time to evaluate : 0.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 LYS cc_start: 0.7635 (mttt) cc_final: 0.7374 (ttmm) REVERT: A 215 ASP cc_start: 0.6670 (m-30) cc_final: 0.6353 (m-30) REVERT: A 319 MET cc_start: 0.8650 (mtp) cc_final: 0.8216 (mtm) REVERT: A 425 CYS cc_start: 0.8496 (t) cc_final: 0.8268 (m) REVERT: B 327 LYS cc_start: 0.8753 (mttt) cc_final: 0.8406 (mtpt) REVERT: B 428 GLU cc_start: 0.8531 (mm-30) cc_final: 0.7968 (mt-10) REVERT: B 574 ILE cc_start: 0.8045 (mt) cc_final: 0.7807 (tp) REVERT: B 684 GLU cc_start: 0.7958 (OUTLIER) cc_final: 0.7227 (mp0) REVERT: B 687 GLU cc_start: 0.8463 (pt0) cc_final: 0.8204 (pp20) outliers start: 12 outliers final: 5 residues processed: 94 average time/residue: 0.2063 time to fit residues: 24.9907 Evaluate side-chains 77 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 71 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 511 GLN Chi-restraints excluded: chain B residue 684 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 21 optimal weight: 2.9990 chunk 66 optimal weight: 0.2980 chunk 76 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 68 optimal weight: 0.5980 chunk 53 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 67 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.128616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.109314 restraints weight = 32103.205| |-----------------------------------------------------------------------------| r_work (start): 0.3725 rms_B_bonded: 2.73 r_work: 0.3614 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7319 moved from start: 0.3400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 6617 Z= 0.147 Angle : 0.599 6.776 8956 Z= 0.321 Chirality : 0.043 0.145 991 Planarity : 0.003 0.032 1140 Dihedral : 8.158 62.975 967 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer: Outliers : 1.69 % Allowed : 13.34 % Favored : 84.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.49 (0.28), residues: 782 helix: -1.94 (0.49), residues: 98 sheet: -1.52 (0.46), residues: 119 loop : -1.73 (0.25), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 336 TYR 0.019 0.002 TYR A 224 PHE 0.012 0.001 PHE B 326 TRP 0.008 0.001 TRP A 176 HIS 0.005 0.001 HIS B 406 Details of bonding type rmsd covalent geometry : bond 0.00332 ( 6595) covalent geometry : angle 0.59219 ( 8908) SS BOND : bond 0.00252 ( 18) SS BOND : angle 1.23069 ( 36) hydrogen bonds : bond 0.03765 ( 127) hydrogen bonds : angle 5.97796 ( 297) link_NAG-ASN : bond 0.00200 ( 4) link_NAG-ASN : angle 1.82170 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 84 time to evaluate : 0.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 LYS cc_start: 0.7650 (mttt) cc_final: 0.7403 (ttmm) REVERT: A 215 ASP cc_start: 0.6679 (m-30) cc_final: 0.6329 (m-30) REVERT: A 319 MET cc_start: 0.8674 (mtp) cc_final: 0.8198 (mtm) REVERT: B 327 LYS cc_start: 0.8788 (mttt) cc_final: 0.8412 (mtpt) REVERT: B 428 GLU cc_start: 0.8462 (mm-30) cc_final: 0.7937 (mt-10) REVERT: B 574 ILE cc_start: 0.8100 (mt) cc_final: 0.7825 (tp) REVERT: B 674 LYS cc_start: 0.8891 (pttm) cc_final: 0.8688 (ptmm) REVERT: B 684 GLU cc_start: 0.7981 (OUTLIER) cc_final: 0.7127 (mp0) REVERT: B 687 GLU cc_start: 0.8476 (pt0) cc_final: 0.8163 (pp20) outliers start: 12 outliers final: 8 residues processed: 94 average time/residue: 0.1644 time to fit residues: 20.8685 Evaluate side-chains 82 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 73 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 467 SER Chi-restraints excluded: chain B residue 511 GLN Chi-restraints excluded: chain B residue 684 GLU Chi-restraints excluded: chain B residue 702 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 9 optimal weight: 1.9990 chunk 53 optimal weight: 0.0670 chunk 47 optimal weight: 2.9990 chunk 66 optimal weight: 0.0980 chunk 4 optimal weight: 1.9990 chunk 19 optimal weight: 0.3980 chunk 2 optimal weight: 0.9980 chunk 14 optimal weight: 0.2980 chunk 15 optimal weight: 0.5980 chunk 7 optimal weight: 0.6980 chunk 28 optimal weight: 0.2980 overall best weight: 0.2318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 ASN A 102 ASN A 338 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.130940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.111382 restraints weight = 32160.372| |-----------------------------------------------------------------------------| r_work (start): 0.3754 rms_B_bonded: 2.79 r_work: 0.3643 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7277 moved from start: 0.3738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 6617 Z= 0.095 Angle : 0.547 6.734 8956 Z= 0.292 Chirality : 0.042 0.148 991 Planarity : 0.003 0.030 1140 Dihedral : 7.750 61.748 967 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 2.11 % Allowed : 13.62 % Favored : 84.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.25 (0.28), residues: 782 helix: -1.64 (0.50), residues: 99 sheet: -1.37 (0.46), residues: 119 loop : -1.58 (0.25), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 481 TYR 0.016 0.001 TYR A 224 PHE 0.011 0.001 PHE A 371 TRP 0.006 0.001 TRP A 176 HIS 0.004 0.001 HIS B 406 Details of bonding type rmsd covalent geometry : bond 0.00217 ( 6595) covalent geometry : angle 0.54234 ( 8908) SS BOND : bond 0.00500 ( 18) SS BOND : angle 0.91142 ( 36) hydrogen bonds : bond 0.03146 ( 127) hydrogen bonds : angle 5.52615 ( 297) link_NAG-ASN : bond 0.00218 ( 4) link_NAG-ASN : angle 1.45297 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 87 time to evaluate : 0.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 215 ASP cc_start: 0.6518 (m-30) cc_final: 0.6158 (m-30) REVERT: A 319 MET cc_start: 0.8660 (mtp) cc_final: 0.8121 (mtm) REVERT: A 409 LEU cc_start: 0.7645 (OUTLIER) cc_final: 0.7177 (tt) REVERT: B 327 LYS cc_start: 0.8705 (mttt) cc_final: 0.8305 (mtpt) REVERT: B 428 GLU cc_start: 0.8381 (mm-30) cc_final: 0.7898 (mt-10) REVERT: B 467 SER cc_start: 0.8239 (OUTLIER) cc_final: 0.8017 (p) REVERT: B 574 ILE cc_start: 0.7967 (mt) cc_final: 0.7729 (tp) REVERT: B 684 GLU cc_start: 0.7980 (OUTLIER) cc_final: 0.7195 (mp0) REVERT: B 687 GLU cc_start: 0.8477 (pt0) cc_final: 0.8167 (pp20) REVERT: I 44 GLU cc_start: 0.7454 (tt0) cc_final: 0.7193 (tt0) outliers start: 15 outliers final: 6 residues processed: 102 average time/residue: 0.1491 time to fit residues: 21.2153 Evaluate side-chains 83 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 74 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 467 SER Chi-restraints excluded: chain B residue 511 GLN Chi-restraints excluded: chain B residue 684 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 47 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 chunk 44 optimal weight: 0.5980 chunk 75 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.127521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.108155 restraints weight = 32424.073| |-----------------------------------------------------------------------------| r_work (start): 0.3702 rms_B_bonded: 2.77 r_work: 0.3590 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.4075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6617 Z= 0.175 Angle : 0.599 7.105 8956 Z= 0.318 Chirality : 0.043 0.141 991 Planarity : 0.004 0.032 1140 Dihedral : 7.861 63.031 967 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.31 % Favored : 91.69 % Rotamer: Outliers : 1.83 % Allowed : 14.04 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.43 (0.28), residues: 782 helix: -1.60 (0.51), residues: 99 sheet: -1.60 (0.44), residues: 119 loop : -1.72 (0.25), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 474 TYR 0.016 0.002 TYR A 224 PHE 0.019 0.002 PHE A 371 TRP 0.008 0.001 TRP A 244 HIS 0.006 0.001 HIS B 406 Details of bonding type rmsd covalent geometry : bond 0.00397 ( 6595) covalent geometry : angle 0.59017 ( 8908) SS BOND : bond 0.00253 ( 18) SS BOND : angle 1.41019 ( 36) hydrogen bonds : bond 0.03538 ( 127) hydrogen bonds : angle 5.65433 ( 297) link_NAG-ASN : bond 0.00161 ( 4) link_NAG-ASN : angle 1.81083 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 82 time to evaluate : 0.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 215 ASP cc_start: 0.6671 (m-30) cc_final: 0.6337 (m-30) REVERT: A 319 MET cc_start: 0.8667 (mtp) cc_final: 0.8118 (mtm) REVERT: A 409 LEU cc_start: 0.7835 (OUTLIER) cc_final: 0.7377 (tt) REVERT: B 327 LYS cc_start: 0.8758 (mttt) cc_final: 0.8389 (mtpt) REVERT: B 329 ASN cc_start: 0.7417 (OUTLIER) cc_final: 0.7076 (p0) REVERT: B 428 GLU cc_start: 0.8520 (mm-30) cc_final: 0.8011 (mt-10) REVERT: B 574 ILE cc_start: 0.8008 (mt) cc_final: 0.7766 (tp) REVERT: B 674 LYS cc_start: 0.8932 (pttm) cc_final: 0.8713 (ptmm) REVERT: B 684 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.7665 (mp0) outliers start: 13 outliers final: 9 residues processed: 93 average time/residue: 0.1662 time to fit residues: 21.0481 Evaluate side-chains 86 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 74 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain B residue 329 ASN Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 467 SER Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 511 GLN Chi-restraints excluded: chain B residue 684 GLU Chi-restraints excluded: chain B residue 702 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 48 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 chunk 45 optimal weight: 0.9990 chunk 56 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 374 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.126843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.107657 restraints weight = 32312.836| |-----------------------------------------------------------------------------| r_work (start): 0.3697 rms_B_bonded: 2.75 r_work: 0.3589 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7353 moved from start: 0.4262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 6617 Z= 0.165 Angle : 0.586 7.928 8956 Z= 0.311 Chirality : 0.042 0.142 991 Planarity : 0.003 0.031 1140 Dihedral : 7.770 64.401 967 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.82 % Favored : 91.18 % Rotamer: Outliers : 1.54 % Allowed : 14.89 % Favored : 83.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.53 (0.28), residues: 782 helix: -1.59 (0.51), residues: 99 sheet: -1.67 (0.44), residues: 119 loop : -1.81 (0.25), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 474 TYR 0.016 0.001 TYR A 224 PHE 0.012 0.001 PHE A 371 TRP 0.007 0.001 TRP A 176 HIS 0.005 0.001 HIS B 406 Details of bonding type rmsd covalent geometry : bond 0.00377 ( 6595) covalent geometry : angle 0.57899 ( 8908) SS BOND : bond 0.00249 ( 18) SS BOND : angle 1.22897 ( 36) hydrogen bonds : bond 0.03394 ( 127) hydrogen bonds : angle 5.50895 ( 297) link_NAG-ASN : bond 0.00169 ( 4) link_NAG-ASN : angle 1.77903 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 77 time to evaluate : 0.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 ASP cc_start: 0.7443 (t0) cc_final: 0.7167 (m-30) REVERT: A 319 MET cc_start: 0.8695 (mtp) cc_final: 0.8131 (mtm) REVERT: A 409 LEU cc_start: 0.7837 (OUTLIER) cc_final: 0.7368 (tt) REVERT: B 327 LYS cc_start: 0.8752 (mttt) cc_final: 0.8366 (mtpt) REVERT: B 329 ASN cc_start: 0.7608 (OUTLIER) cc_final: 0.7274 (p0) REVERT: B 428 GLU cc_start: 0.8505 (mm-30) cc_final: 0.7994 (mt-10) REVERT: B 574 ILE cc_start: 0.8007 (mt) cc_final: 0.7755 (tp) REVERT: B 674 LYS cc_start: 0.8974 (pttm) cc_final: 0.8730 (ptmm) REVERT: B 684 GLU cc_start: 0.7919 (OUTLIER) cc_final: 0.7111 (mp0) REVERT: B 687 GLU cc_start: 0.8536 (pt0) cc_final: 0.8175 (pp20) outliers start: 11 outliers final: 8 residues processed: 87 average time/residue: 0.1439 time to fit residues: 17.4661 Evaluate side-chains 86 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 75 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain B residue 329 ASN Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 467 SER Chi-restraints excluded: chain B residue 511 GLN Chi-restraints excluded: chain B residue 684 GLU Chi-restraints excluded: chain B residue 702 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 40 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 76 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 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 = 0.3954 r_free = 0.3954 target = 0.126112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.106967 restraints weight = 32233.031| |-----------------------------------------------------------------------------| r_work (start): 0.3682 rms_B_bonded: 2.75 r_work: 0.3574 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7368 moved from start: 0.4419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 6617 Z= 0.177 Angle : 0.597 8.644 8956 Z= 0.316 Chirality : 0.043 0.141 991 Planarity : 0.004 0.035 1140 Dihedral : 7.723 65.853 967 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.85 % Favored : 90.15 % Rotamer: Outliers : 1.83 % Allowed : 15.17 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.62 (0.28), residues: 782 helix: -1.59 (0.51), residues: 99 sheet: -1.79 (0.44), residues: 114 loop : -1.87 (0.25), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 474 TYR 0.017 0.002 TYR A 224 PHE 0.012 0.001 PHE B 326 TRP 0.007 0.001 TRP A 244 HIS 0.006 0.001 HIS B 406 Details of bonding type rmsd covalent geometry : bond 0.00401 ( 6595) covalent geometry : angle 0.59067 ( 8908) SS BOND : bond 0.00311 ( 18) SS BOND : angle 1.03731 ( 36) hydrogen bonds : bond 0.03596 ( 127) hydrogen bonds : angle 5.57082 ( 297) link_NAG-ASN : bond 0.00147 ( 4) link_NAG-ASN : angle 1.94417 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 75 time to evaluate : 0.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 319 MET cc_start: 0.8752 (mtp) cc_final: 0.8164 (mtm) REVERT: A 409 LEU cc_start: 0.7858 (OUTLIER) cc_final: 0.7394 (tt) REVERT: B 327 LYS cc_start: 0.8762 (mttt) cc_final: 0.8368 (mtpt) REVERT: B 329 ASN cc_start: 0.7627 (OUTLIER) cc_final: 0.7286 (p0) REVERT: B 416 MET cc_start: 0.8533 (ptp) cc_final: 0.8099 (ptp) REVERT: B 428 GLU cc_start: 0.8523 (mm-30) cc_final: 0.8009 (mt-10) REVERT: B 574 ILE cc_start: 0.8024 (mt) cc_final: 0.7762 (tp) REVERT: B 674 LYS cc_start: 0.9007 (pttm) cc_final: 0.8747 (ptmm) REVERT: B 684 GLU cc_start: 0.7848 (OUTLIER) cc_final: 0.7096 (mp0) REVERT: B 687 GLU cc_start: 0.8609 (pt0) cc_final: 0.8199 (pp20) outliers start: 13 outliers final: 8 residues processed: 86 average time/residue: 0.1432 time to fit residues: 17.1949 Evaluate side-chains 82 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 71 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain B residue 329 ASN Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 467 SER Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 511 GLN Chi-restraints excluded: chain B residue 684 GLU Chi-restraints excluded: chain B residue 702 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 48 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 4 optimal weight: 0.3980 chunk 12 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 chunk 41 optimal weight: 0.0570 chunk 46 optimal weight: 0.9980 chunk 45 optimal weight: 0.8980 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.127312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.108225 restraints weight = 32347.064| |-----------------------------------------------------------------------------| r_work (start): 0.3706 rms_B_bonded: 2.76 r_work: 0.3594 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 moved from start: 0.4555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6617 Z= 0.121 Angle : 0.558 8.939 8956 Z= 0.296 Chirality : 0.042 0.145 991 Planarity : 0.003 0.031 1140 Dihedral : 7.518 65.815 967 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer: Outliers : 1.97 % Allowed : 15.59 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.49 (0.28), residues: 782 helix: -1.45 (0.51), residues: 98 sheet: -1.66 (0.45), residues: 114 loop : -1.81 (0.25), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 474 TYR 0.017 0.001 TYR A 224 PHE 0.011 0.001 PHE A 371 TRP 0.007 0.001 TRP A 176 HIS 0.004 0.001 HIS B 406 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 6595) covalent geometry : angle 0.55343 ( 8908) SS BOND : bond 0.00203 ( 18) SS BOND : angle 0.85653 ( 36) hydrogen bonds : bond 0.03232 ( 127) hydrogen bonds : angle 5.32433 ( 297) link_NAG-ASN : bond 0.00208 ( 4) link_NAG-ASN : angle 1.65808 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 77 time to evaluate : 0.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 THR cc_start: 0.8770 (m) cc_final: 0.8552 (m) REVERT: A 132 ASP cc_start: 0.7337 (t0) cc_final: 0.7073 (m-30) REVERT: A 319 MET cc_start: 0.8690 (mtp) cc_final: 0.8120 (mtm) REVERT: A 409 LEU cc_start: 0.7840 (OUTLIER) cc_final: 0.7381 (tt) REVERT: B 327 LYS cc_start: 0.8683 (mttt) cc_final: 0.8286 (mtpt) REVERT: B 329 ASN cc_start: 0.7575 (OUTLIER) cc_final: 0.7253 (p0) REVERT: B 428 GLU cc_start: 0.8475 (mm-30) cc_final: 0.8008 (mt-10) REVERT: B 460 SER cc_start: 0.7366 (OUTLIER) cc_final: 0.6801 (p) REVERT: B 574 ILE cc_start: 0.8022 (mt) cc_final: 0.7766 (tp) REVERT: B 674 LYS cc_start: 0.8989 (pttm) cc_final: 0.8731 (ptmm) REVERT: B 684 GLU cc_start: 0.7848 (OUTLIER) cc_final: 0.7091 (mp0) REVERT: B 687 GLU cc_start: 0.8602 (pt0) cc_final: 0.8183 (pp20) REVERT: B 688 TYR cc_start: 0.8532 (t80) cc_final: 0.8331 (t80) outliers start: 14 outliers final: 8 residues processed: 90 average time/residue: 0.1500 time to fit residues: 18.7401 Evaluate side-chains 86 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 74 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ASN Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain B residue 329 ASN Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 467 SER Chi-restraints excluded: chain B residue 511 GLN Chi-restraints excluded: chain B residue 554 VAL Chi-restraints excluded: chain B residue 684 GLU Chi-restraints excluded: chain B residue 702 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 29 optimal weight: 0.9980 chunk 17 optimal weight: 0.1980 chunk 59 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 63 optimal weight: 0.1980 chunk 11 optimal weight: 0.9980 chunk 64 optimal weight: 0.8980 chunk 7 optimal weight: 0.4980 chunk 0 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 21 optimal weight: 0.8980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.127976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.108534 restraints weight = 32327.528| |-----------------------------------------------------------------------------| r_work (start): 0.3704 rms_B_bonded: 2.82 r_work: 0.3594 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7342 moved from start: 0.4633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6617 Z= 0.118 Angle : 0.558 9.546 8956 Z= 0.294 Chirality : 0.042 0.143 991 Planarity : 0.003 0.033 1140 Dihedral : 7.298 65.675 966 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.21 % Favored : 90.79 % Rotamer: Outliers : 1.69 % Allowed : 15.59 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.47 (0.28), residues: 782 helix: -1.38 (0.51), residues: 98 sheet: -1.70 (0.45), residues: 115 loop : -1.78 (0.25), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 474 TYR 0.018 0.001 TYR A 224 PHE 0.010 0.001 PHE A 371 TRP 0.006 0.001 TRP A 244 HIS 0.004 0.001 HIS B 406 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 6595) covalent geometry : angle 0.54877 ( 8908) SS BOND : bond 0.00392 ( 18) SS BOND : angle 1.44755 ( 36) hydrogen bonds : bond 0.03166 ( 127) hydrogen bonds : angle 5.26335 ( 297) link_NAG-ASN : bond 0.00173 ( 4) link_NAG-ASN : angle 1.65774 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 77 time to evaluate : 0.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 VAL cc_start: 0.8766 (t) cc_final: 0.8488 (m) REVERT: A 132 ASP cc_start: 0.7332 (t0) cc_final: 0.7033 (m-30) REVERT: A 215 ASP cc_start: 0.6615 (m-30) cc_final: 0.6298 (m-30) REVERT: A 319 MET cc_start: 0.8667 (mtp) cc_final: 0.8069 (mtm) REVERT: A 409 LEU cc_start: 0.7833 (OUTLIER) cc_final: 0.7384 (tt) REVERT: B 327 LYS cc_start: 0.8682 (mttt) cc_final: 0.8283 (mtpt) REVERT: B 329 ASN cc_start: 0.7535 (OUTLIER) cc_final: 0.7180 (p0) REVERT: B 428 GLU cc_start: 0.8482 (mm-30) cc_final: 0.8015 (mt-10) REVERT: B 460 SER cc_start: 0.7366 (OUTLIER) cc_final: 0.6812 (p) REVERT: B 467 SER cc_start: 0.8343 (OUTLIER) cc_final: 0.8111 (p) REVERT: B 574 ILE cc_start: 0.8027 (mt) cc_final: 0.7725 (tp) REVERT: B 674 LYS cc_start: 0.9001 (pttm) cc_final: 0.8765 (ptmm) REVERT: B 684 GLU cc_start: 0.7844 (OUTLIER) cc_final: 0.7121 (mp0) REVERT: B 687 GLU cc_start: 0.8613 (pt0) cc_final: 0.8181 (pp20) REVERT: B 688 TYR cc_start: 0.8543 (t80) cc_final: 0.8339 (t80) outliers start: 12 outliers final: 7 residues processed: 88 average time/residue: 0.1458 time to fit residues: 18.1494 Evaluate side-chains 85 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 73 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ASN Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain B residue 329 ASN Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 467 SER Chi-restraints excluded: chain B residue 511 GLN Chi-restraints excluded: chain B residue 554 VAL Chi-restraints excluded: chain B residue 684 GLU Chi-restraints excluded: chain B residue 702 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 54 optimal weight: 0.7980 chunk 11 optimal weight: 0.9980 chunk 4 optimal weight: 0.7980 chunk 46 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 59 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 chunk 36 optimal weight: 0.1980 chunk 69 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 chunk 76 optimal weight: 0.1980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 442 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.127544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.108448 restraints weight = 32265.854| |-----------------------------------------------------------------------------| r_work (start): 0.3711 rms_B_bonded: 2.76 r_work: 0.3600 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7342 moved from start: 0.4708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6617 Z= 0.120 Angle : 0.555 9.246 8956 Z= 0.293 Chirality : 0.042 0.144 991 Planarity : 0.003 0.032 1140 Dihedral : 7.231 65.918 966 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.70 % Favored : 91.30 % Rotamer: Outliers : 1.83 % Allowed : 16.29 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.47 (0.28), residues: 782 helix: -1.35 (0.51), residues: 98 sheet: -1.73 (0.45), residues: 115 loop : -1.78 (0.25), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 474 TYR 0.017 0.001 TYR A 224 PHE 0.010 0.001 PHE A 371 TRP 0.006 0.001 TRP A 244 HIS 0.004 0.001 HIS B 406 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 6595) covalent geometry : angle 0.54736 ( 8908) SS BOND : bond 0.00223 ( 18) SS BOND : angle 1.25115 ( 36) hydrogen bonds : bond 0.03126 ( 127) hydrogen bonds : angle 5.21970 ( 297) link_NAG-ASN : bond 0.00174 ( 4) link_NAG-ASN : angle 1.64441 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3075.57 seconds wall clock time: 52 minutes 46.46 seconds (3166.46 seconds total)