Starting phenix.real_space_refine on Thu Sep 26 10:25:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vwg_21415/09_2024/6vwg_21415_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vwg_21415/09_2024/6vwg_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vwg_21415/09_2024/6vwg_21415.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vwg_21415/09_2024/6vwg_21415.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vwg_21415/09_2024/6vwg_21415_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vwg_21415/09_2024/6vwg_21415_trim.cif" } resolution = 3.21 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= 0.001 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/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: 7.45, per 1000 atoms: 0.58 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: 3.20 Conformation dependent library (CDL) restraints added in 965.1 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: 1.12 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: 4.80 Time building geometry restraints manager: 3.80 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.110 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: 0.200 Extract box with map and model: 0.430 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 31.210 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:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.900 ------------------------------------------------------------------------------- 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 6595 Z= 0.438 Angle : 0.890 8.179 8908 Z= 0.509 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 : 4.30 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 (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: -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 TRP 0.035 0.007 TRP A 244 HIS 0.009 0.003 HIS B 480 PHE 0.021 0.003 PHE A 418 TYR 0.027 0.006 TYR B 496 ARG 0.092 0.011 ARG A 112 *********************** 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 fitting. rotamer outliers: 9 poor density : 137 time to evaluate : 0.953 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 164 LYS cc_start: 0.8522 (mppt) cc_final: 0.8280 (mtpt) REVERT: A 215 ASP cc_start: 0.6290 (m-30) cc_final: 0.6083 (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: 0.7677 (m) REVERT: A 400 GLN cc_start: 0.7603 (OUTLIER) cc_final: 0.7397 (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: 0.6133 (p0) REVERT: B 489 ASP cc_start: 0.7735 (m-30) cc_final: 0.7307 (m-30) REVERT: B 574 ILE cc_start: 0.7629 (mt) cc_final: 0.7404 (tp) outliers start: 9 outliers final: 4 residues processed: 145 average time/residue: 0.4698 time to fit residues: 86.0973 Evaluate side-chains 76 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 71 time to evaluate : 1.073 ------------------------------------------------------------------------------- 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 65 optimal weight: 0.7980 chunk 59 optimal weight: 0.0040 chunk 32 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 39 optimal weight: 0.9980 chunk 31 optimal weight: 0.5980 chunk 61 optimal weight: 0.1980 chunk 23 optimal weight: 0.8980 chunk 37 optimal weight: 0.6980 chunk 45 optimal weight: 0.5980 chunk 70 optimal weight: 0.0770 overall best weight: 0.2950 ------------------------------------------------------------------------------- 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 B 406 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7135 moved from start: 0.2469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6595 Z= 0.186 Angle : 0.670 5.606 8908 Z= 0.365 Chirality : 0.044 0.153 991 Planarity : 0.004 0.052 1140 Dihedral : 9.356 61.812 972 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 1.54 % Allowed : 11.38 % Favored : 87.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.39 % 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: -2.39 (0.29), residues: 782 helix: -2.56 (0.44), residues: 104 sheet: -0.87 (0.50), residues: 119 loop : -1.65 (0.26), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 244 HIS 0.004 0.001 HIS B 406 PHE 0.013 0.001 PHE B 326 TYR 0.032 0.002 TYR A 224 ARG 0.005 0.001 ARG A 41 *********************** 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 97 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 86 time to evaluate : 1.031 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: A 164 LYS cc_start: 0.8496 (mppt) cc_final: 0.8186 (mtpt) REVERT: A 215 ASP cc_start: 0.6398 (m-30) cc_final: 0.6190 (m-30) REVERT: A 319 MET cc_start: 0.7836 (mtp) cc_final: 0.7594 (mtm) REVERT: B 552 LYS cc_start: 0.8275 (tttt) cc_final: 0.8015 (tttp) REVERT: B 574 ILE cc_start: 0.7896 (mt) cc_final: 0.7607 (tp) outliers start: 11 outliers final: 8 residues processed: 97 average time/residue: 0.4586 time to fit residues: 57.2307 Evaluate side-chains 80 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 72 time to evaluate : 1.076 ------------------------------------------------------------------------------- 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 39 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 76 optimal weight: 0.8980 chunk 63 optimal weight: 0.9990 chunk 24 optimal weight: 0.7980 chunk 56 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 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 223 HIS B 396 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7214 moved from start: 0.3059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6595 Z= 0.277 Angle : 0.637 5.921 8908 Z= 0.346 Chirality : 0.044 0.154 991 Planarity : 0.004 0.033 1140 Dihedral : 8.580 62.783 969 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.31 % Favored : 91.69 % Rotamer: Outliers : 1.54 % Allowed : 12.78 % Favored : 85.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: -2.34 (0.29), residues: 782 helix: -2.26 (0.48), residues: 98 sheet: -1.23 (0.49), residues: 115 loop : -1.58 (0.26), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 176 HIS 0.005 0.001 HIS B 406 PHE 0.015 0.001 PHE B 326 TYR 0.025 0.002 TYR A 224 ARG 0.003 0.000 ARG A 41 *********************** 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 93 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 82 time to evaluate : 1.055 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: A 164 LYS cc_start: 0.8557 (mppt) cc_final: 0.8269 (mtpt) REVERT: A 215 ASP cc_start: 0.6476 (m-30) cc_final: 0.6190 (m-30) REVERT: A 319 MET cc_start: 0.7900 (mtp) cc_final: 0.7635 (mtm) REVERT: B 574 ILE cc_start: 0.7917 (mt) cc_final: 0.7668 (tp) REVERT: B 684 GLU cc_start: 0.7784 (OUTLIER) cc_final: 0.6987 (mp0) outliers start: 11 outliers final: 5 residues processed: 93 average time/residue: 0.4484 time to fit residues: 54.5577 Evaluate side-chains 76 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 70 time to evaluate : 1.021 ------------------------------------------------------------------------------- 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 36 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 33 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 chunk 71 optimal weight: 0.7980 chunk 75 optimal weight: 0.8980 chunk 37 optimal weight: 0.9990 chunk 67 optimal weight: 0.8980 chunk 20 optimal weight: 0.8980 chunk 62 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7224 moved from start: 0.3519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 6595 Z= 0.246 Angle : 0.610 6.564 8908 Z= 0.328 Chirality : 0.043 0.144 991 Planarity : 0.004 0.028 1140 Dihedral : 8.205 62.887 967 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 2.11 % Allowed : 12.78 % Favored : 85.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: -2.51 (0.28), residues: 782 helix: -2.04 (0.49), residues: 98 sheet: -1.59 (0.45), residues: 120 loop : -1.71 (0.25), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 176 HIS 0.005 0.001 HIS B 406 PHE 0.013 0.001 PHE B 326 TYR 0.020 0.002 TYR A 224 ARG 0.003 0.000 ARG A 41 *********************** 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 93 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 78 time to evaluate : 1.072 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 215 ASP cc_start: 0.6485 (m-30) cc_final: 0.6173 (m-30) REVERT: A 272 GLU cc_start: 0.5306 (OUTLIER) cc_final: 0.4986 (mm-30) REVERT: A 303 GLU cc_start: 0.6943 (OUTLIER) cc_final: 0.6723 (pp20) REVERT: A 319 MET cc_start: 0.7948 (mtp) cc_final: 0.7627 (mtm) REVERT: A 409 LEU cc_start: 0.7861 (OUTLIER) cc_final: 0.7453 (tt) REVERT: B 574 ILE cc_start: 0.7949 (mt) cc_final: 0.7676 (tp) REVERT: B 684 GLU cc_start: 0.7629 (OUTLIER) cc_final: 0.7179 (mp0) outliers start: 15 outliers final: 8 residues processed: 89 average time/residue: 0.3832 time to fit residues: 46.3298 Evaluate side-chains 83 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 71 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 272 GLU Chi-restraints excluded: chain A residue 303 GLU 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 549 VAL 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 1 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 0 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 14 optimal weight: 0.4980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 ASN A 451 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7247 moved from start: 0.3884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 6595 Z= 0.241 Angle : 0.594 6.660 8908 Z= 0.319 Chirality : 0.043 0.144 991 Planarity : 0.004 0.029 1140 Dihedral : 7.953 63.477 967 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.95 % Favored : 91.05 % Rotamer: Outliers : 2.81 % Allowed : 13.76 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: -2.59 (0.28), residues: 782 helix: -1.93 (0.49), residues: 99 sheet: -1.65 (0.46), residues: 110 loop : -1.80 (0.25), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 176 HIS 0.005 0.001 HIS B 406 PHE 0.011 0.001 PHE B 326 TYR 0.019 0.002 TYR A 224 ARG 0.002 0.000 ARG A 174 *********************** 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 95 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 75 time to evaluate : 0.952 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 164 LYS cc_start: 0.8668 (mppt) cc_final: 0.8363 (mtpt) REVERT: A 303 GLU cc_start: 0.7117 (OUTLIER) cc_final: 0.6845 (pp20) REVERT: A 319 MET cc_start: 0.8012 (mtp) cc_final: 0.7652 (mtm) REVERT: A 409 LEU cc_start: 0.7913 (OUTLIER) cc_final: 0.7445 (tt) REVERT: B 329 ASN cc_start: 0.7298 (OUTLIER) cc_final: 0.6898 (p0) REVERT: B 574 ILE cc_start: 0.7857 (mt) cc_final: 0.7616 (tp) REVERT: B 684 GLU cc_start: 0.7516 (OUTLIER) cc_final: 0.7088 (mp0) outliers start: 20 outliers final: 12 residues processed: 91 average time/residue: 0.3301 time to fit residues: 42.1539 Evaluate side-chains 85 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 69 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 148 CYS Chi-restraints excluded: chain A residue 272 GLU Chi-restraints excluded: chain A residue 303 GLU 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 549 VAL Chi-restraints excluded: chain B residue 684 GLU Chi-restraints excluded: chain B residue 702 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 44 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 chunk 42 optimal weight: 0.6980 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7261 moved from start: 0.4072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6595 Z= 0.261 Angle : 0.598 7.089 8908 Z= 0.321 Chirality : 0.043 0.143 991 Planarity : 0.003 0.030 1140 Dihedral : 7.774 64.120 966 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer: Outliers : 2.53 % Allowed : 13.90 % 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 (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: -2.73 (0.28), residues: 782 helix: -2.00 (0.48), residues: 105 sheet: -1.72 (0.46), residues: 109 loop : -1.92 (0.25), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 244 HIS 0.006 0.001 HIS B 406 PHE 0.011 0.001 PHE B 326 TYR 0.019 0.002 TYR A 224 ARG 0.002 0.000 ARG B 481 *********************** 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 88 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 70 time to evaluate : 1.094 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: A 49 THR cc_start: 0.8640 (m) cc_final: 0.8424 (m) REVERT: A 272 GLU cc_start: 0.5419 (OUTLIER) cc_final: 0.5197 (mm-30) REVERT: A 319 MET cc_start: 0.8030 (mtp) cc_final: 0.7655 (mtm) REVERT: A 409 LEU cc_start: 0.7933 (OUTLIER) cc_final: 0.7486 (tt) REVERT: B 574 ILE cc_start: 0.7893 (mt) cc_final: 0.7646 (tp) REVERT: B 684 GLU cc_start: 0.7504 (OUTLIER) cc_final: 0.7187 (mp0) outliers start: 18 outliers final: 11 residues processed: 86 average time/residue: 0.3326 time to fit residues: 40.6654 Evaluate side-chains 81 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 67 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 CYS Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 272 GLU 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 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 55 optimal weight: 0.2980 chunk 42 optimal weight: 2.9990 chunk 63 optimal weight: 0.7980 chunk 75 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 chunk 30 optimal weight: 0.8980 chunk 44 optimal weight: 0.5980 chunk 22 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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** B 396 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7248 moved from start: 0.4241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6595 Z= 0.203 Angle : 0.565 8.218 8908 Z= 0.302 Chirality : 0.042 0.145 991 Planarity : 0.003 0.030 1140 Dihedral : 7.597 64.200 966 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.70 % Favored : 91.30 % Rotamer: Outliers : 2.39 % Allowed : 14.04 % 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 (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: -2.59 (0.28), residues: 782 helix: -1.68 (0.50), residues: 99 sheet: -1.62 (0.47), residues: 109 loop : -1.88 (0.25), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 176 HIS 0.005 0.001 HIS B 406 PHE 0.024 0.001 PHE A 371 TYR 0.018 0.001 TYR A 224 ARG 0.002 0.000 ARG B 481 *********************** 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 90 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 73 time to evaluate : 1.030 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 319 MET cc_start: 0.8015 (mtp) cc_final: 0.7645 (mtm) REVERT: A 409 LEU cc_start: 0.7895 (OUTLIER) cc_final: 0.7437 (tt) REVERT: B 329 ASN cc_start: 0.7193 (OUTLIER) cc_final: 0.6895 (p0) REVERT: B 574 ILE cc_start: 0.7892 (mt) cc_final: 0.7644 (tp) REVERT: B 684 GLU cc_start: 0.7456 (OUTLIER) cc_final: 0.7025 (mp0) outliers start: 17 outliers final: 11 residues processed: 89 average time/residue: 0.3825 time to fit residues: 48.8715 Evaluate side-chains 82 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 68 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ASN Chi-restraints excluded: chain A residue 148 CYS 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 511 GLN Chi-restraints excluded: chain B residue 545 THR 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 14 optimal weight: 0.6980 chunk 47 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 72 optimal weight: 0.9990 chunk 65 optimal weight: 0.8980 chunk 70 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 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** B 374 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7269 moved from start: 0.4392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 6595 Z= 0.256 Angle : 0.592 8.499 8908 Z= 0.316 Chirality : 0.043 0.141 991 Planarity : 0.003 0.032 1140 Dihedral : 7.621 65.271 966 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.21 % Favored : 90.79 % Rotamer: Outliers : 2.11 % Allowed : 14.47 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: -2.63 (0.28), residues: 782 helix: -1.72 (0.50), residues: 99 sheet: -1.63 (0.48), residues: 104 loop : -1.91 (0.25), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 244 HIS 0.006 0.001 HIS B 406 PHE 0.011 0.001 PHE B 326 TYR 0.020 0.002 TYR A 224 ARG 0.002 0.000 ARG A 240 *********************** 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 85 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 70 time to evaluate : 0.955 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: A 319 MET cc_start: 0.8026 (mtp) cc_final: 0.7642 (mtm) REVERT: A 409 LEU cc_start: 0.7945 (OUTLIER) cc_final: 0.7500 (tt) REVERT: B 329 ASN cc_start: 0.7185 (OUTLIER) cc_final: 0.6956 (p0) REVERT: B 574 ILE cc_start: 0.7908 (mt) cc_final: 0.7657 (tp) REVERT: B 684 GLU cc_start: 0.7517 (OUTLIER) cc_final: 0.7232 (mp0) outliers start: 15 outliers final: 12 residues processed: 83 average time/residue: 0.3188 time to fit residues: 37.5232 Evaluate side-chains 83 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 68 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ASN Chi-restraints excluded: chain A residue 148 CYS 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 469 THR Chi-restraints excluded: chain B residue 511 GLN Chi-restraints excluded: chain B residue 545 THR 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 30 optimal weight: 0.3980 chunk 55 optimal weight: 0.6980 chunk 21 optimal weight: 0.8980 chunk 63 optimal weight: 0.5980 chunk 66 optimal weight: 0.4980 chunk 69 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 74 optimal weight: 0.2980 chunk 45 optimal weight: 0.9980 chunk 35 optimal weight: 0.4980 chunk 51 optimal weight: 0.8980 overall best weight: 0.4580 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7231 moved from start: 0.4529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 6595 Z= 0.161 Angle : 0.545 8.798 8908 Z= 0.292 Chirality : 0.042 0.146 991 Planarity : 0.003 0.029 1140 Dihedral : 7.380 65.396 966 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer: Outliers : 1.83 % Allowed : 14.75 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: -2.50 (0.28), residues: 782 helix: -1.53 (0.50), residues: 98 sheet: -1.51 (0.47), residues: 115 loop : -1.83 (0.25), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 176 HIS 0.005 0.001 HIS B 406 PHE 0.013 0.001 PHE A 371 TYR 0.020 0.001 TYR A 224 ARG 0.002 0.000 ARG B 481 *********************** 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 93 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 80 time to evaluate : 1.022 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: A 319 MET cc_start: 0.8018 (mtp) cc_final: 0.7650 (mtm) REVERT: A 409 LEU cc_start: 0.7896 (OUTLIER) cc_final: 0.7409 (tt) REVERT: B 329 ASN cc_start: 0.7072 (OUTLIER) cc_final: 0.6804 (p0) REVERT: B 460 SER cc_start: 0.7086 (OUTLIER) cc_final: 0.6566 (p) REVERT: B 574 ILE cc_start: 0.7889 (mt) cc_final: 0.7646 (tp) REVERT: B 684 GLU cc_start: 0.7471 (OUTLIER) cc_final: 0.7146 (mp0) outliers start: 13 outliers final: 9 residues processed: 92 average time/residue: 0.3172 time to fit residues: 41.3128 Evaluate side-chains 84 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 71 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ASN Chi-restraints excluded: chain A residue 148 CYS 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 511 GLN Chi-restraints excluded: chain B residue 545 THR 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 77 optimal weight: 0.7980 chunk 71 optimal weight: 0.5980 chunk 61 optimal weight: 0.4980 chunk 6 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 65 optimal weight: 0.9980 chunk 18 optimal weight: 0.6980 chunk 57 optimal weight: 0.9990 chunk 9 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7249 moved from start: 0.4602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6595 Z= 0.210 Angle : 0.569 9.207 8908 Z= 0.303 Chirality : 0.042 0.139 991 Planarity : 0.003 0.030 1140 Dihedral : 7.412 65.764 966 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.21 % Favored : 90.79 % Rotamer: Outliers : 1.97 % Allowed : 15.17 % Favored : 82.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: -2.50 (0.28), residues: 782 helix: -1.48 (0.50), residues: 98 sheet: -1.51 (0.47), residues: 115 loop : -1.85 (0.25), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 244 HIS 0.005 0.001 HIS B 406 PHE 0.011 0.001 PHE A 371 TYR 0.018 0.001 TYR A 224 ARG 0.002 0.000 ARG B 481 ********************** 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 87 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 73 time to evaluate : 0.981 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 319 MET cc_start: 0.7993 (mtp) cc_final: 0.7538 (mtm) REVERT: A 409 LEU cc_start: 0.8005 (OUTLIER) cc_final: 0.7656 (tt) REVERT: B 329 ASN cc_start: 0.7114 (OUTLIER) cc_final: 0.6843 (p0) REVERT: B 460 SER cc_start: 0.7114 (OUTLIER) cc_final: 0.6580 (p) REVERT: B 574 ILE cc_start: 0.7914 (mt) cc_final: 0.7666 (tp) REVERT: B 684 GLU cc_start: 0.7493 (OUTLIER) cc_final: 0.7210 (mp0) outliers start: 14 outliers final: 10 residues processed: 86 average time/residue: 0.3334 time to fit residues: 40.5341 Evaluate side-chains 85 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 71 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ASN Chi-restraints excluded: chain A residue 148 CYS 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 511 GLN Chi-restraints excluded: chain B residue 545 THR 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 17 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 chunk 63 optimal weight: 0.7980 chunk 7 optimal weight: 0.0970 chunk 11 optimal weight: 0.9980 chunk 54 optimal weight: 0.7980 chunk 3 optimal weight: 0.9990 chunk 44 optimal weight: 0.8980 chunk 70 optimal weight: 3.9990 chunk 41 optimal weight: 0.7980 overall best weight: 0.6378 ------------------------------------------------------------------------------- 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 = 0.3968 r_free = 0.3968 target = 0.127026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.107737 restraints weight = 32386.313| |-----------------------------------------------------------------------------| r_work (start): 0.3698 rms_B_bonded: 2.77 r_work: 0.3589 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 moved from start: 0.4695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6595 Z= 0.197 Angle : 0.559 9.338 8908 Z= 0.297 Chirality : 0.042 0.142 991 Planarity : 0.003 0.029 1140 Dihedral : 7.409 66.297 966 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.44 % Favored : 91.56 % 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 (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: -2.49 (0.28), residues: 782 helix: -1.43 (0.51), residues: 98 sheet: -1.48 (0.47), residues: 115 loop : -1.85 (0.25), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 176 HIS 0.005 0.001 HIS B 406 PHE 0.011 0.001 PHE A 371 TYR 0.019 0.001 TYR A 224 ARG 0.002 0.000 ARG B 481 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3672.25 seconds wall clock time: 64 minutes 27.53 seconds (3867.53 seconds total)