Starting phenix.real_space_refine on Fri Sep 11 18:38:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9w4d_65625/09_2026/9w4d_65625.cif Found real_map, /net/cci-nas-00/data/ceres_data/9w4d_65625/09_2026/9w4d_65625.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9w4d_65625/09_2026/9w4d_65625.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9w4d_65625/09_2026/9w4d_65625.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9w4d_65625/09_2026/9w4d_65625.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9w4d_65625/09_2026/9w4d_65625.map" } resolution = 2.9 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= 0.118 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 78 5.16 5 C 6729 2.51 5 N 1785 2.21 5 O 1998 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10590 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3502 Classifications: {'peptide': 428} Link IDs: {'PTRANS': 13, 'TRANS': 414} Chain breaks: 1 Chain: "B" Number of atoms: 3502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3502 Classifications: {'peptide': 428} Link IDs: {'PTRANS': 13, 'TRANS': 414} Chain breaks: 1 Chain: "C" Number of atoms: 3502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3502 Classifications: {'peptide': 428} Link IDs: {'PTRANS': 13, 'TRANS': 414} Chain breaks: 1 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 2.49, per 1000 atoms: 0.24 Number of scatterers: 10590 At special positions: 0 Unit cell: (87.4, 91.2, 147.25, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 78 16.00 O 1998 8.00 N 1785 7.00 C 6729 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS A 108 " - pdb=" SG CYS A 241 " distance=2.03 Simple disulfide: pdb=" SG CYS A 358 " - pdb=" SG CYS A 365 " distance=2.03 Simple disulfide: pdb=" SG CYS A 393 " - pdb=" SG CYS A 403 " distance=2.03 Simple disulfide: pdb=" SG CYS A 418 " - pdb=" SG CYS A 436 " distance=2.03 Simple disulfide: pdb=" SG CYS A 471 " - pdb=" SG CYS A 495 " distance=2.03 Simple disulfide: pdb=" SG CYS B 108 " - pdb=" SG CYS B 241 " distance=2.03 Simple disulfide: pdb=" SG CYS B 358 " - pdb=" SG CYS B 365 " distance=2.03 Simple disulfide: pdb=" SG CYS B 393 " - pdb=" SG CYS B 403 " distance=2.03 Simple disulfide: pdb=" SG CYS B 418 " - pdb=" SG CYS B 436 " distance=2.03 Simple disulfide: pdb=" SG CYS B 471 " - pdb=" SG CYS B 495 " distance=2.03 Simple disulfide: pdb=" SG CYS C 108 " - pdb=" SG CYS C 241 " distance=2.03 Simple disulfide: pdb=" SG CYS C 358 " - pdb=" SG CYS C 365 " distance=2.03 Simple disulfide: pdb=" SG CYS C 393 " - pdb=" SG CYS C 403 " distance=2.03 Simple disulfide: pdb=" SG CYS C 418 " - pdb=" SG CYS C 436 " distance=2.03 Simple disulfide: pdb=" SG CYS C 471 " - pdb=" SG CYS C 495 " 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 A 701 " - " ASN A 293 " " NAG A 702 " - " ASN A 526 " " NAG B 701 " - " ASN B 293 " " NAG B 702 " - " ASN B 526 " " NAG C 701 " - " ASN C 293 " " NAG C 702 " - " ASN C 526 " Time building additional restraints: 0.87 Conformation dependent library (CDL) restraints added in 357.2 milliseconds 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2514 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 13 sheets defined 38.1% alpha, 24.5% 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 40 through 44 Processing helix chain 'A' and resid 79 through 103 Processing helix chain 'A' and resid 114 through 140 removed outlier: 3.884A pdb=" N ALA A 140 " --> pdb=" O ILE A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 240 removed outlier: 3.604A pdb=" N THR A 240 " --> pdb=" O MET A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 274 removed outlier: 3.541A pdb=" N VAL A 244 " --> pdb=" O THR A 240 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N THR A 245 " --> pdb=" O CYS A 241 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N TYR A 274 " --> pdb=" O ASP A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 293 Processing helix chain 'A' and resid 294 through 298 Processing helix chain 'A' and resid 309 through 320 removed outlier: 4.202A pdb=" N HIS A 314 " --> pdb=" O VAL A 310 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ALA A 315 " --> pdb=" O ASN A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 424 Processing helix chain 'A' and resid 526 through 543 Processing helix chain 'B' and resid 40 through 44 Processing helix chain 'B' and resid 79 through 103 Processing helix chain 'B' and resid 114 through 140 removed outlier: 3.863A pdb=" N ALA B 140 " --> pdb=" O ILE B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 240 Processing helix chain 'B' and resid 240 through 274 removed outlier: 3.578A pdb=" N VAL B 244 " --> pdb=" O THR B 240 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N THR B 245 " --> pdb=" O CYS B 241 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TYR B 274 " --> pdb=" O ASP B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 294 Processing helix chain 'B' and resid 309 through 320 removed outlier: 4.086A pdb=" N HIS B 314 " --> pdb=" O VAL B 310 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ALA B 315 " --> pdb=" O ASN B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 424 Processing helix chain 'B' and resid 526 through 543 Processing helix chain 'C' and resid 40 through 44 Processing helix chain 'C' and resid 79 through 103 removed outlier: 3.554A pdb=" N PHE C 83 " --> pdb=" O HIS C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 140 removed outlier: 3.857A pdb=" N ALA C 140 " --> pdb=" O ILE C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 240 removed outlier: 3.592A pdb=" N THR C 240 " --> pdb=" O MET C 236 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 273 Processing helix chain 'C' and resid 283 through 294 Processing helix chain 'C' and resid 309 through 320 removed outlier: 4.075A pdb=" N HIS C 314 " --> pdb=" O VAL C 310 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ALA C 315 " --> pdb=" O ASN C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 424 Processing helix chain 'C' and resid 431 through 436 removed outlier: 3.648A pdb=" N CYS C 436 " --> pdb=" O LEU C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 526 through 543 Processing sheet with id=AA1, first strand: chain 'A' and resid 46 through 50 removed outlier: 4.358A pdb=" N VAL A 484 " --> pdb=" O LEU A 50 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 393 through 395 removed outlier: 8.536A pdb=" N LYS A 401 " --> pdb=" O ILE A 61 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N GLN A 63 " --> pdb=" O LYS A 401 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N CYS A 403 " --> pdb=" O GLN A 63 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ARG A 65 " --> pdb=" O CYS A 403 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N LEU A 349 " --> pdb=" O ILE A 61 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N GLN A 63 " --> pdb=" O TYR A 347 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N TYR A 347 " --> pdb=" O GLN A 63 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N ASN A 383 " --> pdb=" O SER A 378 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 322 through 327 removed outlier: 3.542A pdb=" N ILE B 515 " --> pdb=" O HIS A 72 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 357 through 358 Processing sheet with id=AA5, first strand: chain 'A' and resid 478 through 480 removed outlier: 5.897A pdb=" N ASN C 383 " --> pdb=" O SER C 378 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N TYR C 62 " --> pdb=" O LEU C 349 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ASN C 351 " --> pdb=" O LYS C 60 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N LYS C 60 " --> pdb=" O ASN C 351 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N VAL C 353 " --> pdb=" O PHE C 58 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N PHE C 58 " --> pdb=" O VAL C 353 " (cutoff:3.500A) removed outlier: 8.596A pdb=" N LYS C 401 " --> pdb=" O ILE C 61 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N GLN C 63 " --> pdb=" O LYS C 401 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N CYS C 403 " --> pdb=" O GLN C 63 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ARG C 65 " --> pdb=" O CYS C 403 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 514 through 518 removed outlier: 5.986A pdb=" N ILE A 515 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N GLU C 76 " --> pdb=" O ILE A 515 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N GLU A 517 " --> pdb=" O GLU C 76 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N ASP C 78 " --> pdb=" O GLU A 517 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N THR C 332 " --> pdb=" O THR C 328 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 46 through 50 removed outlier: 4.412A pdb=" N VAL B 484 " --> pdb=" O LEU B 50 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 322 through 327 removed outlier: 7.153A pdb=" N LEU B 349 " --> pdb=" O ILE B 61 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N GLN B 63 " --> pdb=" O TYR B 347 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N TYR B 347 " --> pdb=" O GLN B 63 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N ASN B 383 " --> pdb=" O SER B 378 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 393 through 395 removed outlier: 8.551A pdb=" N LYS B 401 " --> pdb=" O ILE B 61 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N GLN B 63 " --> pdb=" O LYS B 401 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N CYS B 403 " --> pdb=" O GLN B 63 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ARG B 65 " --> pdb=" O CYS B 403 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 357 through 358 Processing sheet with id=AB2, first strand: chain 'C' and resid 46 through 50 removed outlier: 4.399A pdb=" N VAL C 484 " --> pdb=" O LEU C 50 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 365 through 368 Processing sheet with id=AB4, first strand: chain 'C' and resid 478 through 480 561 hydrogen bonds defined for protein. 1563 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.66 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: 1.22 - 1.34: 3465 1.34 - 1.46: 2341 1.46 - 1.58: 4856 1.58 - 1.70: 0 1.70 - 1.82: 123 Bond restraints: 10785 Sorted by residual: bond pdb=" C1 NAG C 701 " pdb=" O5 NAG C 701 " ideal model delta sigma weight residual 1.406 1.472 -0.066 2.00e-02 2.50e+03 1.10e+01 bond pdb=" C1 NAG A 701 " pdb=" O5 NAG A 701 " ideal model delta sigma weight residual 1.406 1.454 -0.048 2.00e-02 2.50e+03 5.79e+00 bond pdb=" C1 NAG C 702 " pdb=" O5 NAG C 702 " ideal model delta sigma weight residual 1.406 1.445 -0.039 2.00e-02 2.50e+03 3.80e+00 bond pdb=" C1 NAG B 701 " pdb=" O5 NAG B 701 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.21e+00 bond pdb=" C5 NAG A 701 " pdb=" O5 NAG A 701 " ideal model delta sigma weight residual 1.413 1.441 -0.028 2.00e-02 2.50e+03 1.92e+00 ... (remaining 10780 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.90: 14422 1.90 - 3.80: 185 3.80 - 5.70: 9 5.70 - 7.60: 2 7.60 - 9.50: 1 Bond angle restraints: 14619 Sorted by residual: angle pdb=" CB MET A 377 " pdb=" CG MET A 377 " pdb=" SD MET A 377 " ideal model delta sigma weight residual 112.70 105.35 7.35 3.00e+00 1.11e-01 6.01e+00 angle pdb=" N LEU A 308 " pdb=" CA LEU A 308 " pdb=" C LEU A 308 " ideal model delta sigma weight residual 108.63 112.33 -3.70 1.60e+00 3.91e-01 5.36e+00 angle pdb=" C SER C 111 " pdb=" N GLU C 112 " pdb=" CA GLU C 112 " ideal model delta sigma weight residual 121.54 125.90 -4.36 1.91e+00 2.74e-01 5.22e+00 angle pdb=" CA GLU A 128 " pdb=" CB GLU A 128 " pdb=" CG GLU A 128 " ideal model delta sigma weight residual 114.10 117.90 -3.80 2.00e+00 2.50e-01 3.60e+00 angle pdb=" C1 NAG A 701 " pdb=" O5 NAG A 701 " pdb=" C5 NAG A 701 " ideal model delta sigma weight residual 113.21 118.71 -5.50 3.00e+00 1.11e-01 3.37e+00 ... (remaining 14614 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.06: 6263 23.06 - 46.11: 376 46.11 - 69.16: 37 69.16 - 92.22: 12 92.22 - 115.27: 20 Dihedral angle restraints: 6708 sinusoidal: 2859 harmonic: 3849 Sorted by residual: dihedral pdb=" CB CYS A 418 " pdb=" SG CYS A 418 " pdb=" SG CYS A 436 " pdb=" CB CYS A 436 " ideal model delta sinusoidal sigma weight residual 93.00 141.66 -48.66 1 1.00e+01 1.00e-02 3.26e+01 dihedral pdb=" CB CYS B 418 " pdb=" SG CYS B 418 " pdb=" SG CYS B 436 " pdb=" CB CYS B 436 " ideal model delta sinusoidal sigma weight residual 93.00 136.66 -43.66 1 1.00e+01 1.00e-02 2.66e+01 dihedral pdb=" CB CYS C 418 " pdb=" SG CYS C 418 " pdb=" SG CYS C 436 " pdb=" CB CYS C 436 " ideal model delta sinusoidal sigma weight residual 93.00 131.14 -38.14 1 1.00e+01 1.00e-02 2.05e+01 ... (remaining 6705 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1240 0.042 - 0.084: 348 0.084 - 0.125: 102 0.125 - 0.167: 17 0.167 - 0.209: 3 Chirality restraints: 1710 Sorted by residual: chirality pdb=" C1 NAG A 701 " pdb=" ND2 ASN A 293 " pdb=" C2 NAG A 701 " pdb=" O5 NAG A 701 " both_signs ideal model delta sigma weight residual False -2.40 -2.19 -0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" C1 NAG C 701 " pdb=" ND2 ASN C 293 " pdb=" C2 NAG C 701 " pdb=" O5 NAG C 701 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-01 2.50e+01 8.55e-01 chirality pdb=" CB VAL A 294 " pdb=" CA VAL A 294 " pdb=" CG1 VAL A 294 " pdb=" CG2 VAL A 294 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 7.50e-01 ... (remaining 1707 not shown) Planarity restraints: 1860 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 328 " 0.037 5.00e-02 4.00e+02 5.67e-02 5.14e+00 pdb=" N PRO A 329 " -0.098 5.00e-02 4.00e+02 pdb=" CA PRO A 329 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 329 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 328 " -0.029 5.00e-02 4.00e+02 4.36e-02 3.04e+00 pdb=" N PRO C 329 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO C 329 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO C 329 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 328 " 0.028 5.00e-02 4.00e+02 4.23e-02 2.86e+00 pdb=" N PRO B 329 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO B 329 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 329 " 0.024 5.00e-02 4.00e+02 ... (remaining 1857 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 970 2.75 - 3.29: 10051 3.29 - 3.82: 17330 3.82 - 4.36: 21172 4.36 - 4.90: 36563 Nonbonded interactions: 86086 Sorted by model distance: nonbonded pdb=" OG SER C 378 " pdb=" OD1 ASP C 380 " model vdw 2.212 3.040 nonbonded pdb=" OG SER B 378 " pdb=" OD1 ASP B 380 " model vdw 2.217 3.040 nonbonded pdb=" OG SER A 378 " pdb=" OD1 ASP A 380 " model vdw 2.250 3.040 nonbonded pdb=" OE1 GLU A 68 " pdb=" OH TYR B 494 " model vdw 2.252 3.040 nonbonded pdb=" NH2 ARG B 362 " pdb=" O PHE B 443 " model vdw 2.286 3.120 ... (remaining 86081 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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: 3.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 10.700 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 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 : 0.003 0.066 10806 Z= 0.131 Angle : 0.523 9.496 14667 Z= 0.272 Chirality : 0.043 0.209 1710 Planarity : 0.004 0.057 1854 Dihedral : 15.841 115.275 4149 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.11 (0.24), residues: 1272 helix: 2.64 (0.24), residues: 441 sheet: 0.47 (0.26), residues: 417 loop : -1.11 (0.29), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 276 TYR 0.014 0.001 TYR C 274 PHE 0.012 0.001 PHE A 527 TRP 0.006 0.001 TRP B 99 HIS 0.002 0.000 HIS A 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 (10785) covalent geometry : angle 0.51577 / 0.27 (14619) SS BOND : bond 0.00199 / 0.12 ( 15) SS BOND : angle 0.97871 / 0.62 ( 30) hydrogen bonds : bond 0.10216 / 6.34 ( 561) hydrogen bonds : angle 4.97638 / 3.48 ( 1563) link_NAG-ASN : bond 0.00524 / 0.25 ( 6) link_NAG-ASN : angle 2.35344 / 1.36 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 187 time to evaluate : 0.428 Fit side-chains REVERT: B 357 MET cc_start: 0.8633 (ptt) cc_final: 0.8229 (ptt) outliers start: 0 outliers final: 2 residues processed: 187 average time/residue: 0.5625 time to fit residues: 113.0395 Evaluate side-chains 134 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 132 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 307 GLU Chi-restraints excluded: chain C residue 444 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 108 optimal weight: 5.9990 chunk 49 optimal weight: 5.9990 chunk 97 optimal weight: 2.9990 chunk 113 optimal weight: 0.7980 chunk 53 optimal weight: 7.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.3980 chunk 123 optimal weight: 3.9990 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 0.9980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 383 ASN ** B 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 63 GLN C 383 ASN C 449 HIS C 507 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.163970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.122968 restraints weight = 11212.442| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 1.79 r_work: 0.3055 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2892 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.0986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 10806 Z= 0.156 Angle : 0.561 9.647 14667 Z= 0.283 Chirality : 0.045 0.240 1710 Planarity : 0.004 0.055 1854 Dihedral : 10.188 159.303 1529 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.99 % Allowed : 9.68 % Favored : 88.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.24), residues: 1272 helix: 2.43 (0.24), residues: 447 sheet: 0.49 (0.26), residues: 417 loop : -1.07 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 532 TYR 0.014 0.002 TYR C 274 PHE 0.010 0.001 PHE B 83 TRP 0.007 0.001 TRP A 71 HIS 0.009 0.001 HIS C 449 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.16 (10785) covalent geometry : angle 0.54630 / 0.28 (14619) SS BOND : bond 0.00216 / 0.11 ( 15) SS BOND : angle 0.92710 / 0.59 ( 30) hydrogen bonds : bond 0.04059 / 2.71 ( 561) hydrogen bonds : angle 4.52851 / 3.15 ( 1563) link_NAG-ASN : bond 0.00656 / 0.32 ( 6) link_NAG-ASN : angle 3.54254 / 2.09 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 146 time to evaluate : 0.445 Fit side-chains revert: symmetry clash REVERT: A 532 ARG cc_start: 0.7784 (mtm110) cc_final: 0.7447 (ttp-110) REVERT: B 373 LYS cc_start: 0.8758 (OUTLIER) cc_final: 0.8325 (tmtm) REVERT: B 430 MET cc_start: 0.7808 (ptt) cc_final: 0.7491 (ptt) REVERT: C 373 LYS cc_start: 0.8724 (OUTLIER) cc_final: 0.8337 (tmtm) REVERT: C 442 ARG cc_start: 0.8149 (mpt-90) cc_final: 0.7944 (mtm180) outliers start: 24 outliers final: 11 residues processed: 163 average time/residue: 0.5804 time to fit residues: 102.0557 Evaluate side-chains 144 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 131 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 380 ASP Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain A residue 453 ASP Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain B residue 373 LYS Chi-restraints excluded: chain B residue 380 ASP Chi-restraints excluded: chain B residue 419 ASP Chi-restraints excluded: chain C residue 373 LYS Chi-restraints excluded: chain C residue 380 ASP Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 453 ASP Chi-restraints excluded: chain C residue 498 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 98 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 100 optimal weight: 0.5980 chunk 105 optimal weight: 0.0670 chunk 18 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 83 optimal weight: 0.7980 chunk 27 optimal weight: 0.5980 chunk 33 optimal weight: 0.7980 chunk 124 optimal weight: 4.9990 chunk 78 optimal weight: 3.9990 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 449 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.165720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.125753 restraints weight = 11283.883| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 1.86 r_work: 0.3114 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.1127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 10806 Z= 0.112 Angle : 0.517 10.169 14667 Z= 0.262 Chirality : 0.044 0.466 1710 Planarity : 0.004 0.060 1854 Dihedral : 7.112 70.907 1524 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.23 % Allowed : 12.24 % Favored : 85.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.24), residues: 1272 helix: 2.55 (0.24), residues: 447 sheet: 0.51 (0.26), residues: 417 loop : -1.03 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 532 TYR 0.013 0.001 TYR C 274 PHE 0.007 0.001 PHE C 260 TRP 0.004 0.001 TRP C 99 HIS 0.009 0.001 HIS C 449 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.11 (10785) covalent geometry : angle 0.50196 / 0.26 (14619) SS BOND : bond 0.00154 / 0.08 ( 15) SS BOND : angle 0.83816 / 0.52 ( 30) hydrogen bonds : bond 0.03528 / 2.37 ( 561) hydrogen bonds : angle 4.40259 / 3.07 ( 1563) link_NAG-ASN : bond 0.00671 / 0.32 ( 6) link_NAG-ASN : angle 3.50286 / 1.88 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 142 time to evaluate : 0.310 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 532 ARG cc_start: 0.7771 (mtm110) cc_final: 0.7412 (ttp-110) REVERT: B 373 LYS cc_start: 0.8698 (OUTLIER) cc_final: 0.8230 (tmtm) REVERT: B 430 MET cc_start: 0.7752 (ptt) cc_final: 0.7465 (ptt) REVERT: C 292 ARG cc_start: 0.8088 (ttp-170) cc_final: 0.7851 (tmm160) REVERT: C 311 ASN cc_start: 0.8087 (OUTLIER) cc_final: 0.7836 (m-40) REVERT: C 373 LYS cc_start: 0.8669 (OUTLIER) cc_final: 0.8219 (tmtm) outliers start: 27 outliers final: 11 residues processed: 159 average time/residue: 0.5350 time to fit residues: 91.9895 Evaluate side-chains 145 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 131 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 357 MET Chi-restraints excluded: chain A residue 380 ASP Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain B residue 357 MET Chi-restraints excluded: chain B residue 373 LYS Chi-restraints excluded: chain B residue 380 ASP Chi-restraints excluded: chain C residue 293 ASN Chi-restraints excluded: chain C residue 311 ASN Chi-restraints excluded: chain C residue 373 LYS Chi-restraints excluded: chain C residue 380 ASP Chi-restraints excluded: chain C residue 413 ASN Chi-restraints excluded: chain C residue 453 ASP Chi-restraints excluded: chain C residue 498 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 93 optimal weight: 0.9990 chunk 3 optimal weight: 3.9990 chunk 101 optimal weight: 0.9990 chunk 26 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 40 optimal weight: 0.0060 chunk 43 optimal weight: 0.7980 chunk 75 optimal weight: 0.5980 chunk 39 optimal weight: 5.9990 overall best weight: 0.6800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 507 HIS ** B 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 449 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.165586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.126656 restraints weight = 11224.711| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 1.88 r_work: 0.3125 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.1346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 10806 Z= 0.118 Angle : 0.497 8.158 14667 Z= 0.257 Chirality : 0.044 0.389 1710 Planarity : 0.004 0.059 1854 Dihedral : 6.233 70.149 1524 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 3.14 % Allowed : 13.73 % Favored : 83.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.18 (0.24), residues: 1272 helix: 2.57 (0.24), residues: 447 sheet: 0.54 (0.26), residues: 417 loop : -1.00 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 532 TYR 0.012 0.001 TYR C 274 PHE 0.007 0.001 PHE B 58 TRP 0.006 0.001 TRP C 99 HIS 0.009 0.001 HIS C 449 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 (10785) covalent geometry : angle 0.48765 / 0.25 (14619) SS BOND : bond 0.00159 / 0.09 ( 15) SS BOND : angle 0.84952 / 0.53 ( 30) hydrogen bonds : bond 0.03470 / 2.33 ( 561) hydrogen bonds : angle 4.34059 / 3.03 ( 1563) link_NAG-ASN : bond 0.00519 / 0.24 ( 6) link_NAG-ASN : angle 2.68830 / 1.33 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 146 time to evaluate : 0.377 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 373 LYS cc_start: 0.8565 (tmtm) cc_final: 0.8288 (tmtm) REVERT: A 430 MET cc_start: 0.7573 (ptt) cc_final: 0.7178 (ptp) REVERT: A 442 ARG cc_start: 0.8114 (OUTLIER) cc_final: 0.7743 (mmt-90) REVERT: A 532 ARG cc_start: 0.7899 (mtm110) cc_final: 0.7541 (ttp-110) REVERT: B 101 LYS cc_start: 0.7496 (ttmm) cc_final: 0.7250 (tttt) REVERT: B 357 MET cc_start: 0.8393 (OUTLIER) cc_final: 0.7985 (ptm) REVERT: B 373 LYS cc_start: 0.8755 (OUTLIER) cc_final: 0.8337 (tmtm) REVERT: B 430 MET cc_start: 0.7834 (ptt) cc_final: 0.7517 (ptt) REVERT: C 311 ASN cc_start: 0.8133 (OUTLIER) cc_final: 0.7890 (m-40) REVERT: C 373 LYS cc_start: 0.8705 (OUTLIER) cc_final: 0.8305 (tmtm) REVERT: C 433 MET cc_start: 0.5934 (OUTLIER) cc_final: 0.5659 (mmm) REVERT: C 521 MET cc_start: 0.8278 (mmt) cc_final: 0.7799 (mmp) REVERT: C 537 MET cc_start: 0.7101 (OUTLIER) cc_final: 0.6786 (ptt) outliers start: 38 outliers final: 16 residues processed: 166 average time/residue: 0.5526 time to fit residues: 98.9774 Evaluate side-chains 156 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 133 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 357 MET Chi-restraints excluded: chain A residue 380 ASP Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain A residue 442 ARG Chi-restraints excluded: chain A residue 471 CYS Chi-restraints excluded: chain B residue 357 MET Chi-restraints excluded: chain B residue 373 LYS Chi-restraints excluded: chain B residue 380 ASP Chi-restraints excluded: chain B residue 419 ASP Chi-restraints excluded: chain B residue 471 CYS Chi-restraints excluded: chain B residue 521 MET Chi-restraints excluded: chain C residue 293 ASN Chi-restraints excluded: chain C residue 311 ASN Chi-restraints excluded: chain C residue 373 LYS Chi-restraints excluded: chain C residue 380 ASP Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 413 ASN Chi-restraints excluded: chain C residue 433 MET Chi-restraints excluded: chain C residue 471 CYS Chi-restraints excluded: chain C residue 498 SER Chi-restraints excluded: chain C residue 526 ASN Chi-restraints excluded: chain C residue 537 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 54 optimal weight: 4.9990 chunk 121 optimal weight: 5.9990 chunk 86 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 27 optimal weight: 0.0870 chunk 57 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 119 optimal weight: 2.9990 chunk 50 optimal weight: 0.6980 overall best weight: 1.5564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 507 HIS C 449 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.158171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.117827 restraints weight = 11285.213| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 1.96 r_work: 0.2971 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2807 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.1550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 10806 Z= 0.206 Angle : 0.569 7.332 14667 Z= 0.295 Chirality : 0.047 0.334 1710 Planarity : 0.004 0.058 1854 Dihedral : 6.378 69.552 1524 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.72 % Allowed : 15.14 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.24), residues: 1272 helix: 2.29 (0.24), residues: 447 sheet: 0.45 (0.26), residues: 417 loop : -1.03 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 532 TYR 0.017 0.002 TYR B 274 PHE 0.012 0.001 PHE B 83 TRP 0.010 0.002 TRP A 71 HIS 0.008 0.001 HIS C 449 Details of bonding type rmsd/Z covalent geometry : bond 0.00511 / 0.21 (10785) covalent geometry : angle 0.55911 / 0.29 (14619) SS BOND : bond 0.00206 / 0.11 ( 15) SS BOND : angle 0.99002 / 0.62 ( 30) hydrogen bonds : bond 0.04229 / 2.84 ( 561) hydrogen bonds : angle 4.53141 / 3.17 ( 1563) link_NAG-ASN : bond 0.00532 / 0.26 ( 6) link_NAG-ASN : angle 2.80090 / 1.39 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 134 time to evaluate : 0.412 Fit side-chains revert: symmetry clash REVERT: A 373 LYS cc_start: 0.8629 (OUTLIER) cc_final: 0.8371 (tmtm) REVERT: A 430 MET cc_start: 0.7612 (ptt) cc_final: 0.7280 (ptp) REVERT: A 433 MET cc_start: 0.6795 (mmm) cc_final: 0.6550 (mmp) REVERT: A 442 ARG cc_start: 0.8052 (OUTLIER) cc_final: 0.7831 (mmt-90) REVERT: A 532 ARG cc_start: 0.7907 (mtm110) cc_final: 0.7531 (ttp-110) REVERT: B 373 LYS cc_start: 0.8764 (OUTLIER) cc_final: 0.8289 (tmtm) REVERT: B 430 MET cc_start: 0.7892 (ptt) cc_final: 0.7599 (ptt) REVERT: C 373 LYS cc_start: 0.8706 (OUTLIER) cc_final: 0.8296 (tmtm) REVERT: C 521 MET cc_start: 0.8309 (mmt) cc_final: 0.7884 (mmp) REVERT: C 537 MET cc_start: 0.7079 (OUTLIER) cc_final: 0.6708 (ptt) outliers start: 45 outliers final: 22 residues processed: 163 average time/residue: 0.5298 time to fit residues: 93.5233 Evaluate side-chains 147 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 120 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 ASP Chi-restraints excluded: chain A residue 357 MET Chi-restraints excluded: chain A residue 373 LYS Chi-restraints excluded: chain A residue 380 ASP Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 442 ARG Chi-restraints excluded: chain A residue 453 ASP Chi-restraints excluded: chain A residue 471 CYS Chi-restraints excluded: chain B residue 357 MET Chi-restraints excluded: chain B residue 373 LYS Chi-restraints excluded: chain B residue 380 ASP Chi-restraints excluded: chain B residue 419 ASP Chi-restraints excluded: chain B residue 471 CYS Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 521 MET Chi-restraints excluded: chain B residue 523 SER Chi-restraints excluded: chain C residue 373 LYS Chi-restraints excluded: chain C residue 380 ASP Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 413 ASN Chi-restraints excluded: chain C residue 471 CYS Chi-restraints excluded: chain C residue 498 SER Chi-restraints excluded: chain C residue 526 ASN Chi-restraints excluded: chain C residue 537 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 36 optimal weight: 4.9990 chunk 119 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 1 optimal weight: 0.8980 chunk 40 optimal weight: 3.9990 chunk 112 optimal weight: 2.9990 chunk 105 optimal weight: 0.0000 chunk 33 optimal weight: 0.8980 chunk 54 optimal weight: 5.9990 chunk 30 optimal weight: 0.8980 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 449 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.159830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.119571 restraints weight = 11419.420| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 1.97 r_work: 0.3021 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2859 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.1531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 10806 Z= 0.141 Angle : 0.518 7.553 14667 Z= 0.268 Chirality : 0.044 0.192 1710 Planarity : 0.004 0.059 1854 Dihedral : 5.931 66.071 1524 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 3.47 % Allowed : 16.13 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.24), residues: 1272 helix: 2.44 (0.24), residues: 447 sheet: 0.44 (0.26), residues: 417 loop : -1.01 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 532 TYR 0.015 0.001 TYR C 274 PHE 0.008 0.001 PHE B 58 TRP 0.005 0.001 TRP C 99 HIS 0.009 0.001 HIS C 449 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.14 (10785) covalent geometry : angle 0.50806 / 0.27 (14619) SS BOND : bond 0.00169 / 0.10 ( 15) SS BOND : angle 0.87901 / 0.53 ( 30) hydrogen bonds : bond 0.03690 / 2.47 ( 561) hydrogen bonds : angle 4.42785 / 3.08 ( 1563) link_NAG-ASN : bond 0.00481 / 0.23 ( 6) link_NAG-ASN : angle 2.71380 / 1.37 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 131 time to evaluate : 0.423 Fit side-chains revert: symmetry clash REVERT: A 143 MET cc_start: 0.6213 (mmt) cc_final: 0.5770 (mmt) REVERT: A 373 LYS cc_start: 0.8635 (OUTLIER) cc_final: 0.8339 (tmtm) REVERT: A 430 MET cc_start: 0.7632 (ptt) cc_final: 0.7287 (ptp) REVERT: A 442 ARG cc_start: 0.8081 (OUTLIER) cc_final: 0.7790 (mmt-90) REVERT: A 532 ARG cc_start: 0.7901 (mtm110) cc_final: 0.7525 (ttp-110) REVERT: B 373 LYS cc_start: 0.8763 (OUTLIER) cc_final: 0.8300 (tmtm) REVERT: B 430 MET cc_start: 0.7880 (ptt) cc_final: 0.7577 (ptt) REVERT: C 373 LYS cc_start: 0.8695 (OUTLIER) cc_final: 0.8273 (tmtm) REVERT: C 433 MET cc_start: 0.5802 (OUTLIER) cc_final: 0.5575 (mmm) REVERT: C 521 MET cc_start: 0.8331 (mmt) cc_final: 0.7839 (mmp) REVERT: C 537 MET cc_start: 0.7109 (OUTLIER) cc_final: 0.6764 (ptt) outliers start: 42 outliers final: 27 residues processed: 158 average time/residue: 0.5197 time to fit residues: 89.1383 Evaluate side-chains 162 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 129 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 ASP Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 357 MET Chi-restraints excluded: chain A residue 373 LYS Chi-restraints excluded: chain A residue 380 ASP Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain A residue 442 ARG Chi-restraints excluded: chain A residue 453 ASP Chi-restraints excluded: chain A residue 471 CYS Chi-restraints excluded: chain B residue 292 ARG Chi-restraints excluded: chain B residue 357 MET Chi-restraints excluded: chain B residue 373 LYS Chi-restraints excluded: chain B residue 380 ASP Chi-restraints excluded: chain B residue 419 ASP Chi-restraints excluded: chain B residue 471 CYS Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 521 MET Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain C residue 311 ASN Chi-restraints excluded: chain C residue 373 LYS Chi-restraints excluded: chain C residue 380 ASP Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 413 ASN Chi-restraints excluded: chain C residue 433 MET Chi-restraints excluded: chain C residue 453 ASP Chi-restraints excluded: chain C residue 471 CYS Chi-restraints excluded: chain C residue 498 SER Chi-restraints excluded: chain C residue 526 ASN Chi-restraints excluded: chain C residue 537 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 112 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 37 optimal weight: 0.7980 chunk 114 optimal weight: 0.8980 chunk 21 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 99 optimal weight: 0.6980 chunk 4 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 chunk 118 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 449 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.160737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.120289 restraints weight = 11236.190| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 1.98 r_work: 0.3020 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2857 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.1580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 10806 Z= 0.130 Angle : 0.511 7.638 14667 Z= 0.265 Chirality : 0.044 0.199 1710 Planarity : 0.004 0.061 1854 Dihedral : 5.651 59.810 1524 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.98 % Allowed : 17.20 % Favored : 79.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.24), residues: 1272 helix: 2.50 (0.24), residues: 447 sheet: 0.45 (0.26), residues: 417 loop : -1.03 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 532 TYR 0.015 0.001 TYR C 274 PHE 0.008 0.001 PHE B 58 TRP 0.006 0.001 TRP C 99 HIS 0.009 0.001 HIS C 449 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.13 (10785) covalent geometry : angle 0.50177 / 0.26 (14619) SS BOND : bond 0.00165 / 0.10 ( 15) SS BOND : angle 0.87344 / 0.54 ( 30) hydrogen bonds : bond 0.03553 / 2.38 ( 561) hydrogen bonds : angle 4.38040 / 3.05 ( 1563) link_NAG-ASN : bond 0.00443 / 0.21 ( 6) link_NAG-ASN : angle 2.61735 / 1.34 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 138 time to evaluate : 0.269 Fit side-chains revert: symmetry clash REVERT: A 143 MET cc_start: 0.6368 (mmt) cc_final: 0.5815 (mmt) REVERT: A 373 LYS cc_start: 0.8635 (OUTLIER) cc_final: 0.8337 (tmtm) REVERT: A 430 MET cc_start: 0.7668 (ptt) cc_final: 0.7285 (ptp) REVERT: A 442 ARG cc_start: 0.8085 (OUTLIER) cc_final: 0.7787 (mmt-90) REVERT: A 532 ARG cc_start: 0.7929 (mtm110) cc_final: 0.7556 (ttp-110) REVERT: B 373 LYS cc_start: 0.8757 (OUTLIER) cc_final: 0.8305 (tmtm) REVERT: B 379 GLN cc_start: 0.9009 (mm110) cc_final: 0.8712 (mm110) REVERT: B 430 MET cc_start: 0.7894 (ptt) cc_final: 0.7595 (ptt) REVERT: C 373 LYS cc_start: 0.8697 (OUTLIER) cc_final: 0.8289 (tmtm) REVERT: C 537 MET cc_start: 0.7050 (OUTLIER) cc_final: 0.6712 (ptt) outliers start: 36 outliers final: 24 residues processed: 160 average time/residue: 0.5096 time to fit residues: 88.4102 Evaluate side-chains 155 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 126 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 ASP Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 357 MET Chi-restraints excluded: chain A residue 373 LYS Chi-restraints excluded: chain A residue 380 ASP Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain A residue 442 ARG Chi-restraints excluded: chain A residue 453 ASP Chi-restraints excluded: chain A residue 471 CYS Chi-restraints excluded: chain B residue 292 ARG Chi-restraints excluded: chain B residue 357 MET Chi-restraints excluded: chain B residue 373 LYS Chi-restraints excluded: chain B residue 380 ASP Chi-restraints excluded: chain B residue 419 ASP Chi-restraints excluded: chain B residue 471 CYS Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 521 MET Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain C residue 311 ASN Chi-restraints excluded: chain C residue 373 LYS Chi-restraints excluded: chain C residue 380 ASP Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 413 ASN Chi-restraints excluded: chain C residue 471 CYS Chi-restraints excluded: chain C residue 498 SER Chi-restraints excluded: chain C residue 526 ASN Chi-restraints excluded: chain C residue 537 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 122 optimal weight: 0.9990 chunk 102 optimal weight: 2.9990 chunk 50 optimal weight: 0.5980 chunk 10 optimal weight: 10.0000 chunk 112 optimal weight: 0.9980 chunk 83 optimal weight: 1.9990 chunk 36 optimal weight: 0.0270 chunk 56 optimal weight: 0.5980 chunk 16 optimal weight: 0.0050 chunk 72 optimal weight: 0.7980 chunk 94 optimal weight: 2.9990 overall best weight: 0.4052 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 43 ASN C 449 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.166895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.126384 restraints weight = 11134.078| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 1.78 r_work: 0.3146 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.1619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 10806 Z= 0.096 Angle : 0.486 8.253 14667 Z= 0.249 Chirality : 0.043 0.185 1710 Planarity : 0.004 0.063 1854 Dihedral : 5.186 50.769 1524 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.81 % Allowed : 17.70 % Favored : 79.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.24), residues: 1272 helix: 2.58 (0.24), residues: 456 sheet: 0.47 (0.26), residues: 420 loop : -0.92 (0.30), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 382 TYR 0.012 0.001 TYR C 274 PHE 0.007 0.001 PHE B 260 TRP 0.005 0.001 TRP C 99 HIS 0.010 0.001 HIS C 449 Details of bonding type rmsd/Z covalent geometry : bond 0.00213 / 0.10 (10785) covalent geometry : angle 0.47734 / 0.25 (14619) SS BOND : bond 0.00151 / 0.09 ( 15) SS BOND : angle 0.78903 / 0.50 ( 30) hydrogen bonds : bond 0.03113 / 2.08 ( 561) hydrogen bonds : angle 4.23317 / 2.95 ( 1563) link_NAG-ASN : bond 0.00433 / 0.21 ( 6) link_NAG-ASN : angle 2.54862 / 1.31 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 144 time to evaluate : 0.394 Fit side-chains revert: symmetry clash REVERT: A 430 MET cc_start: 0.7694 (ptt) cc_final: 0.7304 (ptp) REVERT: A 532 ARG cc_start: 0.7907 (mtm110) cc_final: 0.7560 (ttp-110) REVERT: B 270 ASP cc_start: 0.8283 (m-30) cc_final: 0.8061 (m-30) REVERT: B 373 LYS cc_start: 0.8738 (OUTLIER) cc_final: 0.8317 (tmtm) REVERT: B 379 GLN cc_start: 0.8971 (mm110) cc_final: 0.8669 (mm110) REVERT: B 430 MET cc_start: 0.7839 (ptt) cc_final: 0.7540 (ptt) REVERT: B 479 GLN cc_start: 0.8307 (mt0) cc_final: 0.8085 (tt0) REVERT: C 357 MET cc_start: 0.7549 (ptm) cc_final: 0.7343 (ptm) REVERT: C 373 LYS cc_start: 0.8674 (OUTLIER) cc_final: 0.8296 (tmtm) REVERT: C 532 ARG cc_start: 0.7990 (mtm110) cc_final: 0.7648 (mtm-85) outliers start: 34 outliers final: 21 residues processed: 169 average time/residue: 0.5446 time to fit residues: 99.7204 Evaluate side-chains 154 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 131 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 ASP Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 357 MET Chi-restraints excluded: chain A residue 380 ASP Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain A residue 471 CYS Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 292 ARG Chi-restraints excluded: chain B residue 373 LYS Chi-restraints excluded: chain B residue 380 ASP Chi-restraints excluded: chain B residue 471 CYS Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain B residue 521 MET Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain C residue 373 LYS Chi-restraints excluded: chain C residue 380 ASP Chi-restraints excluded: chain C residue 413 ASN Chi-restraints excluded: chain C residue 471 CYS Chi-restraints excluded: chain C residue 498 SER Chi-restraints excluded: chain C residue 526 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 123 optimal weight: 5.9990 chunk 29 optimal weight: 0.6980 chunk 30 optimal weight: 0.8980 chunk 17 optimal weight: 0.9990 chunk 72 optimal weight: 0.0570 chunk 43 optimal weight: 0.9980 chunk 37 optimal weight: 6.9990 chunk 74 optimal weight: 0.9990 chunk 103 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 overall best weight: 0.7300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 43 ASN B 507 HIS B 511 ASN C 449 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.165414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.124725 restraints weight = 11119.847| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 1.76 r_work: 0.3088 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2923 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.1688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 10806 Z= 0.122 Angle : 0.512 7.499 14667 Z= 0.265 Chirality : 0.044 0.185 1710 Planarity : 0.004 0.061 1854 Dihedral : 5.177 51.066 1524 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 2.48 % Allowed : 18.36 % Favored : 79.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.18 (0.24), residues: 1272 helix: 2.50 (0.24), residues: 456 sheet: 0.54 (0.26), residues: 417 loop : -1.00 (0.30), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 456 TYR 0.014 0.001 TYR C 274 PHE 0.008 0.001 PHE B 58 TRP 0.007 0.001 TRP C 99 HIS 0.010 0.001 HIS C 449 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.12 (10785) covalent geometry : angle 0.50332 / 0.26 (14619) SS BOND : bond 0.00161 / 0.09 ( 15) SS BOND : angle 0.83135 / 0.52 ( 30) hydrogen bonds : bond 0.03436 / 2.31 ( 561) hydrogen bonds : angle 4.28382 / 2.99 ( 1563) link_NAG-ASN : bond 0.00460 / 0.22 ( 6) link_NAG-ASN : angle 2.65019 / 1.36 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 136 time to evaluate : 0.535 Fit side-chains revert: symmetry clash REVERT: A 430 MET cc_start: 0.7646 (ptt) cc_final: 0.7292 (ptp) REVERT: A 532 ARG cc_start: 0.8003 (mtm110) cc_final: 0.7647 (ttp-110) REVERT: B 373 LYS cc_start: 0.8751 (OUTLIER) cc_final: 0.8329 (tmtm) REVERT: B 430 MET cc_start: 0.7841 (ptt) cc_final: 0.7541 (ptt) REVERT: B 479 GLN cc_start: 0.8357 (mt0) cc_final: 0.8145 (tt0) REVERT: C 373 LYS cc_start: 0.8694 (OUTLIER) cc_final: 0.8294 (tmtm) REVERT: C 532 ARG cc_start: 0.7966 (mtm110) cc_final: 0.7610 (mtm-85) outliers start: 30 outliers final: 23 residues processed: 158 average time/residue: 0.5399 time to fit residues: 92.2627 Evaluate side-chains 156 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 131 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 ASP Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 357 MET Chi-restraints excluded: chain A residue 380 ASP Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain A residue 471 CYS Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 373 LYS Chi-restraints excluded: chain B residue 380 ASP Chi-restraints excluded: chain B residue 471 CYS Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain B residue 521 MET Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain C residue 311 ASN Chi-restraints excluded: chain C residue 373 LYS Chi-restraints excluded: chain C residue 380 ASP Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 413 ASN Chi-restraints excluded: chain C residue 471 CYS Chi-restraints excluded: chain C residue 498 SER Chi-restraints excluded: chain C residue 526 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 21 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 8 optimal weight: 0.5980 chunk 40 optimal weight: 0.8980 chunk 105 optimal weight: 0.0770 chunk 27 optimal weight: 0.9990 chunk 116 optimal weight: 0.7980 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 110 ASN B 63 GLN C 449 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.165899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.125260 restraints weight = 11149.153| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 1.78 r_work: 0.3140 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.1714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 10806 Z= 0.113 Angle : 0.511 8.882 14667 Z= 0.262 Chirality : 0.043 0.184 1710 Planarity : 0.004 0.060 1854 Dihedral : 5.059 50.894 1524 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 2.40 % Allowed : 18.78 % Favored : 78.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.19 (0.24), residues: 1272 helix: 2.52 (0.24), residues: 456 sheet: 0.50 (0.26), residues: 420 loop : -0.95 (0.30), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 382 TYR 0.014 0.001 TYR C 274 PHE 0.008 0.001 PHE A 326 TRP 0.005 0.001 TRP C 99 HIS 0.011 0.001 HIS C 449 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.11 (10785) covalent geometry : angle 0.50251 / 0.26 (14619) SS BOND : bond 0.00161 / 0.10 ( 15) SS BOND : angle 0.79292 / 0.50 ( 30) hydrogen bonds : bond 0.03350 / 2.24 ( 561) hydrogen bonds : angle 4.26995 / 2.98 ( 1563) link_NAG-ASN : bond 0.00458 / 0.22 ( 6) link_NAG-ASN : angle 2.63697 / 1.35 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 133 time to evaluate : 0.285 Fit side-chains revert: symmetry clash REVERT: A 430 MET cc_start: 0.7652 (ptt) cc_final: 0.7300 (ptp) REVERT: A 532 ARG cc_start: 0.7890 (mtm110) cc_final: 0.7573 (ttp-110) REVERT: B 373 LYS cc_start: 0.8745 (OUTLIER) cc_final: 0.8328 (tmtm) REVERT: B 430 MET cc_start: 0.7850 (ptt) cc_final: 0.7538 (ptt) REVERT: B 479 GLN cc_start: 0.8348 (mt0) cc_final: 0.8134 (tt0) REVERT: C 373 LYS cc_start: 0.8686 (OUTLIER) cc_final: 0.8298 (tmtm) REVERT: C 532 ARG cc_start: 0.7973 (mtm110) cc_final: 0.7621 (mtm-85) outliers start: 29 outliers final: 25 residues processed: 155 average time/residue: 0.5084 time to fit residues: 84.9616 Evaluate side-chains 157 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 130 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 ASN Chi-restraints excluded: chain A residue 117 ASP Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 357 MET Chi-restraints excluded: chain A residue 380 ASP Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain A residue 471 CYS Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 292 ARG Chi-restraints excluded: chain B residue 373 LYS Chi-restraints excluded: chain B residue 380 ASP Chi-restraints excluded: chain B residue 471 CYS Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain B residue 521 MET Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain C residue 311 ASN Chi-restraints excluded: chain C residue 373 LYS Chi-restraints excluded: chain C residue 380 ASP Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 413 ASN Chi-restraints excluded: chain C residue 471 CYS Chi-restraints excluded: chain C residue 498 SER Chi-restraints excluded: chain C residue 526 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 14 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 chunk 41 optimal weight: 0.5980 chunk 20 optimal weight: 2.9990 chunk 62 optimal weight: 0.0970 chunk 95 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 15 optimal weight: 0.5980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 110 ASN C 449 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.164136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.123263 restraints weight = 11213.504| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 1.78 r_work: 0.3056 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2891 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 10806 Z= 0.154 Angle : 0.543 9.840 14667 Z= 0.278 Chirality : 0.045 0.181 1710 Planarity : 0.004 0.059 1854 Dihedral : 5.156 50.803 1524 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.56 % Allowed : 18.94 % Favored : 78.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.24), residues: 1272 helix: 2.39 (0.24), residues: 456 sheet: 0.50 (0.25), residues: 417 loop : -1.01 (0.30), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 382 TYR 0.017 0.002 TYR C 274 PHE 0.010 0.001 PHE A 326 TRP 0.009 0.001 TRP A 71 HIS 0.010 0.001 HIS C 449 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.15 (10785) covalent geometry : angle 0.53353 / 0.28 (14619) SS BOND : bond 0.00185 / 0.11 ( 15) SS BOND : angle 0.86142 / 0.55 ( 30) hydrogen bonds : bond 0.03711 / 2.49 ( 561) hydrogen bonds : angle 4.36570 / 3.05 ( 1563) link_NAG-ASN : bond 0.00458 / 0.22 ( 6) link_NAG-ASN : angle 2.74063 / 1.40 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3643.56 seconds wall clock time: 62 minutes 50.61 seconds (3770.61 seconds total)