Starting phenix.real_space_refine on Mon Dec 30 02:17:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ze3_60022/12_2024/8ze3_60022_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ze3_60022/12_2024/8ze3_60022.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ze3_60022/12_2024/8ze3_60022.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ze3_60022/12_2024/8ze3_60022.map" model { file = "/net/cci-nas-00/data/ceres_data/8ze3_60022/12_2024/8ze3_60022_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ze3_60022/12_2024/8ze3_60022_trim.cif" } resolution = 3.17 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= 0.017 sd= 0.119 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 80 5.16 5 C 7868 2.51 5 N 2012 2.21 5 O 2112 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 12072 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 3006 Classifications: {'peptide': 374} Link IDs: {'PTRANS': 6, 'TRANS': 367} Chain breaks: 2 Chain: "B" Number of atoms: 3006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 3006 Classifications: {'peptide': 374} Link IDs: {'PTRANS': 6, 'TRANS': 367} Chain breaks: 2 Chain: "C" Number of atoms: 3006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 3006 Classifications: {'peptide': 374} Link IDs: {'PTRANS': 6, 'TRANS': 367} Chain breaks: 2 Chain: "D" Number of atoms: 3006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 3006 Classifications: {'peptide': 374} Link IDs: {'PTRANS': 6, 'TRANS': 367} Chain breaks: 2 Chain: "A" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'FRU': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'FRU': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'FRU': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'FRU': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.10, per 1000 atoms: 0.59 Number of scatterers: 12072 At special positions: 0 Unit cell: (97.86, 97.86, 98.792, 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 80 16.00 O 2112 8.00 N 2012 7.00 C 7868 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.15 Conformation dependent library (CDL) restraints added in 1.6 seconds 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2864 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 4 sheets defined 83.7% alpha, 2.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.96 Creating SS restraints... Processing helix chain 'A' and resid 8 through 17 Processing helix chain 'A' and resid 37 through 64 removed outlier: 3.505A pdb=" N ILE A 42 " --> pdb=" O TRP A 38 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TYR A 43 " --> pdb=" O LEU A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 100 removed outlier: 4.009A pdb=" N VAL A 78 " --> pdb=" O ALA A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 118 removed outlier: 3.576A pdb=" N THR A 118 " --> pdb=" O LYS A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 161 removed outlier: 3.792A pdb=" N ASP A 128 " --> pdb=" O ASN A 124 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N MET A 161 " --> pdb=" O MET A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 174 Processing helix chain 'A' and resid 175 through 214 removed outlier: 3.553A pdb=" N LEU A 210 " --> pdb=" O LEU A 206 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N TYR A 214 " --> pdb=" O LEU A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 292 removed outlier: 4.168A pdb=" N SER A 268 " --> pdb=" O THR A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 321 removed outlier: 3.729A pdb=" N ALA A 311 " --> pdb=" O LEU A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 342 removed outlier: 3.936A pdb=" N VAL A 327 " --> pdb=" O ASP A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 357 Processing helix chain 'A' and resid 358 through 368 removed outlier: 4.929A pdb=" N GLU A 364 " --> pdb=" O GLN A 360 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ILE A 365 " --> pdb=" O ILE A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 388 removed outlier: 3.711A pdb=" N GLU A 376 " --> pdb=" O PRO A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 424 removed outlier: 3.690A pdb=" N THR A 406 " --> pdb=" O ARG A 402 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N THR A 414 " --> pdb=" O SER A 410 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ILE A 420 " --> pdb=" O LEU A 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 17 Processing helix chain 'B' and resid 37 through 64 removed outlier: 3.505A pdb=" N ILE B 42 " --> pdb=" O TRP B 38 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N TYR B 43 " --> pdb=" O LEU B 39 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 100 removed outlier: 4.009A pdb=" N VAL B 78 " --> pdb=" O ALA B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 118 removed outlier: 3.576A pdb=" N THR B 118 " --> pdb=" O LYS B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 161 removed outlier: 3.793A pdb=" N ASP B 128 " --> pdb=" O ASN B 124 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N MET B 161 " --> pdb=" O MET B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 174 Processing helix chain 'B' and resid 175 through 214 removed outlier: 3.553A pdb=" N LEU B 210 " --> pdb=" O LEU B 206 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N TYR B 214 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 292 removed outlier: 4.168A pdb=" N SER B 268 " --> pdb=" O THR B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 321 removed outlier: 3.729A pdb=" N ALA B 311 " --> pdb=" O LEU B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 342 removed outlier: 3.936A pdb=" N VAL B 327 " --> pdb=" O ASP B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 357 Processing helix chain 'B' and resid 358 through 368 removed outlier: 4.929A pdb=" N GLU B 364 " --> pdb=" O GLN B 360 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ILE B 365 " --> pdb=" O ILE B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 388 removed outlier: 3.709A pdb=" N GLU B 376 " --> pdb=" O PRO B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 424 removed outlier: 3.690A pdb=" N THR B 406 " --> pdb=" O ARG B 402 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N THR B 414 " --> pdb=" O SER B 410 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ILE B 420 " --> pdb=" O LEU B 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 17 Processing helix chain 'C' and resid 37 through 64 removed outlier: 3.505A pdb=" N ILE C 42 " --> pdb=" O TRP C 38 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TYR C 43 " --> pdb=" O LEU C 39 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 100 removed outlier: 4.010A pdb=" N VAL C 78 " --> pdb=" O ALA C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 118 removed outlier: 3.576A pdb=" N THR C 118 " --> pdb=" O LYS C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 124 through 161 removed outlier: 3.792A pdb=" N ASP C 128 " --> pdb=" O ASN C 124 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N MET C 161 " --> pdb=" O MET C 157 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 174 Processing helix chain 'C' and resid 175 through 214 removed outlier: 3.553A pdb=" N LEU C 210 " --> pdb=" O LEU C 206 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N TYR C 214 " --> pdb=" O LEU C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 292 removed outlier: 4.168A pdb=" N SER C 268 " --> pdb=" O THR C 264 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 321 removed outlier: 3.730A pdb=" N ALA C 311 " --> pdb=" O LEU C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 323 through 342 removed outlier: 3.937A pdb=" N VAL C 327 " --> pdb=" O ASP C 323 " (cutoff:3.500A) Processing helix chain 'C' and resid 344 through 357 Processing helix chain 'C' and resid 358 through 368 removed outlier: 4.929A pdb=" N GLU C 364 " --> pdb=" O GLN C 360 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ILE C 365 " --> pdb=" O ILE C 361 " (cutoff:3.500A) Processing helix chain 'C' and resid 371 through 388 removed outlier: 3.710A pdb=" N GLU C 376 " --> pdb=" O PRO C 372 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 424 removed outlier: 3.690A pdb=" N THR C 406 " --> pdb=" O ARG C 402 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N THR C 414 " --> pdb=" O SER C 410 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ILE C 420 " --> pdb=" O LEU C 416 " (cutoff:3.500A) Processing helix chain 'D' and resid 8 through 17 Processing helix chain 'D' and resid 37 through 64 removed outlier: 3.505A pdb=" N ILE D 42 " --> pdb=" O TRP D 38 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TYR D 43 " --> pdb=" O LEU D 39 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 100 removed outlier: 4.009A pdb=" N VAL D 78 " --> pdb=" O ALA D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 118 removed outlier: 3.577A pdb=" N THR D 118 " --> pdb=" O LYS D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 124 through 161 removed outlier: 3.792A pdb=" N ASP D 128 " --> pdb=" O ASN D 124 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N MET D 161 " --> pdb=" O MET D 157 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 174 Processing helix chain 'D' and resid 175 through 214 removed outlier: 3.552A pdb=" N LEU D 210 " --> pdb=" O LEU D 206 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N TYR D 214 " --> pdb=" O LEU D 210 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 292 removed outlier: 4.168A pdb=" N SER D 268 " --> pdb=" O THR D 264 " (cutoff:3.500A) Processing helix chain 'D' and resid 292 through 321 removed outlier: 3.730A pdb=" N ALA D 311 " --> pdb=" O LEU D 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 323 through 342 removed outlier: 3.937A pdb=" N VAL D 327 " --> pdb=" O ASP D 323 " (cutoff:3.500A) Processing helix chain 'D' and resid 344 through 357 Processing helix chain 'D' and resid 358 through 368 removed outlier: 4.930A pdb=" N GLU D 364 " --> pdb=" O GLN D 360 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ILE D 365 " --> pdb=" O ILE D 361 " (cutoff:3.500A) Processing helix chain 'D' and resid 371 through 388 removed outlier: 3.710A pdb=" N GLU D 376 " --> pdb=" O PRO D 372 " (cutoff:3.500A) Processing helix chain 'D' and resid 402 through 424 removed outlier: 3.690A pdb=" N THR D 406 " --> pdb=" O ARG D 402 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N THR D 414 " --> pdb=" O SER D 410 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ILE D 420 " --> pdb=" O LEU D 416 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 22 through 27 removed outlier: 4.255A pdb=" N ASN A 27 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N GLN A 31 " --> pdb=" O ASN A 27 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 22 through 27 removed outlier: 4.254A pdb=" N ASN B 27 " --> pdb=" O GLN B 31 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N GLN B 31 " --> pdb=" O ASN B 27 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 22 through 27 removed outlier: 4.254A pdb=" N ASN C 27 " --> pdb=" O GLN C 31 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N GLN C 31 " --> pdb=" O ASN C 27 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 22 through 27 removed outlier: 4.255A pdb=" N ASN D 27 " --> pdb=" O GLN D 31 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N GLN D 31 " --> pdb=" O ASN D 27 " (cutoff:3.500A) 976 hydrogen bonds defined for protein. 2928 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: 4.20 Time building geometry restraints manager: 3.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 3724 1.35 - 1.47: 3043 1.47 - 1.58: 5409 1.58 - 1.70: 0 1.70 - 1.82: 128 Bond restraints: 12304 Sorted by residual: bond pdb=" C2 FRU B 501 " pdb=" C3 FRU B 501 " ideal model delta sigma weight residual 1.541 1.463 0.078 2.00e-02 2.50e+03 1.54e+01 bond pdb=" C2 FRU C 501 " pdb=" C3 FRU C 501 " ideal model delta sigma weight residual 1.541 1.463 0.078 2.00e-02 2.50e+03 1.54e+01 bond pdb=" C2 FRU A 501 " pdb=" C3 FRU A 501 " ideal model delta sigma weight residual 1.541 1.463 0.078 2.00e-02 2.50e+03 1.54e+01 bond pdb=" C2 FRU D 501 " pdb=" C3 FRU D 501 " ideal model delta sigma weight residual 1.541 1.463 0.078 2.00e-02 2.50e+03 1.54e+01 bond pdb=" C3 FRU C 501 " pdb=" C4 FRU C 501 " ideal model delta sigma weight residual 1.519 1.458 0.061 2.00e-02 2.50e+03 9.36e+00 ... (remaining 12299 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.83: 16312 1.83 - 3.66: 241 3.66 - 5.49: 67 5.49 - 7.32: 28 7.32 - 9.15: 12 Bond angle restraints: 16660 Sorted by residual: angle pdb=" CA GLU C 376 " pdb=" CB GLU C 376 " pdb=" CG GLU C 376 " ideal model delta sigma weight residual 114.10 120.37 -6.27 2.00e+00 2.50e-01 9.81e+00 angle pdb=" CA GLU D 376 " pdb=" CB GLU D 376 " pdb=" CG GLU D 376 " ideal model delta sigma weight residual 114.10 120.36 -6.26 2.00e+00 2.50e-01 9.81e+00 angle pdb=" CA GLU A 376 " pdb=" CB GLU A 376 " pdb=" CG GLU A 376 " ideal model delta sigma weight residual 114.10 120.35 -6.25 2.00e+00 2.50e-01 9.76e+00 angle pdb=" CA GLU B 376 " pdb=" CB GLU B 376 " pdb=" CG GLU B 376 " ideal model delta sigma weight residual 114.10 120.32 -6.22 2.00e+00 2.50e-01 9.67e+00 angle pdb=" C2 FRU D 501 " pdb=" O5 FRU D 501 " pdb=" C5 FRU D 501 " ideal model delta sigma weight residual 112.00 102.85 9.15 3.00e+00 1.11e-01 9.31e+00 ... (remaining 16655 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 6136 17.84 - 35.68: 896 35.68 - 53.52: 292 53.52 - 71.36: 56 71.36 - 89.20: 20 Dihedral angle restraints: 7400 sinusoidal: 2984 harmonic: 4416 Sorted by residual: dihedral pdb=" CA LYS A 26 " pdb=" C LYS A 26 " pdb=" N ASN A 27 " pdb=" CA ASN A 27 " ideal model delta harmonic sigma weight residual 180.00 162.84 17.16 0 5.00e+00 4.00e-02 1.18e+01 dihedral pdb=" CA LYS B 26 " pdb=" C LYS B 26 " pdb=" N ASN B 27 " pdb=" CA ASN B 27 " ideal model delta harmonic sigma weight residual 180.00 162.86 17.14 0 5.00e+00 4.00e-02 1.18e+01 dihedral pdb=" CA LYS C 26 " pdb=" C LYS C 26 " pdb=" N ASN C 27 " pdb=" CA ASN C 27 " ideal model delta harmonic sigma weight residual 180.00 162.86 17.14 0 5.00e+00 4.00e-02 1.17e+01 ... (remaining 7397 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1370 0.032 - 0.065: 404 0.065 - 0.097: 182 0.097 - 0.129: 20 0.129 - 0.162: 8 Chirality restraints: 1984 Sorted by residual: chirality pdb=" CG LEU D 60 " pdb=" CB LEU D 60 " pdb=" CD1 LEU D 60 " pdb=" CD2 LEU D 60 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.53e-01 chirality pdb=" CG LEU C 60 " pdb=" CB LEU C 60 " pdb=" CD1 LEU C 60 " pdb=" CD2 LEU C 60 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.47e-01 chirality pdb=" CG LEU A 60 " pdb=" CB LEU A 60 " pdb=" CD1 LEU A 60 " pdb=" CD2 LEU A 60 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.38e-01 ... (remaining 1981 not shown) Planarity restraints: 2008 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU B 376 " 0.006 2.00e-02 2.50e+03 1.31e-02 1.71e+00 pdb=" CD GLU B 376 " -0.023 2.00e-02 2.50e+03 pdb=" OE1 GLU B 376 " 0.008 2.00e-02 2.50e+03 pdb=" OE2 GLU B 376 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU C 376 " 0.006 2.00e-02 2.50e+03 1.28e-02 1.65e+00 pdb=" CD GLU C 376 " -0.022 2.00e-02 2.50e+03 pdb=" OE1 GLU C 376 " 0.008 2.00e-02 2.50e+03 pdb=" OE2 GLU C 376 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU D 376 " -0.006 2.00e-02 2.50e+03 1.27e-02 1.63e+00 pdb=" CD GLU D 376 " 0.022 2.00e-02 2.50e+03 pdb=" OE1 GLU D 376 " -0.008 2.00e-02 2.50e+03 pdb=" OE2 GLU D 376 " -0.008 2.00e-02 2.50e+03 ... (remaining 2005 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 138 2.63 - 3.20: 10906 3.20 - 3.77: 20108 3.77 - 4.33: 25412 4.33 - 4.90: 43261 Nonbonded interactions: 99825 Sorted by model distance: nonbonded pdb=" OE1 GLU A 279 " pdb=" NH2 ARG B 367 " model vdw 2.064 3.120 nonbonded pdb=" NH2 ARG A 367 " pdb=" OE1 GLU D 279 " model vdw 2.119 3.120 nonbonded pdb=" O THR B 212 " pdb=" OG SER B 216 " model vdw 2.178 3.040 nonbonded pdb=" O THR D 212 " pdb=" OG SER D 216 " model vdw 2.179 3.040 nonbonded pdb=" O THR C 212 " pdb=" OG SER C 216 " model vdw 2.179 3.040 ... (remaining 99820 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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 0.730 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: 0.020 Extract box with map and model: 0.450 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 29.050 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.060 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: 0.010 Load rotamer database and sin/cos tables:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7387 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 12304 Z= 0.250 Angle : 0.683 9.152 16660 Z= 0.348 Chirality : 0.038 0.162 1984 Planarity : 0.004 0.046 2008 Dihedral : 19.034 89.200 4536 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.88 % Allowed : 34.70 % Favored : 62.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.22), residues: 1472 helix: 1.45 (0.14), residues: 1224 sheet: -1.39 (0.74), residues: 40 loop : -2.98 (0.37), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 328 HIS 0.003 0.001 HIS A 278 PHE 0.008 0.001 PHE A 192 TYR 0.013 0.001 TYR D 326 ARG 0.008 0.000 ARG D 367 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 252 time to evaluate : 1.749 Fit side-chains REVERT: A 324 ASN cc_start: 0.6854 (p0) cc_final: 0.6505 (m-40) REVERT: B 209 MET cc_start: 0.7656 (tpp) cc_final: 0.7357 (tpt) REVERT: C 22 TYR cc_start: 0.7935 (m-80) cc_final: 0.7570 (m-10) REVERT: C 116 ASP cc_start: 0.7833 (m-30) cc_final: 0.7582 (m-30) REVERT: D 103 ARG cc_start: 0.7194 (tpp-160) cc_final: 0.6774 (mmm-85) REVERT: D 129 ARG cc_start: 0.7815 (ttm170) cc_final: 0.7422 (ttm170) REVERT: D 208 GLN cc_start: 0.7437 (mm-40) cc_final: 0.7103 (tp-100) REVERT: D 324 ASN cc_start: 0.6881 (p0) cc_final: 0.6576 (m-40) outliers start: 38 outliers final: 32 residues processed: 290 average time/residue: 0.2731 time to fit residues: 112.4933 Evaluate side-chains 253 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 221 time to evaluate : 1.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 383 GLN Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 383 GLN Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain C residue 7 ASN Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 37 SER Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 280 SER Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 383 GLN Chi-restraints excluded: chain C residue 417 VAL Chi-restraints excluded: chain D residue 7 ASN Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 37 SER Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 182 TYR Chi-restraints excluded: chain D residue 280 SER Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 383 GLN Chi-restraints excluded: chain D residue 417 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 124 optimal weight: 7.9990 chunk 112 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 chunk 38 optimal weight: 3.9990 chunk 75 optimal weight: 0.9980 chunk 59 optimal weight: 0.9990 chunk 116 optimal weight: 4.9990 chunk 44 optimal weight: 0.8980 chunk 70 optimal weight: 2.9990 chunk 86 optimal weight: 7.9990 chunk 134 optimal weight: 2.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 ASN A 278 HIS A 330 GLN A 384 GLN B 7 ASN B 278 HIS B 330 GLN C 278 HIS C 330 GLN D 278 HIS D 330 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 moved from start: 0.1193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12304 Z= 0.196 Angle : 0.512 7.847 16660 Z= 0.262 Chirality : 0.037 0.224 1984 Planarity : 0.003 0.026 2008 Dihedral : 7.245 58.034 1784 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 4.62 % Allowed : 26.89 % Favored : 68.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.96 (0.22), residues: 1472 helix: 2.06 (0.14), residues: 1228 sheet: -1.72 (0.72), residues: 40 loop : -3.00 (0.37), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 328 HIS 0.003 0.001 HIS A 189 PHE 0.015 0.001 PHE C 192 TYR 0.007 0.001 TYR C 182 ARG 0.004 0.000 ARG A 367 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 238 time to evaluate : 1.363 Fit side-chains REVERT: A 324 ASN cc_start: 0.6786 (p0) cc_final: 0.6424 (m-40) REVERT: A 330 GLN cc_start: 0.7179 (OUTLIER) cc_final: 0.5849 (mp-120) REVERT: B 93 THR cc_start: 0.8729 (m) cc_final: 0.8505 (m) REVERT: B 145 ILE cc_start: 0.8099 (mp) cc_final: 0.7813 (mp) REVERT: B 324 ASN cc_start: 0.7034 (p0) cc_final: 0.6487 (m-40) REVERT: B 330 GLN cc_start: 0.7320 (OUTLIER) cc_final: 0.6065 (mp-120) REVERT: B 346 GLU cc_start: 0.8382 (mm-30) cc_final: 0.8007 (tp30) REVERT: C 324 ASN cc_start: 0.6768 (p0) cc_final: 0.6330 (m-40) REVERT: C 330 GLN cc_start: 0.7379 (OUTLIER) cc_final: 0.6214 (mp-120) REVERT: D 116 ASP cc_start: 0.8101 (m-30) cc_final: 0.7853 (m-30) REVERT: D 129 ARG cc_start: 0.7796 (ttm170) cc_final: 0.7410 (ttm170) REVERT: D 145 ILE cc_start: 0.7983 (mp) cc_final: 0.7682 (mp) REVERT: D 324 ASN cc_start: 0.6804 (p0) cc_final: 0.6502 (m-40) REVERT: D 330 GLN cc_start: 0.7201 (OUTLIER) cc_final: 0.5825 (mp-120) outliers start: 61 outliers final: 34 residues processed: 281 average time/residue: 0.2298 time to fit residues: 94.0682 Evaluate side-chains 254 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 216 time to evaluate : 1.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 283 LYS Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 330 GLN Chi-restraints excluded: chain A residue 343 MET Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain B residue 7 ASN Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 283 LYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 330 GLN Chi-restraints excluded: chain B residue 343 MET Chi-restraints excluded: chain B residue 361 ILE Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 271 ILE Chi-restraints excluded: chain C residue 283 LYS Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 330 GLN Chi-restraints excluded: chain C residue 343 MET Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 271 ILE Chi-restraints excluded: chain D residue 283 LYS Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 330 GLN Chi-restraints excluded: chain D residue 343 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 74 optimal weight: 10.0000 chunk 41 optimal weight: 3.9990 chunk 111 optimal weight: 10.0000 chunk 91 optimal weight: 0.7980 chunk 37 optimal weight: 10.0000 chunk 134 optimal weight: 2.9990 chunk 145 optimal weight: 0.0470 chunk 119 optimal weight: 4.9990 chunk 133 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 chunk 108 optimal weight: 0.0970 overall best weight: 1.1880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 ASN A 330 GLN A 383 GLN B 330 GLN C 330 GLN C 383 GLN C 384 GLN D 330 GLN D 384 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.1589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12304 Z= 0.203 Angle : 0.499 7.525 16660 Z= 0.257 Chirality : 0.036 0.140 1984 Planarity : 0.003 0.025 2008 Dihedral : 5.008 41.578 1744 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 5.00 % Allowed : 25.53 % Favored : 69.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.13 (0.22), residues: 1472 helix: 2.20 (0.14), residues: 1228 sheet: -2.03 (0.64), residues: 40 loop : -3.00 (0.37), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 328 HIS 0.004 0.001 HIS D 189 PHE 0.012 0.001 PHE C 192 TYR 0.015 0.001 TYR B 326 ARG 0.006 0.000 ARG D 367 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 229 time to evaluate : 1.410 Fit side-chains REVERT: A 22 TYR cc_start: 0.8384 (m-80) cc_final: 0.8161 (m-10) REVERT: A 324 ASN cc_start: 0.6821 (p0) cc_final: 0.6401 (m-40) REVERT: A 330 GLN cc_start: 0.7090 (OUTLIER) cc_final: 0.5906 (mp-120) REVERT: B 145 ILE cc_start: 0.8056 (OUTLIER) cc_final: 0.7670 (mp) REVERT: B 324 ASN cc_start: 0.7055 (p0) cc_final: 0.6479 (m-40) REVERT: B 330 GLN cc_start: 0.7214 (OUTLIER) cc_final: 0.5970 (mp-120) REVERT: C 33 GLU cc_start: 0.7729 (tt0) cc_final: 0.7177 (pt0) REVERT: C 324 ASN cc_start: 0.6806 (p0) cc_final: 0.6333 (m-40) REVERT: C 330 GLN cc_start: 0.7267 (OUTLIER) cc_final: 0.6118 (mp-120) REVERT: D 116 ASP cc_start: 0.8143 (m-30) cc_final: 0.7862 (m-30) REVERT: D 129 ARG cc_start: 0.7714 (ttm170) cc_final: 0.7357 (ttm170) REVERT: D 145 ILE cc_start: 0.8098 (OUTLIER) cc_final: 0.7733 (mp) REVERT: D 324 ASN cc_start: 0.6609 (p0) cc_final: 0.6268 (m-40) REVERT: D 330 GLN cc_start: 0.7060 (OUTLIER) cc_final: 0.6036 (mp-120) outliers start: 66 outliers final: 36 residues processed: 273 average time/residue: 0.2176 time to fit residues: 88.1600 Evaluate side-chains 245 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 203 time to evaluate : 1.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 283 LYS Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 330 GLN Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 330 GLN Chi-restraints excluded: chain B residue 361 ILE Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 271 ILE Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 330 GLN Chi-restraints excluded: chain C residue 361 ILE Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 271 ILE Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 330 GLN Chi-restraints excluded: chain D residue 361 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 133 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 chunk 64 optimal weight: 4.9990 chunk 90 optimal weight: 20.0000 chunk 135 optimal weight: 3.9990 chunk 143 optimal weight: 9.9990 chunk 70 optimal weight: 0.6980 chunk 128 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 ASN A 330 GLN B 173 GLN B 330 GLN C 7 ASN C 330 GLN D 7 ASN D 173 GLN D 330 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.1887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12304 Z= 0.223 Angle : 0.502 8.136 16660 Z= 0.259 Chirality : 0.037 0.267 1984 Planarity : 0.003 0.025 2008 Dihedral : 4.719 37.998 1744 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 5.08 % Allowed : 25.98 % Favored : 68.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.19 (0.21), residues: 1472 helix: 2.25 (0.14), residues: 1228 sheet: -1.97 (0.65), residues: 40 loop : -3.03 (0.36), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 328 HIS 0.003 0.001 HIS D 189 PHE 0.012 0.001 PHE C 192 TYR 0.011 0.001 TYR C 326 ARG 0.004 0.000 ARG C 367 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 220 time to evaluate : 1.269 Fit side-chains REVERT: A 116 ASP cc_start: 0.7958 (m-30) cc_final: 0.7610 (m-30) REVERT: A 209 MET cc_start: 0.7975 (tpp) cc_final: 0.7769 (tpt) REVERT: A 324 ASN cc_start: 0.6787 (p0) cc_final: 0.6331 (m-40) REVERT: A 330 GLN cc_start: 0.7052 (OUTLIER) cc_final: 0.5859 (mp-120) REVERT: B 22 TYR cc_start: 0.8330 (m-10) cc_final: 0.8123 (m-10) REVERT: B 145 ILE cc_start: 0.8120 (OUTLIER) cc_final: 0.7869 (mt) REVERT: B 182 TYR cc_start: 0.8139 (OUTLIER) cc_final: 0.7756 (m-80) REVERT: B 324 ASN cc_start: 0.6889 (p0) cc_final: 0.6361 (m-40) REVERT: B 364 GLU cc_start: 0.7127 (mp0) cc_final: 0.6721 (mp0) REVERT: C 25 LYS cc_start: 0.7361 (mmmm) cc_final: 0.7068 (mmmm) REVERT: C 33 GLU cc_start: 0.7748 (tt0) cc_final: 0.7223 (pt0) REVERT: C 209 MET cc_start: 0.8261 (tpp) cc_final: 0.8042 (tpt) REVERT: C 324 ASN cc_start: 0.6789 (p0) cc_final: 0.6222 (m-40) REVERT: C 364 GLU cc_start: 0.7114 (mp0) cc_final: 0.6716 (mp0) REVERT: C 376 GLU cc_start: 0.8007 (tp30) cc_final: 0.7723 (tp30) REVERT: D 33 GLU cc_start: 0.7768 (tt0) cc_final: 0.7198 (pt0) REVERT: D 116 ASP cc_start: 0.8178 (m-30) cc_final: 0.7907 (m-30) REVERT: D 129 ARG cc_start: 0.7695 (ttm170) cc_final: 0.7356 (ttm170) REVERT: D 145 ILE cc_start: 0.8132 (OUTLIER) cc_final: 0.7745 (mp) REVERT: D 324 ASN cc_start: 0.6644 (p0) cc_final: 0.6217 (m-40) outliers start: 67 outliers final: 40 residues processed: 265 average time/residue: 0.2192 time to fit residues: 85.7881 Evaluate side-chains 246 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 202 time to evaluate : 1.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 283 LYS Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 330 GLN Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 182 TYR Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 283 LYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 361 ILE Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 271 ILE Chi-restraints excluded: chain C residue 283 LYS Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 361 ILE Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 271 ILE Chi-restraints excluded: chain D residue 283 LYS Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 361 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 119 optimal weight: 0.8980 chunk 81 optimal weight: 2.9990 chunk 2 optimal weight: 9.9990 chunk 106 optimal weight: 2.9990 chunk 59 optimal weight: 9.9990 chunk 122 optimal weight: 8.9990 chunk 98 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 73 optimal weight: 4.9990 chunk 128 optimal weight: 0.7980 chunk 36 optimal weight: 0.7980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 ASN A 330 GLN A 384 GLN B 173 GLN B 330 GLN C 7 ASN C 173 GLN C 330 GLN D 7 ASN D 173 GLN D 330 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12304 Z= 0.219 Angle : 0.494 8.900 16660 Z= 0.255 Chirality : 0.037 0.307 1984 Planarity : 0.003 0.025 2008 Dihedral : 4.429 36.928 1744 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 4.70 % Allowed : 26.67 % Favored : 68.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.33 (0.21), residues: 1472 helix: 2.34 (0.14), residues: 1228 sheet: -1.89 (0.67), residues: 40 loop : -3.02 (0.36), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 328 HIS 0.003 0.001 HIS D 189 PHE 0.012 0.001 PHE C 192 TYR 0.012 0.001 TYR D 214 ARG 0.004 0.000 ARG C 367 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 224 time to evaluate : 1.440 Fit side-chains REVERT: A 116 ASP cc_start: 0.8010 (m-30) cc_final: 0.7711 (m-30) REVERT: A 324 ASN cc_start: 0.6815 (p0) cc_final: 0.6289 (m-40) REVERT: A 376 GLU cc_start: 0.8047 (tp30) cc_final: 0.7682 (tp30) REVERT: A 384 GLN cc_start: 0.8217 (tt0) cc_final: 0.7956 (tt0) REVERT: B 116 ASP cc_start: 0.7974 (m-30) cc_final: 0.7756 (m-30) REVERT: B 145 ILE cc_start: 0.8140 (OUTLIER) cc_final: 0.7889 (mt) REVERT: B 182 TYR cc_start: 0.8156 (OUTLIER) cc_final: 0.7813 (m-80) REVERT: B 324 ASN cc_start: 0.6887 (p0) cc_final: 0.6371 (m-40) REVERT: C 25 LYS cc_start: 0.7446 (mmmm) cc_final: 0.7139 (mmmm) REVERT: C 33 GLU cc_start: 0.7729 (tt0) cc_final: 0.7241 (pt0) REVERT: C 360 GLN cc_start: 0.8868 (mt0) cc_final: 0.8641 (mt0) REVERT: C 376 GLU cc_start: 0.7990 (tp30) cc_final: 0.7647 (tp30) REVERT: C 397 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8424 (mt) REVERT: D 25 LYS cc_start: 0.7622 (mmmm) cc_final: 0.7301 (mmmm) REVERT: D 33 GLU cc_start: 0.7800 (tt0) cc_final: 0.7271 (pt0) REVERT: D 129 ARG cc_start: 0.7725 (ttm170) cc_final: 0.7408 (ttm170) REVERT: D 145 ILE cc_start: 0.8128 (OUTLIER) cc_final: 0.7744 (mp) REVERT: D 209 MET cc_start: 0.7706 (tpt) cc_final: 0.7368 (tpt) REVERT: D 324 ASN cc_start: 0.6752 (p0) cc_final: 0.6323 (m-40) REVERT: D 376 GLU cc_start: 0.8002 (tp30) cc_final: 0.7668 (tp30) outliers start: 62 outliers final: 38 residues processed: 268 average time/residue: 0.2352 time to fit residues: 92.1922 Evaluate side-chains 239 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 197 time to evaluate : 1.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 182 TYR Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 283 LYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 361 ILE Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 271 ILE Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 361 ILE Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 72 LYS Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 271 ILE Chi-restraints excluded: chain D residue 283 LYS Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 361 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 48 optimal weight: 7.9990 chunk 128 optimal weight: 4.9990 chunk 28 optimal weight: 5.9990 chunk 83 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 143 optimal weight: 3.9990 chunk 118 optimal weight: 0.6980 chunk 66 optimal weight: 0.6980 chunk 11 optimal weight: 10.0000 chunk 47 optimal weight: 0.6980 chunk 75 optimal weight: 2.9990 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 ASN A 330 GLN C 7 ASN C 173 GLN D 7 ASN D 173 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.2348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12304 Z= 0.250 Angle : 0.519 9.465 16660 Z= 0.267 Chirality : 0.038 0.308 1984 Planarity : 0.003 0.024 2008 Dihedral : 4.303 36.822 1744 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 5.00 % Allowed : 27.50 % Favored : 67.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.34 (0.21), residues: 1472 helix: 2.36 (0.14), residues: 1228 sheet: -1.74 (0.68), residues: 40 loop : -3.05 (0.36), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 328 HIS 0.003 0.001 HIS D 189 PHE 0.013 0.001 PHE D 192 TYR 0.012 0.001 TYR D 214 ARG 0.004 0.000 ARG C 367 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 215 time to evaluate : 1.254 Fit side-chains REVERT: A 324 ASN cc_start: 0.6769 (p0) cc_final: 0.6256 (m-40) REVERT: A 376 GLU cc_start: 0.8000 (tp30) cc_final: 0.7604 (tp30) REVERT: A 397 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8436 (mp) REVERT: B 145 ILE cc_start: 0.8188 (OUTLIER) cc_final: 0.7922 (mt) REVERT: B 182 TYR cc_start: 0.8219 (OUTLIER) cc_final: 0.7910 (m-80) REVERT: B 324 ASN cc_start: 0.6845 (p0) cc_final: 0.6378 (m-40) REVERT: B 397 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.8438 (mp) REVERT: C 25 LYS cc_start: 0.7556 (mmmm) cc_final: 0.7259 (mmmm) REVERT: C 33 GLU cc_start: 0.7756 (tt0) cc_final: 0.7261 (pt0) REVERT: C 157 MET cc_start: 0.8015 (mtp) cc_final: 0.7349 (mtp) REVERT: C 161 MET cc_start: 0.6050 (OUTLIER) cc_final: 0.5788 (pmt) REVERT: C 182 TYR cc_start: 0.8223 (OUTLIER) cc_final: 0.7928 (m-80) REVERT: C 376 GLU cc_start: 0.7959 (tp30) cc_final: 0.7582 (tp30) REVERT: C 397 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8460 (mt) REVERT: D 129 ARG cc_start: 0.7767 (ttm170) cc_final: 0.7463 (ttm170) REVERT: D 145 ILE cc_start: 0.8129 (OUTLIER) cc_final: 0.7869 (mt) REVERT: D 209 MET cc_start: 0.7747 (tpt) cc_final: 0.7397 (tpt) REVERT: D 324 ASN cc_start: 0.6803 (p0) cc_final: 0.6338 (m-40) REVERT: D 376 GLU cc_start: 0.8040 (tp30) cc_final: 0.7677 (tp30) REVERT: D 397 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8447 (mp) outliers start: 66 outliers final: 42 residues processed: 265 average time/residue: 0.2393 time to fit residues: 90.8223 Evaluate side-chains 254 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 203 time to evaluate : 1.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 72 LYS Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 283 LYS Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 72 LYS Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 182 TYR Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 283 LYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 361 ILE Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 72 LYS Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain C residue 161 MET Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain C residue 271 ILE Chi-restraints excluded: chain C residue 283 LYS Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 361 ILE Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 271 ILE Chi-restraints excluded: chain D residue 283 LYS Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 361 ILE Chi-restraints excluded: chain D residue 397 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 138 optimal weight: 1.9990 chunk 16 optimal weight: 7.9990 chunk 81 optimal weight: 5.9990 chunk 104 optimal weight: 4.9990 chunk 120 optimal weight: 5.9990 chunk 79 optimal weight: 0.9990 chunk 142 optimal weight: 6.9990 chunk 89 optimal weight: 0.9990 chunk 86 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 88 optimal weight: 0.6980 overall best weight: 1.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 ASN A 278 HIS A 423 GLN B 173 GLN B 278 HIS C 7 ASN C 173 GLN C 278 HIS D 7 ASN D 173 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.2392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12304 Z= 0.188 Angle : 0.505 9.731 16660 Z= 0.255 Chirality : 0.038 0.276 1984 Planarity : 0.003 0.025 2008 Dihedral : 4.132 36.763 1744 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 4.85 % Allowed : 28.26 % Favored : 66.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.48 (0.21), residues: 1472 helix: 2.45 (0.14), residues: 1228 sheet: -1.68 (0.66), residues: 40 loop : -3.02 (0.36), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 328 HIS 0.003 0.001 HIS D 189 PHE 0.012 0.001 PHE B 53 TYR 0.010 0.001 TYR D 214 ARG 0.003 0.000 ARG C 367 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 222 time to evaluate : 1.351 Fit side-chains REVERT: A 324 ASN cc_start: 0.6742 (p0) cc_final: 0.6315 (m-40) REVERT: A 376 GLU cc_start: 0.8021 (tp30) cc_final: 0.7596 (tp30) REVERT: A 397 LEU cc_start: 0.8724 (OUTLIER) cc_final: 0.8456 (mt) REVERT: B 145 ILE cc_start: 0.8170 (OUTLIER) cc_final: 0.7926 (mt) REVERT: B 161 MET cc_start: 0.6102 (OUTLIER) cc_final: 0.5831 (pmt) REVERT: B 182 TYR cc_start: 0.8117 (OUTLIER) cc_final: 0.7786 (m-80) REVERT: B 324 ASN cc_start: 0.6794 (p0) cc_final: 0.6314 (m110) REVERT: B 397 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8451 (mt) REVERT: C 25 LYS cc_start: 0.7563 (mmmm) cc_final: 0.7299 (mmmm) REVERT: C 33 GLU cc_start: 0.7737 (tt0) cc_final: 0.7240 (pt0) REVERT: C 157 MET cc_start: 0.8006 (mtp) cc_final: 0.7367 (mtp) REVERT: C 161 MET cc_start: 0.6044 (OUTLIER) cc_final: 0.5774 (pmt) REVERT: C 182 TYR cc_start: 0.8151 (OUTLIER) cc_final: 0.7805 (m-80) REVERT: C 376 GLU cc_start: 0.7926 (tp30) cc_final: 0.7530 (tp30) REVERT: C 397 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.8474 (mt) REVERT: D 33 GLU cc_start: 0.7742 (tt0) cc_final: 0.7189 (pt0) REVERT: D 129 ARG cc_start: 0.7742 (ttm170) cc_final: 0.7408 (ttm170) REVERT: D 145 ILE cc_start: 0.8101 (OUTLIER) cc_final: 0.7843 (mt) REVERT: D 157 MET cc_start: 0.8167 (mtp) cc_final: 0.7388 (mtp) REVERT: D 209 MET cc_start: 0.7681 (tpt) cc_final: 0.7321 (tpt) REVERT: D 376 GLU cc_start: 0.8030 (tp30) cc_final: 0.7634 (tp30) REVERT: D 397 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8446 (mt) outliers start: 64 outliers final: 39 residues processed: 266 average time/residue: 0.2278 time to fit residues: 88.6513 Evaluate side-chains 258 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 209 time to evaluate : 1.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ASN Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 72 LYS Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 72 LYS Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 161 MET Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 182 TYR Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 361 ILE Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain C residue 7 ASN Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 72 LYS Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain C residue 161 MET Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain C residue 271 ILE Chi-restraints excluded: chain C residue 361 ILE Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain D residue 7 ASN Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 72 LYS Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 271 ILE Chi-restraints excluded: chain D residue 361 ILE Chi-restraints excluded: chain D residue 397 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 56 optimal weight: 5.9990 chunk 85 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 27 optimal weight: 0.6980 chunk 90 optimal weight: 7.9990 chunk 97 optimal weight: 1.9990 chunk 70 optimal weight: 7.9990 chunk 13 optimal weight: 6.9990 chunk 112 optimal weight: 4.9990 chunk 129 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 ASN B 173 GLN B 278 HIS C 7 ASN C 173 GLN D 7 ASN D 173 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.2483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12304 Z= 0.224 Angle : 0.526 9.996 16660 Z= 0.266 Chirality : 0.039 0.312 1984 Planarity : 0.003 0.042 2008 Dihedral : 3.927 36.635 1740 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 4.47 % Allowed : 28.56 % Favored : 66.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.46 (0.21), residues: 1472 helix: 2.43 (0.14), residues: 1228 sheet: -1.56 (0.67), residues: 40 loop : -3.03 (0.36), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 328 HIS 0.002 0.001 HIS D 189 PHE 0.012 0.001 PHE C 192 TYR 0.014 0.001 TYR C 22 ARG 0.006 0.000 ARG B 367 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 215 time to evaluate : 1.343 Fit side-chains REVERT: A 209 MET cc_start: 0.7564 (tpt) cc_final: 0.7251 (tpt) REVERT: A 324 ASN cc_start: 0.6735 (p0) cc_final: 0.6302 (m-40) REVERT: A 376 GLU cc_start: 0.8031 (tp30) cc_final: 0.7605 (tp30) REVERT: A 397 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.8445 (mp) REVERT: B 145 ILE cc_start: 0.8182 (OUTLIER) cc_final: 0.7926 (mt) REVERT: B 182 TYR cc_start: 0.8166 (OUTLIER) cc_final: 0.7851 (m-80) REVERT: B 324 ASN cc_start: 0.6782 (p0) cc_final: 0.6297 (m110) REVERT: B 397 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8464 (mt) REVERT: C 25 LYS cc_start: 0.7564 (mmmm) cc_final: 0.7288 (mmmm) REVERT: C 33 GLU cc_start: 0.7753 (tt0) cc_final: 0.7247 (pt0) REVERT: C 157 MET cc_start: 0.8022 (mtp) cc_final: 0.7374 (mtp) REVERT: C 161 MET cc_start: 0.6080 (OUTLIER) cc_final: 0.5819 (pmt) REVERT: C 171 ASN cc_start: 0.7507 (t0) cc_final: 0.7267 (t0) REVERT: C 182 TYR cc_start: 0.8168 (OUTLIER) cc_final: 0.7834 (m-80) REVERT: C 209 MET cc_start: 0.7579 (tpt) cc_final: 0.7310 (tpt) REVERT: C 376 GLU cc_start: 0.7932 (tp30) cc_final: 0.7525 (tp30) REVERT: C 397 LEU cc_start: 0.8754 (OUTLIER) cc_final: 0.8483 (mp) REVERT: D 33 GLU cc_start: 0.7770 (tt0) cc_final: 0.7212 (pt0) REVERT: D 129 ARG cc_start: 0.7740 (ttm170) cc_final: 0.7427 (ttm170) REVERT: D 145 ILE cc_start: 0.8121 (OUTLIER) cc_final: 0.7860 (mt) REVERT: D 157 MET cc_start: 0.8022 (mtp) cc_final: 0.7809 (mtp) REVERT: D 376 GLU cc_start: 0.7941 (tp30) cc_final: 0.7540 (tp30) REVERT: D 397 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.8478 (mt) outliers start: 59 outliers final: 46 residues processed: 262 average time/residue: 0.2379 time to fit residues: 89.7928 Evaluate side-chains 266 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 211 time to evaluate : 1.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ASN Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 72 LYS Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 71 MET Chi-restraints excluded: chain B residue 72 LYS Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 182 TYR Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 361 ILE Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain C residue 7 ASN Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 72 LYS Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain C residue 161 MET Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain C residue 271 ILE Chi-restraints excluded: chain C residue 283 LYS Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 361 ILE Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 72 LYS Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 271 ILE Chi-restraints excluded: chain D residue 361 ILE Chi-restraints excluded: chain D residue 397 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 136 optimal weight: 3.9990 chunk 124 optimal weight: 7.9990 chunk 132 optimal weight: 0.0970 chunk 80 optimal weight: 10.0000 chunk 57 optimal weight: 2.9990 chunk 104 optimal weight: 4.9990 chunk 40 optimal weight: 5.9990 chunk 120 optimal weight: 5.9990 chunk 125 optimal weight: 0.6980 chunk 87 optimal weight: 6.9990 chunk 140 optimal weight: 2.9990 overall best weight: 2.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 ASN A 384 GLN A 423 GLN B 173 GLN C 7 ASN C 173 GLN D 7 ASN D 173 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.2575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 12304 Z= 0.283 Angle : 0.560 10.487 16660 Z= 0.282 Chirality : 0.040 0.295 1984 Planarity : 0.003 0.046 2008 Dihedral : 4.026 36.747 1740 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 4.77 % Allowed : 28.11 % Favored : 67.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.37 (0.22), residues: 1472 helix: 2.36 (0.14), residues: 1228 sheet: -1.39 (0.69), residues: 40 loop : -3.04 (0.37), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 328 HIS 0.002 0.001 HIS D 189 PHE 0.014 0.001 PHE C 192 TYR 0.010 0.001 TYR D 214 ARG 0.006 0.000 ARG B 367 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 207 time to evaluate : 1.396 Fit side-chains REVERT: A 7 ASN cc_start: 0.7822 (OUTLIER) cc_final: 0.7501 (p0) REVERT: A 324 ASN cc_start: 0.6724 (p0) cc_final: 0.6244 (m-40) REVERT: A 376 GLU cc_start: 0.7982 (tp30) cc_final: 0.7541 (tp30) REVERT: A 397 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.8491 (mp) REVERT: B 145 ILE cc_start: 0.8219 (OUTLIER) cc_final: 0.7914 (mt) REVERT: B 161 MET cc_start: 0.6147 (OUTLIER) cc_final: 0.5859 (pmt) REVERT: B 182 TYR cc_start: 0.8272 (OUTLIER) cc_final: 0.7987 (m-80) REVERT: B 324 ASN cc_start: 0.6791 (p0) cc_final: 0.6312 (m-40) REVERT: B 376 GLU cc_start: 0.8024 (tp30) cc_final: 0.7570 (tp30) REVERT: B 397 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8483 (mp) REVERT: C 157 MET cc_start: 0.8068 (mtp) cc_final: 0.7420 (mtp) REVERT: C 161 MET cc_start: 0.6132 (OUTLIER) cc_final: 0.5851 (pmt) REVERT: C 171 ASN cc_start: 0.7624 (t0) cc_final: 0.7389 (t0) REVERT: C 182 TYR cc_start: 0.8239 (OUTLIER) cc_final: 0.7964 (m-80) REVERT: C 209 MET cc_start: 0.7599 (tpt) cc_final: 0.7241 (tpt) REVERT: C 376 GLU cc_start: 0.7931 (tp30) cc_final: 0.7516 (tp30) REVERT: C 397 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.8488 (mt) REVERT: D 145 ILE cc_start: 0.8173 (OUTLIER) cc_final: 0.7905 (mt) REVERT: D 157 MET cc_start: 0.8051 (mtp) cc_final: 0.7821 (mtp) REVERT: D 324 ASN cc_start: 0.6764 (p0) cc_final: 0.6279 (m-40) REVERT: D 376 GLU cc_start: 0.7948 (tp30) cc_final: 0.7535 (tp30) REVERT: D 397 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8472 (mp) outliers start: 63 outliers final: 45 residues processed: 257 average time/residue: 0.2224 time to fit residues: 83.1392 Evaluate side-chains 257 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 201 time to evaluate : 1.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ASN Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 72 LYS Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 283 LYS Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain B residue 71 MET Chi-restraints excluded: chain B residue 72 LYS Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 161 MET Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 182 TYR Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 283 LYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 361 ILE Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 72 LYS Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain C residue 161 MET Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain C residue 271 ILE Chi-restraints excluded: chain C residue 283 LYS Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 361 ILE Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain D residue 7 ASN Chi-restraints excluded: chain D residue 72 LYS Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 271 ILE Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 361 ILE Chi-restraints excluded: chain D residue 397 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 85 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 97 optimal weight: 1.9990 chunk 147 optimal weight: 3.9990 chunk 135 optimal weight: 1.9990 chunk 117 optimal weight: 4.9990 chunk 12 optimal weight: 7.9990 chunk 90 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 93 optimal weight: 0.8980 chunk 125 optimal weight: 0.7980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 423 GLN B 173 GLN C 7 ASN C 173 GLN D 7 ASN D 173 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.2579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.099 12304 Z= 0.264 Angle : 0.841 59.197 16660 Z= 0.477 Chirality : 0.039 0.275 1984 Planarity : 0.005 0.135 2008 Dihedral : 3.982 36.659 1738 Min Nonbonded Distance : 1.590 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 4.24 % Allowed : 29.02 % Favored : 66.74 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.39 (0.22), residues: 1472 helix: 2.38 (0.14), residues: 1228 sheet: -1.40 (0.69), residues: 40 loop : -3.07 (0.37), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 328 HIS 0.003 0.001 HIS D 189 PHE 0.014 0.001 PHE C 192 TYR 0.010 0.001 TYR B 56 ARG 0.006 0.000 ARG B 367 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 200 time to evaluate : 1.340 Fit side-chains REVERT: A 324 ASN cc_start: 0.6724 (p0) cc_final: 0.6243 (m-40) REVERT: A 376 GLU cc_start: 0.7980 (tp30) cc_final: 0.7537 (tp30) REVERT: A 397 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8487 (mp) REVERT: B 145 ILE cc_start: 0.8217 (OUTLIER) cc_final: 0.7913 (mt) REVERT: B 161 MET cc_start: 0.6147 (OUTLIER) cc_final: 0.5857 (pmt) REVERT: B 182 TYR cc_start: 0.8277 (OUTLIER) cc_final: 0.7991 (m-80) REVERT: B 324 ASN cc_start: 0.6789 (p0) cc_final: 0.6311 (m-40) REVERT: B 376 GLU cc_start: 0.8021 (tp30) cc_final: 0.7566 (tp30) REVERT: B 397 LEU cc_start: 0.8752 (OUTLIER) cc_final: 0.8479 (mp) REVERT: C 157 MET cc_start: 0.8078 (mtp) cc_final: 0.7426 (mtp) REVERT: C 161 MET cc_start: 0.6131 (OUTLIER) cc_final: 0.5851 (pmt) REVERT: C 171 ASN cc_start: 0.7621 (t0) cc_final: 0.7383 (t0) REVERT: C 182 TYR cc_start: 0.8241 (OUTLIER) cc_final: 0.7964 (m-80) REVERT: C 209 MET cc_start: 0.7591 (tpt) cc_final: 0.7222 (tpt) REVERT: C 376 GLU cc_start: 0.7930 (tp30) cc_final: 0.7512 (tp30) REVERT: C 397 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8483 (mt) REVERT: D 145 ILE cc_start: 0.8171 (OUTLIER) cc_final: 0.7903 (mt) REVERT: D 157 MET cc_start: 0.8058 (mtp) cc_final: 0.7821 (mtp) REVERT: D 324 ASN cc_start: 0.6762 (p0) cc_final: 0.6278 (m-40) REVERT: D 376 GLU cc_start: 0.7929 (tp30) cc_final: 0.7523 (tp30) REVERT: D 397 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8471 (mp) outliers start: 56 outliers final: 43 residues processed: 244 average time/residue: 0.2368 time to fit residues: 83.6882 Evaluate side-chains 253 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 200 time to evaluate : 1.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ASN Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 71 MET Chi-restraints excluded: chain B residue 72 LYS Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 161 MET Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 182 TYR Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 283 LYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 361 ILE Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 72 LYS Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain C residue 161 MET Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain C residue 271 ILE Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 361 ILE Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain D residue 7 ASN Chi-restraints excluded: chain D residue 72 LYS Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 271 ILE Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 361 ILE Chi-restraints excluded: chain D residue 397 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 35 optimal weight: 1.9990 chunk 108 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 32 optimal weight: 0.8980 chunk 117 optimal weight: 6.9990 chunk 49 optimal weight: 3.9990 chunk 120 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 21 optimal weight: 0.0570 chunk 103 optimal weight: 1.9990 chunk 6 optimal weight: 5.9990 overall best weight: 1.3904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 423 GLN B 173 GLN C 7 ASN C 173 GLN ** D 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 173 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.161727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.123629 restraints weight = 14155.918| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 2.17 r_work: 0.3180 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.2579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.203 12304 Z= 0.289 Angle : 0.698 28.122 16660 Z= 0.402 Chirality : 0.039 0.275 1984 Planarity : 0.005 0.135 2008 Dihedral : 3.982 36.659 1738 Min Nonbonded Distance : 1.590 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 4.09 % Allowed : 29.17 % Favored : 66.74 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.39 (0.22), residues: 1472 helix: 2.38 (0.14), residues: 1228 sheet: -1.40 (0.69), residues: 40 loop : -3.07 (0.37), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 328 HIS 0.003 0.001 HIS D 189 PHE 0.014 0.001 PHE C 192 TYR 0.010 0.001 TYR B 56 ARG 0.006 0.000 ARG B 367 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2517.37 seconds wall clock time: 47 minutes 18.82 seconds (2838.82 seconds total)