Starting phenix.real_space_refine on Sat Jan 18 07:52:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ze3_60022/01_2025/8ze3_60022_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ze3_60022/01_2025/8ze3_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_60022/01_2025/8ze3_60022.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ze3_60022/01_2025/8ze3_60022.map" model { file = "/net/cci-nas-00/data/ceres_data/8ze3_60022/01_2025/8ze3_60022_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ze3_60022/01_2025/8ze3_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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: 6.79, per 1000 atoms: 0.56 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: 2.81 Conformation dependent library (CDL) restraints added in 1.5 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: 0.97 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: 3.58 Time building geometry restraints manager: 3.25 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: 0.08 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' 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: 0.460 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: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 27.260 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.240 ------------------------------------------------------------------------------- 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 : 1.249 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: 0.2485 time to fit residues: 101.9568 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 : 1.372 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.167919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.129497 restraints weight = 14278.626| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 2.17 r_work: 0.3269 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 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 : 1.734 Fit side-chains REVERT: A 324 ASN cc_start: 0.7097 (p0) cc_final: 0.6777 (m-40) REVERT: A 330 GLN cc_start: 0.8179 (OUTLIER) cc_final: 0.6836 (mp-120) REVERT: B 93 THR cc_start: 0.8998 (m) cc_final: 0.8751 (m) REVERT: B 145 ILE cc_start: 0.8390 (mp) cc_final: 0.8045 (mp) REVERT: B 324 ASN cc_start: 0.7300 (p0) cc_final: 0.6825 (m-40) REVERT: B 330 GLN cc_start: 0.8273 (OUTLIER) cc_final: 0.7003 (mp-120) REVERT: B 346 GLU cc_start: 0.8432 (mm-30) cc_final: 0.8215 (tp30) REVERT: C 324 ASN cc_start: 0.7061 (p0) cc_final: 0.6658 (m-40) REVERT: C 330 GLN cc_start: 0.8329 (OUTLIER) cc_final: 0.7138 (mp-120) REVERT: D 116 ASP cc_start: 0.8320 (m-30) cc_final: 0.8072 (m-30) REVERT: D 129 ARG cc_start: 0.8277 (ttm170) cc_final: 0.7891 (ttm170) REVERT: D 145 ILE cc_start: 0.8266 (mp) cc_final: 0.7913 (mp) REVERT: D 324 ASN cc_start: 0.7083 (p0) cc_final: 0.6785 (m-40) REVERT: D 330 GLN cc_start: 0.8210 (OUTLIER) cc_final: 0.6830 (mp-120) outliers start: 61 outliers final: 34 residues processed: 281 average time/residue: 0.2324 time to fit residues: 95.5228 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 : 1.306 ------------------------------------------------------------------------------- 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 53 optimal weight: 0.9980 chunk 42 optimal weight: 5.9990 chunk 80 optimal weight: 10.0000 chunk 15 optimal weight: 6.9990 chunk 126 optimal weight: 6.9990 chunk 140 optimal weight: 0.7980 chunk 110 optimal weight: 0.6980 chunk 79 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.165496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.126648 restraints weight = 14317.369| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 2.18 r_work: 0.3055 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.1630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12304 Z= 0.214 Angle : 0.503 7.573 16660 Z= 0.260 Chirality : 0.036 0.134 1984 Planarity : 0.003 0.025 2008 Dihedral : 4.991 42.275 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 : 25.61 % Favored : 69.39 % 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: -2.02 (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 B 328 HIS 0.004 0.001 HIS D 189 PHE 0.012 0.001 PHE C 192 TYR 0.014 0.001 TYR B 326 ARG 0.005 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 : 1.438 Fit side-chains REVERT: A 324 ASN cc_start: 0.6989 (p0) cc_final: 0.6590 (m-40) REVERT: A 330 GLN cc_start: 0.7837 (OUTLIER) cc_final: 0.6600 (mp-120) REVERT: B 22 TYR cc_start: 0.8395 (m-10) cc_final: 0.8127 (m-10) REVERT: B 93 THR cc_start: 0.8926 (m) cc_final: 0.8722 (m) REVERT: B 145 ILE cc_start: 0.8419 (OUTLIER) cc_final: 0.7969 (mp) REVERT: B 209 MET cc_start: 0.8295 (tpp) cc_final: 0.8072 (tpt) REVERT: B 324 ASN cc_start: 0.7181 (p0) cc_final: 0.6635 (m-40) REVERT: B 330 GLN cc_start: 0.7886 (OUTLIER) cc_final: 0.6727 (mp-120) REVERT: C 25 LYS cc_start: 0.7621 (mmmm) cc_final: 0.7348 (mmmm) REVERT: C 33 GLU cc_start: 0.7795 (tt0) cc_final: 0.7329 (pt0) REVERT: C 324 ASN cc_start: 0.6935 (p0) cc_final: 0.6466 (m-40) REVERT: C 330 GLN cc_start: 0.7986 (OUTLIER) cc_final: 0.6816 (mp-120) REVERT: C 376 GLU cc_start: 0.8010 (tp30) cc_final: 0.7803 (tp30) REVERT: D 116 ASP cc_start: 0.8286 (m-30) cc_final: 0.7959 (m-30) REVERT: D 129 ARG cc_start: 0.8024 (ttm170) cc_final: 0.7653 (ttm170) REVERT: D 145 ILE cc_start: 0.8428 (OUTLIER) cc_final: 0.7996 (mp) REVERT: D 324 ASN cc_start: 0.6792 (p0) cc_final: 0.6444 (m-40) REVERT: D 330 GLN cc_start: 0.7849 (OUTLIER) cc_final: 0.6788 (mp-120) outliers start: 66 outliers final: 37 residues processed: 273 average time/residue: 0.2222 time to fit residues: 89.4102 Evaluate side-chains 246 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 203 time to evaluate : 1.464 ------------------------------------------------------------------------------- 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 71 MET 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 104 optimal weight: 3.9990 chunk 143 optimal weight: 6.9990 chunk 92 optimal weight: 3.9990 chunk 55 optimal weight: 5.9990 chunk 91 optimal weight: 2.9990 chunk 145 optimal weight: 0.6980 chunk 37 optimal weight: 10.0000 chunk 39 optimal weight: 7.9990 chunk 74 optimal weight: 10.0000 chunk 23 optimal weight: 2.9990 chunk 67 optimal weight: 6.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- 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 7 ASN B 173 GLN B 330 GLN C 7 ASN C 173 GLN C 330 GLN D 7 ASN D 330 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.155926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.113889 restraints weight = 14116.347| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 2.27 r_work: 0.3126 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 12304 Z= 0.369 Angle : 0.564 8.308 16660 Z= 0.295 Chirality : 0.040 0.284 1984 Planarity : 0.003 0.023 2008 Dihedral : 4.866 50.370 1744 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 5.23 % Allowed : 25.08 % Favored : 69.70 % 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: 1.97 (0.21), residues: 1472 helix: 2.09 (0.14), residues: 1228 sheet: -1.85 (0.67), residues: 40 loop : -3.07 (0.36), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 328 HIS 0.003 0.001 HIS D 189 PHE 0.016 0.002 PHE C 192 TYR 0.013 0.002 TYR D 214 ARG 0.005 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 278 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 209 time to evaluate : 1.334 Fit side-chains REVERT: A 209 MET cc_start: 0.8228 (tpp) cc_final: 0.7967 (tpt) REVERT: A 324 ASN cc_start: 0.7011 (p0) cc_final: 0.6590 (m-40) REVERT: A 330 GLN cc_start: 0.8042 (OUTLIER) cc_final: 0.6656 (mp-120) REVERT: B 145 ILE cc_start: 0.8588 (OUTLIER) cc_final: 0.8253 (mt) REVERT: B 182 TYR cc_start: 0.8708 (OUTLIER) cc_final: 0.8340 (m-80) REVERT: B 209 MET cc_start: 0.8418 (tpp) cc_final: 0.8211 (tpt) REVERT: B 324 ASN cc_start: 0.7129 (p0) cc_final: 0.6670 (m-40) REVERT: C 182 TYR cc_start: 0.8722 (OUTLIER) cc_final: 0.8465 (m-80) REVERT: C 209 MET cc_start: 0.8489 (tpp) cc_final: 0.8285 (tpt) REVERT: C 324 ASN cc_start: 0.6956 (p0) cc_final: 0.6420 (m-40) REVERT: C 376 GLU cc_start: 0.7997 (tp30) cc_final: 0.7711 (tp30) REVERT: D 129 ARG cc_start: 0.8088 (ttm170) cc_final: 0.7758 (ttm170) REVERT: D 145 ILE cc_start: 0.8600 (OUTLIER) cc_final: 0.8282 (mt) REVERT: D 209 MET cc_start: 0.8463 (tpp) cc_final: 0.8261 (tpt) REVERT: D 324 ASN cc_start: 0.6943 (p0) cc_final: 0.6517 (m-40) REVERT: D 330 GLN cc_start: 0.8035 (OUTLIER) cc_final: 0.6786 (mp-120) REVERT: D 376 GLU cc_start: 0.8017 (tp30) cc_final: 0.7737 (tp30) outliers start: 69 outliers final: 41 residues processed: 261 average time/residue: 0.2246 time to fit residues: 86.3489 Evaluate side-chains 238 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 191 time to evaluate : 1.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 369 VAL Chi-restraints excluded: chain A residue 389 ASP 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 71 MET 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 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 D residue 75 THR Chi-restraints excluded: chain D residue 86 VAL 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 330 GLN 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 58 optimal weight: 0.8980 chunk 146 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 96 optimal weight: 0.9980 chunk 73 optimal weight: 0.9980 chunk 72 optimal weight: 0.9980 chunk 125 optimal weight: 0.6980 chunk 142 optimal weight: 7.9990 chunk 65 optimal weight: 0.9980 chunk 127 optimal weight: 10.0000 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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 7 ASN B 173 GLN B 330 GLN C 7 ASN C 173 GLN C 330 GLN D 7 ASN D 330 GLN D 383 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.160756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.118758 restraints weight = 14154.406| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 2.32 r_work: 0.3185 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.2160 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= 0.179 Angle : 0.491 8.440 16660 Z= 0.252 Chirality : 0.036 0.254 1984 Planarity : 0.003 0.025 2008 Dihedral : 4.475 37.240 1742 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 4.62 % Allowed : 26.67 % Favored : 68.71 % 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: 2.28 (0.21), residues: 1472 helix: 2.31 (0.14), residues: 1228 sheet: -1.86 (0.67), residues: 40 loop : -3.02 (0.36), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 328 HIS 0.003 0.001 HIS D 189 PHE 0.009 0.001 PHE A 192 TYR 0.011 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 281 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 220 time to evaluate : 1.336 Fit side-chains REVERT: A 324 ASN cc_start: 0.6985 (p0) cc_final: 0.6496 (m-40) REVERT: A 330 GLN cc_start: 0.7997 (OUTLIER) cc_final: 0.6728 (mp-120) REVERT: A 376 GLU cc_start: 0.7985 (tp30) cc_final: 0.7626 (tp30) REVERT: A 397 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.8499 (mt) REVERT: B 145 ILE cc_start: 0.8535 (OUTLIER) cc_final: 0.8213 (mt) REVERT: B 182 TYR cc_start: 0.8560 (OUTLIER) cc_final: 0.8217 (m-80) REVERT: B 324 ASN cc_start: 0.7046 (p0) cc_final: 0.6567 (m-40) REVERT: B 397 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8462 (mt) REVERT: C 376 GLU cc_start: 0.7946 (tp30) cc_final: 0.7596 (tp30) REVERT: C 397 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.8468 (mt) REVERT: D 129 ARG cc_start: 0.8053 (ttm170) cc_final: 0.7725 (ttm170) REVERT: D 145 ILE cc_start: 0.8538 (OUTLIER) cc_final: 0.8217 (mt) REVERT: D 324 ASN cc_start: 0.6918 (p0) cc_final: 0.6464 (m-40) REVERT: D 330 GLN cc_start: 0.8076 (OUTLIER) cc_final: 0.6908 (mp-120) REVERT: D 376 GLU cc_start: 0.8058 (tp30) cc_final: 0.7724 (tp30) outliers start: 61 outliers final: 39 residues processed: 263 average time/residue: 0.2185 time to fit residues: 84.6627 Evaluate side-chains 241 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 194 time to evaluate : 1.431 ------------------------------------------------------------------------------- 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 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 330 GLN 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 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 71 MET Chi-restraints excluded: chain C residue 75 THR 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 7 ASN Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 60 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 296 VAL Chi-restraints excluded: chain D residue 330 GLN 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 54 optimal weight: 0.9980 chunk 121 optimal weight: 4.9990 chunk 49 optimal weight: 4.9990 chunk 86 optimal weight: 5.9990 chunk 93 optimal weight: 3.9990 chunk 130 optimal weight: 6.9990 chunk 28 optimal weight: 4.9990 chunk 26 optimal weight: 0.9990 chunk 142 optimal weight: 1.9990 chunk 94 optimal weight: 0.9990 chunk 78 optimal weight: 0.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- 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 7 ASN B 173 GLN C 7 ASN C 173 GLN D 7 ASN D 330 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.160478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.118368 restraints weight = 14319.901| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 2.35 r_work: 0.3194 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.2267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12304 Z= 0.197 Angle : 0.500 8.681 16660 Z= 0.257 Chirality : 0.037 0.224 1984 Planarity : 0.003 0.025 2008 Dihedral : 4.282 36.914 1742 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 4.70 % Allowed : 27.50 % Favored : 67.80 % 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: 2.38 (0.21), residues: 1472 helix: 2.38 (0.14), residues: 1228 sheet: -1.77 (0.67), residues: 40 loop : -3.04 (0.36), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 328 HIS 0.003 0.001 HIS D 189 PHE 0.011 0.001 PHE C 192 TYR 0.016 0.001 TYR D 326 ARG 0.003 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 277 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 215 time to evaluate : 1.349 Fit side-chains REVERT: A 209 MET cc_start: 0.8344 (tpp) cc_final: 0.8099 (tpt) REVERT: A 324 ASN cc_start: 0.7037 (p0) cc_final: 0.6569 (m-40) REVERT: A 376 GLU cc_start: 0.7941 (tp30) cc_final: 0.7567 (tp30) REVERT: A 397 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.8521 (mt) REVERT: B 145 ILE cc_start: 0.8546 (OUTLIER) cc_final: 0.8227 (mt) REVERT: B 182 TYR cc_start: 0.8567 (OUTLIER) cc_final: 0.8228 (m-80) REVERT: B 324 ASN cc_start: 0.7004 (p0) cc_final: 0.6557 (m110) REVERT: B 397 LEU cc_start: 0.8699 (OUTLIER) cc_final: 0.8481 (mt) REVERT: C 161 MET cc_start: 0.6111 (OUTLIER) cc_final: 0.5792 (pmt) REVERT: C 376 GLU cc_start: 0.7968 (tp30) cc_final: 0.7594 (tp30) REVERT: C 397 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.8492 (mt) REVERT: D 33 GLU cc_start: 0.7803 (tt0) cc_final: 0.7364 (pt0) REVERT: D 129 ARG cc_start: 0.8104 (ttm170) cc_final: 0.7779 (ttm170) REVERT: D 145 ILE cc_start: 0.8549 (OUTLIER) cc_final: 0.8228 (mt) REVERT: D 157 MET cc_start: 0.8473 (mtp) cc_final: 0.8233 (mtp) REVERT: D 376 GLU cc_start: 0.7982 (tp30) cc_final: 0.7613 (tp30) REVERT: D 397 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.8495 (mt) outliers start: 62 outliers final: 40 residues processed: 255 average time/residue: 0.2259 time to fit residues: 84.5144 Evaluate side-chains 253 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 205 time to evaluate : 1.273 ------------------------------------------------------------------------------- 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 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 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 7 ASN 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 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 16 LEU Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 71 MET 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 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 60 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 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 121 optimal weight: 4.9990 chunk 57 optimal weight: 4.9990 chunk 143 optimal weight: 3.9990 chunk 141 optimal weight: 3.9990 chunk 37 optimal weight: 10.0000 chunk 136 optimal weight: 4.9990 chunk 31 optimal weight: 0.5980 chunk 113 optimal weight: 9.9990 chunk 23 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 125 optimal weight: 0.7980 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 HIS A 330 GLN B 7 ASN C 173 GLN D 330 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.161021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.122681 restraints weight = 14395.617| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 2.18 r_work: 0.3157 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.2445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 12304 Z= 0.295 Angle : 0.544 9.864 16660 Z= 0.279 Chirality : 0.038 0.299 1984 Planarity : 0.003 0.024 2008 Dihedral : 4.297 36.863 1742 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 5.00 % Allowed : 27.42 % Favored : 67.58 % 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: 2.30 (0.22), residues: 1472 helix: 2.32 (0.14), residues: 1228 sheet: -1.57 (0.68), residues: 40 loop : -3.08 (0.36), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 328 HIS 0.003 0.001 HIS D 189 PHE 0.014 0.001 PHE C 192 TYR 0.010 0.001 TYR D 214 ARG 0.004 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 274 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 208 time to evaluate : 1.447 Fit side-chains REVERT: A 209 MET cc_start: 0.8311 (tpp) cc_final: 0.8107 (tpt) REVERT: A 324 ASN cc_start: 0.6928 (p0) cc_final: 0.6567 (m-40) REVERT: A 376 GLU cc_start: 0.7994 (tp30) cc_final: 0.7597 (tp30) REVERT: B 7 ASN cc_start: 0.8167 (OUTLIER) cc_final: 0.7794 (p0) REVERT: B 145 ILE cc_start: 0.8747 (OUTLIER) cc_final: 0.8365 (mt) REVERT: B 182 TYR cc_start: 0.8738 (OUTLIER) cc_final: 0.8462 (m-80) REVERT: B 324 ASN cc_start: 0.7049 (p0) cc_final: 0.6652 (m-40) REVERT: B 397 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8504 (mp) REVERT: C 157 MET cc_start: 0.8447 (mtp) cc_final: 0.7734 (mtp) REVERT: C 161 MET cc_start: 0.6205 (OUTLIER) cc_final: 0.5845 (pmt) REVERT: C 182 TYR cc_start: 0.8703 (OUTLIER) cc_final: 0.8409 (m-80) REVERT: C 376 GLU cc_start: 0.7868 (tp30) cc_final: 0.7486 (tp30) REVERT: D 33 GLU cc_start: 0.7837 (tt0) cc_final: 0.7406 (pt0) REVERT: D 145 ILE cc_start: 0.8723 (OUTLIER) cc_final: 0.8381 (mt) REVERT: D 157 MET cc_start: 0.8581 (mtp) cc_final: 0.7712 (mtp) REVERT: D 161 MET cc_start: 0.6026 (OUTLIER) cc_final: 0.5801 (pmt) REVERT: D 376 GLU cc_start: 0.7923 (tp30) cc_final: 0.7558 (tp30) outliers start: 66 outliers final: 45 residues processed: 258 average time/residue: 0.2389 time to fit residues: 89.1243 Evaluate side-chains 255 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 202 time to evaluate : 1.307 ------------------------------------------------------------------------------- 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 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 296 VAL Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain B residue 7 ASN 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 91 ILE 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 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 71 MET 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 D residue 60 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 161 MET 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 84 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 chunk 108 optimal weight: 0.0570 chunk 94 optimal weight: 5.9990 chunk 123 optimal weight: 5.9990 chunk 117 optimal weight: 6.9990 chunk 87 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 121 optimal weight: 2.9990 overall best weight: 1.6104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 423 GLN B 7 ASN C 173 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.162220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.124241 restraints weight = 14414.313| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 2.19 r_work: 0.3010 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.2861 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.2487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12304 Z= 0.234 Angle : 0.534 9.467 16660 Z= 0.268 Chirality : 0.038 0.346 1984 Planarity : 0.003 0.028 2008 Dihedral : 4.175 37.123 1742 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 4.85 % Allowed : 27.65 % 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: 2.37 (0.22), residues: 1472 helix: 2.37 (0.14), residues: 1228 sheet: -1.55 (0.67), residues: 40 loop : -3.11 (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 0.011 0.001 PHE C 192 TYR 0.010 0.001 TYR D 214 ARG 0.003 0.000 ARG C 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 268 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 204 time to evaluate : 1.307 Fit side-chains REVERT: A 324 ASN cc_start: 0.6804 (p0) cc_final: 0.6372 (m-40) REVERT: A 376 GLU cc_start: 0.8060 (tp30) cc_final: 0.7640 (tp30) REVERT: A 397 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.8573 (mp) REVERT: B 145 ILE cc_start: 0.8647 (OUTLIER) cc_final: 0.8256 (mt) REVERT: B 157 MET cc_start: 0.8187 (mtp) cc_final: 0.7412 (mtp) REVERT: B 161 MET cc_start: 0.6115 (OUTLIER) cc_final: 0.5815 (pmt) REVERT: B 182 TYR cc_start: 0.8696 (OUTLIER) cc_final: 0.8372 (m-80) REVERT: B 324 ASN cc_start: 0.6863 (p0) cc_final: 0.6390 (m-40) REVERT: B 397 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8570 (mp) REVERT: C 161 MET cc_start: 0.6113 (OUTLIER) cc_final: 0.5837 (pmt) REVERT: C 171 ASN cc_start: 0.7575 (t0) cc_final: 0.7373 (t0) REVERT: C 182 TYR cc_start: 0.8692 (OUTLIER) cc_final: 0.8329 (m-80) REVERT: C 376 GLU cc_start: 0.7942 (tp30) cc_final: 0.7545 (tp30) REVERT: D 145 ILE cc_start: 0.8607 (OUTLIER) cc_final: 0.8271 (mt) REVERT: D 157 MET cc_start: 0.8311 (mtp) cc_final: 0.7452 (mtp) REVERT: D 161 MET cc_start: 0.6033 (OUTLIER) cc_final: 0.5816 (pmt) REVERT: D 376 GLU cc_start: 0.7977 (tp30) cc_final: 0.7596 (tp30) outliers start: 64 outliers final: 41 residues processed: 253 average time/residue: 0.2369 time to fit residues: 86.9838 Evaluate side-chains 249 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 199 time to evaluate : 1.263 ------------------------------------------------------------------------------- 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 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 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 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 71 MET 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 296 VAL Chi-restraints excluded: chain C residue 361 ILE Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 60 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 161 MET Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 271 ILE Chi-restraints excluded: chain D residue 361 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 72 optimal weight: 0.4980 chunk 38 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 30 optimal weight: 9.9990 chunk 74 optimal weight: 10.0000 chunk 102 optimal weight: 1.9990 chunk 42 optimal weight: 0.0370 chunk 39 optimal weight: 0.9990 chunk 122 optimal weight: 0.9980 overall best weight: 0.9062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 423 GLN B 7 ASN C 173 GLN D 7 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.166693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.128992 restraints weight = 14323.959| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 2.18 r_work: 0.3063 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2915 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.2506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12304 Z= 0.176 Angle : 0.523 9.586 16660 Z= 0.260 Chirality : 0.038 0.328 1984 Planarity : 0.003 0.026 2008 Dihedral : 3.944 37.109 1741 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 4.24 % Allowed : 28.56 % Favored : 67.20 % 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: 2.52 (0.22), residues: 1472 helix: 2.48 (0.14), residues: 1228 sheet: -1.44 (0.66), residues: 40 loop : -3.12 (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 0.010 0.001 PHE D 192 TYR 0.009 0.001 TYR B 214 ARG 0.003 0.000 ARG C 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 278 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 222 time to evaluate : 1.314 Fit side-chains REVERT: A 324 ASN cc_start: 0.6815 (p0) cc_final: 0.6334 (m110) REVERT: A 376 GLU cc_start: 0.8050 (tp30) cc_final: 0.7632 (tp30) REVERT: A 397 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.8525 (mp) REVERT: B 145 ILE cc_start: 0.8540 (OUTLIER) cc_final: 0.8228 (mt) REVERT: B 157 MET cc_start: 0.8183 (mtp) cc_final: 0.7386 (mtp) REVERT: B 161 MET cc_start: 0.6114 (OUTLIER) cc_final: 0.5818 (pmt) REVERT: B 182 TYR cc_start: 0.8541 (OUTLIER) cc_final: 0.8168 (m-80) REVERT: B 324 ASN cc_start: 0.6815 (p0) cc_final: 0.6327 (m110) REVERT: B 376 GLU cc_start: 0.8016 (tp30) cc_final: 0.7602 (tp30) REVERT: B 397 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8547 (mt) REVERT: C 157 MET cc_start: 0.8165 (mtp) cc_final: 0.7427 (mtp) REVERT: C 161 MET cc_start: 0.6166 (OUTLIER) cc_final: 0.5883 (pmt) REVERT: C 376 GLU cc_start: 0.7929 (tp30) cc_final: 0.7523 (tp30) REVERT: D 145 ILE cc_start: 0.8473 (OUTLIER) cc_final: 0.8143 (mt) REVERT: D 157 MET cc_start: 0.8286 (mtp) cc_final: 0.7429 (mtp) REVERT: D 376 GLU cc_start: 0.7947 (tp30) cc_final: 0.7554 (tp30) outliers start: 56 outliers final: 39 residues processed: 259 average time/residue: 0.2207 time to fit residues: 84.2613 Evaluate side-chains 257 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 211 time to evaluate : 1.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU 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 397 LEU Chi-restraints excluded: chain B residue 7 ASN 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 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 16 LEU Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 71 MET 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 271 ILE Chi-restraints excluded: chain C residue 361 ILE Chi-restraints excluded: chain D residue 7 ASN Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 60 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 296 VAL Chi-restraints excluded: chain D residue 361 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 115 optimal weight: 7.9990 chunk 72 optimal weight: 3.9990 chunk 141 optimal weight: 3.9990 chunk 118 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 80 optimal weight: 0.0980 chunk 102 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 121 optimal weight: 4.9990 chunk 53 optimal weight: 9.9990 chunk 116 optimal weight: 0.9980 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 ASN A 423 GLN B 7 ASN C 7 ASN D 7 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.164492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.126796 restraints weight = 14356.128| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 2.18 r_work: 0.3120 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2971 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.2538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.189 12304 Z= 0.323 Angle : 0.976 59.200 16660 Z= 0.577 Chirality : 0.040 0.333 1984 Planarity : 0.003 0.057 2008 Dihedral : 3.849 37.075 1738 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 3.94 % Allowed : 29.24 % Favored : 66.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.49 (0.22), residues: 1472 helix: 2.47 (0.14), residues: 1228 sheet: -1.43 (0.66), residues: 40 loop : -3.20 (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 0.010 0.001 PHE D 192 TYR 0.008 0.001 TYR B 214 ARG 0.004 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 260 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 208 time to evaluate : 1.384 Fit side-chains REVERT: A 324 ASN cc_start: 0.6805 (p0) cc_final: 0.6344 (m110) REVERT: A 376 GLU cc_start: 0.8059 (tp30) cc_final: 0.7637 (tp30) REVERT: A 397 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8551 (mp) REVERT: B 145 ILE cc_start: 0.8551 (OUTLIER) cc_final: 0.8243 (mt) REVERT: B 157 MET cc_start: 0.8176 (mtp) cc_final: 0.7383 (mtp) REVERT: B 161 MET cc_start: 0.6113 (OUTLIER) cc_final: 0.5816 (pmt) REVERT: B 182 TYR cc_start: 0.8557 (OUTLIER) cc_final: 0.8185 (m-80) REVERT: B 324 ASN cc_start: 0.6841 (p0) cc_final: 0.6354 (m110) REVERT: B 376 GLU cc_start: 0.8021 (tp30) cc_final: 0.7603 (tp30) REVERT: B 397 LEU cc_start: 0.8769 (OUTLIER) cc_final: 0.8558 (mt) REVERT: C 157 MET cc_start: 0.8169 (mtp) cc_final: 0.7482 (mtp) REVERT: C 161 MET cc_start: 0.6155 (OUTLIER) cc_final: 0.5879 (pmt) REVERT: C 376 GLU cc_start: 0.7936 (tp30) cc_final: 0.7526 (tp30) REVERT: D 145 ILE cc_start: 0.8487 (OUTLIER) cc_final: 0.8157 (mt) REVERT: D 157 MET cc_start: 0.7820 (mtp) cc_final: 0.7597 (mtp) REVERT: D 376 GLU cc_start: 0.7948 (tp30) cc_final: 0.7559 (tp30) outliers start: 52 outliers final: 41 residues processed: 244 average time/residue: 0.2321 time to fit residues: 82.1626 Evaluate side-chains 256 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 208 time to evaluate : 1.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU 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 397 LEU Chi-restraints excluded: chain B residue 7 ASN 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 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 71 MET 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 271 ILE Chi-restraints excluded: chain C residue 361 ILE Chi-restraints excluded: chain D residue 7 ASN Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 60 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 283 LYS Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 361 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 25 optimal weight: 4.9990 chunk 111 optimal weight: 9.9990 chunk 147 optimal weight: 3.9990 chunk 123 optimal weight: 3.9990 chunk 105 optimal weight: 1.9990 chunk 134 optimal weight: 0.7980 chunk 41 optimal weight: 7.9990 chunk 58 optimal weight: 3.9990 chunk 125 optimal weight: 0.9990 chunk 84 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 ASN A 423 GLN ** B 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 7 ASN ** D 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.164483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.127000 restraints weight = 14325.686| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 2.16 r_work: 0.3051 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2905 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.2540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.189 12304 Z= 0.312 Angle : 0.861 58.623 16660 Z= 0.520 Chirality : 0.040 0.333 1984 Planarity : 0.004 0.108 2008 Dihedral : 3.849 37.075 1738 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 3.79 % Allowed : 29.39 % Favored : 66.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.49 (0.22), residues: 1472 helix: 2.47 (0.14), residues: 1228 sheet: -1.43 (0.66), residues: 40 loop : -3.20 (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 0.010 0.001 PHE D 192 TYR 0.008 0.001 TYR B 214 ARG 0.004 0.000 ARG B 367 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4866.10 seconds wall clock time: 87 minutes 48.82 seconds (5268.82 seconds total)