Starting phenix.real_space_refine on Wed Sep 17 22:47:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ze3_60022/09_2025/8ze3_60022_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ze3_60022/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/8ze3_60022/09_2025/8ze3_60022_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ze3_60022/09_2025/8ze3_60022_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ze3_60022/09_2025/8ze3_60022.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ze3_60022/09_2025/8ze3_60022.map" } resolution = 3.17 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.017 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 3.38, per 1000 atoms: 0.28 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: 1.07 Conformation dependent library (CDL) restraints added in 666.1 milliseconds Enol-peptide restraints added in 1.2 microseconds 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: 0.26 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: 2.18 Time building geometry restraints manager: 1.45 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.670 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: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.100 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.950 ------------------------------------------------------------------------------- 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= 0.193 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.008 0.000 ARG D 367 TYR 0.013 0.001 TYR D 326 PHE 0.008 0.001 PHE A 192 TRP 0.011 0.001 TRP C 328 HIS 0.003 0.001 HIS A 278 Details of bonding type rmsd covalent geometry : bond 0.00388 (12304) covalent geometry : angle 0.68328 (16660) hydrogen bonds : bond 0.10926 ( 976) hydrogen bonds : angle 5.29952 ( 2928) *********************** 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 : 0.517 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: 0.1252 time to fit residues: 51.4143 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 : 0.480 ------------------------------------------------------------------------------- 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 98 optimal weight: 1.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 ASN A 330 GLN ** A 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 7 ASN B 330 GLN C 330 GLN D 330 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.163511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.124381 restraints weight = 14279.727| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 2.17 r_work: 0.3043 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.2898 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.1504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12304 Z= 0.169 Angle : 0.537 7.321 16660 Z= 0.277 Chirality : 0.038 0.198 1984 Planarity : 0.003 0.025 2008 Dihedral : 6.979 54.497 1784 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 4.47 % Allowed : 27.95 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.87 (0.22), residues: 1472 helix: 2.00 (0.14), residues: 1228 sheet: -1.68 (0.74), residues: 40 loop : -3.03 (0.37), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 367 TYR 0.010 0.001 TYR C 182 PHE 0.016 0.001 PHE C 192 TRP 0.009 0.001 TRP B 328 HIS 0.003 0.001 HIS D 189 Details of bonding type rmsd covalent geometry : bond 0.00390 (12304) covalent geometry : angle 0.53668 (16660) hydrogen bonds : bond 0.04280 ( 976) hydrogen bonds : angle 3.80151 ( 2928) *********************** 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 286 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 227 time to evaluate : 0.484 Fit side-chains REVERT: A 145 ILE cc_start: 0.8352 (mp) cc_final: 0.8145 (mp) REVERT: A 209 MET cc_start: 0.8229 (tpp) cc_final: 0.7979 (tpt) REVERT: A 324 ASN cc_start: 0.6920 (p0) cc_final: 0.6557 (m-40) REVERT: A 330 GLN cc_start: 0.8071 (OUTLIER) cc_final: 0.6771 (mp-120) REVERT: B 93 THR cc_start: 0.8962 (m) cc_final: 0.8733 (m) REVERT: B 145 ILE cc_start: 0.8449 (mp) cc_final: 0.8010 (mp) REVERT: B 324 ASN cc_start: 0.7175 (p0) cc_final: 0.6687 (m-40) REVERT: B 330 GLN cc_start: 0.8122 (OUTLIER) cc_final: 0.6828 (mp-120) REVERT: C 145 ILE cc_start: 0.8377 (mp) cc_final: 0.8163 (mp) REVERT: C 209 MET cc_start: 0.8228 (tpp) cc_final: 0.7961 (tpt) REVERT: C 324 ASN cc_start: 0.6828 (p0) cc_final: 0.6363 (m-40) REVERT: C 330 GLN cc_start: 0.8211 (OUTLIER) cc_final: 0.6941 (mp-120) REVERT: D 116 ASP cc_start: 0.8253 (m-30) cc_final: 0.7964 (m-30) REVERT: D 129 ARG cc_start: 0.7882 (ttm170) cc_final: 0.7499 (ttm170) REVERT: D 145 ILE cc_start: 0.8422 (mp) cc_final: 0.7981 (mp) REVERT: D 324 ASN cc_start: 0.6914 (p0) cc_final: 0.6546 (m-40) REVERT: D 330 GLN cc_start: 0.8146 (OUTLIER) cc_final: 0.7054 (mp-120) outliers start: 59 outliers final: 34 residues processed: 270 average time/residue: 0.1113 time to fit residues: 43.9189 Evaluate side-chains 235 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 197 time to evaluate : 0.402 ------------------------------------------------------------------------------- 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 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 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 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 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 283 LYS Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 330 GLN 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 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 95 optimal weight: 0.8980 chunk 71 optimal weight: 0.9990 chunk 107 optimal weight: 5.9990 chunk 59 optimal weight: 10.0000 chunk 99 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 chunk 147 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 25 optimal weight: 0.6980 chunk 69 optimal weight: 6.9990 chunk 4 optimal weight: 5.9990 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 173 GLN A 278 HIS A 330 GLN B 7 ASN B 173 GLN B 278 HIS B 330 GLN B 423 GLN C 7 ASN C 173 GLN C 278 HIS C 330 GLN D 7 ASN D 173 GLN D 278 HIS D 330 GLN D 423 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.164541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.125856 restraints weight = 14369.381| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 2.18 r_work: 0.3294 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.1801 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= 0.139 Angle : 0.492 7.354 16660 Z= 0.256 Chirality : 0.037 0.214 1984 Planarity : 0.003 0.025 2008 Dihedral : 5.011 50.477 1744 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 4.62 % Allowed : 25.23 % Favored : 70.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.13 (0.22), residues: 1472 helix: 2.19 (0.14), residues: 1228 sheet: -1.93 (0.68), residues: 40 loop : -2.96 (0.37), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 367 TYR 0.012 0.001 TYR C 326 PHE 0.012 0.001 PHE A 192 TRP 0.008 0.001 TRP B 328 HIS 0.004 0.001 HIS D 189 Details of bonding type rmsd covalent geometry : bond 0.00317 (12304) covalent geometry : angle 0.49191 (16660) hydrogen bonds : bond 0.03933 ( 976) hydrogen bonds : angle 3.58882 ( 2928) *********************** 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 275 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 214 time to evaluate : 0.491 Fit side-chains REVERT: A 116 ASP cc_start: 0.8268 (m-30) cc_final: 0.7919 (m-30) REVERT: A 145 ILE cc_start: 0.8680 (OUTLIER) cc_final: 0.8189 (mp) REVERT: A 324 ASN cc_start: 0.7126 (p0) cc_final: 0.6755 (m-40) REVERT: A 330 GLN cc_start: 0.8116 (OUTLIER) cc_final: 0.6830 (mp-120) REVERT: B 93 THR cc_start: 0.9037 (m) cc_final: 0.8821 (m) REVERT: B 145 ILE cc_start: 0.8678 (OUTLIER) cc_final: 0.8330 (mt) REVERT: B 209 MET cc_start: 0.8254 (tpp) cc_final: 0.8000 (tpt) REVERT: B 324 ASN cc_start: 0.7184 (p0) cc_final: 0.6786 (m-40) REVERT: B 330 GLN cc_start: 0.8224 (OUTLIER) cc_final: 0.6970 (mp-120) REVERT: C 33 GLU cc_start: 0.7807 (tt0) cc_final: 0.7439 (pt0) REVERT: C 145 ILE cc_start: 0.8690 (OUTLIER) cc_final: 0.8208 (mp) REVERT: C 182 TYR cc_start: 0.8611 (OUTLIER) cc_final: 0.8308 (m-80) REVERT: C 324 ASN cc_start: 0.7040 (p0) cc_final: 0.6611 (m-40) REVERT: C 330 GLN cc_start: 0.8262 (OUTLIER) cc_final: 0.7077 (mp-120) REVERT: C 376 GLU cc_start: 0.7928 (tp30) cc_final: 0.7698 (tp30) REVERT: D 116 ASP cc_start: 0.8420 (m-30) cc_final: 0.8123 (m-30) REVERT: D 129 ARG cc_start: 0.8177 (ttm170) cc_final: 0.7828 (ttm170) REVERT: D 145 ILE cc_start: 0.8680 (OUTLIER) cc_final: 0.8409 (mt) REVERT: D 324 ASN cc_start: 0.6972 (p0) cc_final: 0.6632 (m-40) REVERT: D 330 GLN cc_start: 0.8154 (OUTLIER) cc_final: 0.6994 (mp-120) outliers start: 61 outliers final: 31 residues processed: 256 average time/residue: 0.1005 time to fit residues: 38.5873 Evaluate side-chains 239 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 199 time to evaluate : 0.483 ------------------------------------------------------------------------------- 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 145 ILE 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 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 102 LEU 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 102 LEU Chi-restraints excluded: chain C residue 145 ILE 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 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 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 99 optimal weight: 4.9990 chunk 59 optimal weight: 9.9990 chunk 57 optimal weight: 4.9990 chunk 130 optimal weight: 6.9990 chunk 4 optimal weight: 5.9990 chunk 124 optimal weight: 1.9990 chunk 90 optimal weight: 10.0000 chunk 103 optimal weight: 3.9990 chunk 51 optimal weight: 0.6980 chunk 113 optimal weight: 9.9990 chunk 6 optimal weight: 6.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 GLN 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 173 GLN D 330 GLN D 384 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.154807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.112669 restraints weight = 14227.753| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 2.28 r_work: 0.3122 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.2302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 12304 Z= 0.263 Angle : 0.572 8.411 16660 Z= 0.302 Chirality : 0.040 0.310 1984 Planarity : 0.003 0.024 2008 Dihedral : 5.057 58.118 1744 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 5.30 % Allowed : 24.62 % Favored : 70.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.96 (0.21), residues: 1472 helix: 2.07 (0.14), residues: 1228 sheet: -1.72 (0.70), residues: 40 loop : -3.04 (0.37), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 367 TYR 0.011 0.002 TYR C 56 PHE 0.015 0.002 PHE B 192 TRP 0.009 0.001 TRP B 328 HIS 0.004 0.001 HIS D 189 Details of bonding type rmsd covalent geometry : bond 0.00635 (12304) covalent geometry : angle 0.57191 (16660) hydrogen bonds : bond 0.04717 ( 976) hydrogen bonds : angle 3.77591 ( 2928) *********************** 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 284 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 214 time to evaluate : 0.462 Fit side-chains REVERT: A 145 ILE cc_start: 0.8668 (OUTLIER) cc_final: 0.8298 (mt) REVERT: A 182 TYR cc_start: 0.8731 (OUTLIER) cc_final: 0.8506 (m-80) REVERT: A 209 MET cc_start: 0.8412 (tpp) cc_final: 0.8173 (tpt) REVERT: A 324 ASN cc_start: 0.7057 (p0) cc_final: 0.6612 (m-40) REVERT: B 145 ILE cc_start: 0.8647 (OUTLIER) cc_final: 0.8274 (mt) REVERT: B 182 TYR cc_start: 0.8735 (OUTLIER) cc_final: 0.8400 (m-80) REVERT: B 209 MET cc_start: 0.8459 (tpp) cc_final: 0.8256 (tpt) REVERT: B 324 ASN cc_start: 0.7127 (p0) cc_final: 0.6656 (m-40) REVERT: C 145 ILE cc_start: 0.8677 (OUTLIER) cc_final: 0.8306 (mt) REVERT: C 182 TYR cc_start: 0.8765 (OUTLIER) cc_final: 0.8523 (m-80) REVERT: C 209 MET cc_start: 0.8487 (tpp) cc_final: 0.8250 (tpt) REVERT: C 324 ASN cc_start: 0.6968 (p0) cc_final: 0.6430 (m-40) REVERT: C 376 GLU cc_start: 0.8004 (tp30) cc_final: 0.7695 (tp30) REVERT: C 397 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8574 (mp) REVERT: D 129 ARG cc_start: 0.8115 (ttm170) cc_final: 0.7802 (ttm170) REVERT: D 145 ILE cc_start: 0.8594 (OUTLIER) cc_final: 0.8245 (mt) REVERT: D 182 TYR cc_start: 0.8754 (OUTLIER) cc_final: 0.8548 (m-80) REVERT: D 209 MET cc_start: 0.8483 (tpp) cc_final: 0.8256 (tpt) REVERT: D 324 ASN cc_start: 0.6969 (p0) cc_final: 0.6560 (m-40) REVERT: D 376 GLU cc_start: 0.7995 (tp30) cc_final: 0.7686 (tp30) outliers start: 70 outliers final: 43 residues processed: 269 average time/residue: 0.1006 time to fit residues: 40.4358 Evaluate side-chains 243 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 191 time to evaluate : 0.468 ------------------------------------------------------------------------------- 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 145 ILE Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 283 LYS Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 71 MET Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 91 ILE 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 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 87 VAL Chi-restraints excluded: chain C residue 91 ILE Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain C residue 271 ILE Chi-restraints excluded: chain C residue 283 LYS Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 361 ILE Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 182 TYR Chi-restraints excluded: chain D residue 271 ILE Chi-restraints excluded: chain D residue 283 LYS Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 361 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 0 optimal weight: 8.9990 chunk 91 optimal weight: 0.9990 chunk 108 optimal weight: 3.9990 chunk 102 optimal weight: 0.9980 chunk 89 optimal weight: 10.0000 chunk 56 optimal weight: 3.9990 chunk 4 optimal weight: 4.9990 chunk 10 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 chunk 123 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 overall best weight: 0.9386 ------------------------------------------------------------------------------- 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 278 HIS 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: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.160524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.118729 restraints weight = 14207.368| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 2.32 r_work: 0.3199 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.2274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12304 Z= 0.122 Angle : 0.493 8.509 16660 Z= 0.252 Chirality : 0.037 0.278 1984 Planarity : 0.003 0.026 2008 Dihedral : 4.544 56.039 1740 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 4.85 % Allowed : 25.98 % Favored : 69.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.34 (0.22), residues: 1472 helix: 2.35 (0.14), residues: 1228 sheet: -1.77 (0.68), residues: 40 loop : -3.00 (0.37), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 367 TYR 0.010 0.001 TYR D 214 PHE 0.009 0.001 PHE C 192 TRP 0.006 0.001 TRP D 328 HIS 0.003 0.001 HIS D 189 Details of bonding type rmsd covalent geometry : bond 0.00276 (12304) covalent geometry : angle 0.49329 (16660) hydrogen bonds : bond 0.03790 ( 976) hydrogen bonds : angle 3.50982 ( 2928) *********************** 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 285 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 221 time to evaluate : 0.483 Fit side-chains REVERT: A 145 ILE cc_start: 0.8568 (OUTLIER) cc_final: 0.8075 (mp) REVERT: A 324 ASN cc_start: 0.7026 (p0) cc_final: 0.6566 (m-40) REVERT: A 376 GLU cc_start: 0.7910 (tp30) cc_final: 0.7527 (tp30) REVERT: A 397 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8484 (mp) REVERT: B 25 LYS cc_start: 0.7981 (mmmm) cc_final: 0.7638 (mmtt) REVERT: B 145 ILE cc_start: 0.8568 (OUTLIER) cc_final: 0.8226 (mt) REVERT: B 182 TYR cc_start: 0.8561 (OUTLIER) cc_final: 0.8256 (m-80) REVERT: B 324 ASN cc_start: 0.6964 (p0) cc_final: 0.6508 (m-40) REVERT: B 397 LEU cc_start: 0.8668 (OUTLIER) cc_final: 0.8457 (mt) REVERT: C 145 ILE cc_start: 0.8572 (OUTLIER) cc_final: 0.8070 (mp) REVERT: C 182 TYR cc_start: 0.8575 (OUTLIER) cc_final: 0.8298 (m-80) REVERT: C 209 MET cc_start: 0.8414 (tpp) cc_final: 0.8168 (tpt) REVERT: C 376 GLU cc_start: 0.7947 (tp30) cc_final: 0.7581 (tp30) REVERT: D 145 ILE cc_start: 0.8591 (OUTLIER) cc_final: 0.8269 (mt) REVERT: D 209 MET cc_start: 0.8430 (tpp) cc_final: 0.8220 (tpt) REVERT: D 376 GLU cc_start: 0.7996 (tp30) cc_final: 0.7629 (tp30) REVERT: D 397 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8504 (mp) outliers start: 64 outliers final: 37 residues processed: 265 average time/residue: 0.1049 time to fit residues: 41.0568 Evaluate side-chains 248 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 202 time to evaluate : 0.478 ------------------------------------------------------------------------------- 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 102 LEU Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 145 ILE 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 397 LEU Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 60 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 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 102 LEU Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain C residue 145 ILE 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 72 LYS Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 271 ILE Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 361 ILE Chi-restraints excluded: chain D residue 397 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 47 optimal weight: 4.9990 chunk 85 optimal weight: 7.9990 chunk 146 optimal weight: 2.9990 chunk 126 optimal weight: 1.9990 chunk 121 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 99 optimal weight: 4.9990 chunk 98 optimal weight: 0.9990 chunk 64 optimal weight: 3.9990 chunk 102 optimal weight: 1.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 ASN B 7 ASN B 173 GLN B 278 HIS C 7 ASN C 173 GLN D 7 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.157879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.116338 restraints weight = 14163.343| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 2.28 r_work: 0.3178 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.2394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12304 Z= 0.153 Angle : 0.510 8.928 16660 Z= 0.261 Chirality : 0.037 0.212 1984 Planarity : 0.003 0.024 2008 Dihedral : 4.500 59.095 1740 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 4.92 % Allowed : 26.89 % Favored : 68.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.38 (0.21), residues: 1472 helix: 2.38 (0.14), residues: 1228 sheet: -1.66 (0.69), residues: 40 loop : -3.09 (0.36), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 367 TYR 0.010 0.001 TYR B 214 PHE 0.012 0.001 PHE C 192 TRP 0.006 0.001 TRP B 328 HIS 0.004 0.001 HIS D 189 Details of bonding type rmsd covalent geometry : bond 0.00360 (12304) covalent geometry : angle 0.50956 (16660) hydrogen bonds : bond 0.03980 ( 976) hydrogen bonds : angle 3.50591 ( 2928) *********************** 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 278 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 213 time to evaluate : 0.342 Fit side-chains REVERT: A 145 ILE cc_start: 0.8575 (OUTLIER) cc_final: 0.8075 (mp) REVERT: A 324 ASN cc_start: 0.7011 (p0) cc_final: 0.6554 (m-40) REVERT: A 376 GLU cc_start: 0.7972 (tp30) cc_final: 0.7577 (tp30) REVERT: A 397 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8494 (mp) REVERT: B 25 LYS cc_start: 0.8013 (mmmm) cc_final: 0.7682 (mmtt) REVERT: B 145 ILE cc_start: 0.8576 (OUTLIER) cc_final: 0.8228 (mt) REVERT: B 182 TYR cc_start: 0.8618 (OUTLIER) cc_final: 0.8332 (m-80) REVERT: B 324 ASN cc_start: 0.6994 (p0) cc_final: 0.6565 (m110) REVERT: B 397 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8478 (mp) REVERT: C 145 ILE cc_start: 0.8582 (OUTLIER) cc_final: 0.8289 (mt) REVERT: C 157 MET cc_start: 0.8249 (mtp) cc_final: 0.7482 (mtp) REVERT: C 161 MET cc_start: 0.6106 (OUTLIER) cc_final: 0.5775 (pmt) REVERT: C 182 TYR cc_start: 0.8617 (OUTLIER) cc_final: 0.8343 (m-80) REVERT: C 209 MET cc_start: 0.8453 (tpp) cc_final: 0.8207 (tpt) REVERT: C 376 GLU cc_start: 0.7894 (tp30) cc_final: 0.7497 (tp30) REVERT: C 397 LEU cc_start: 0.8717 (OUTLIER) cc_final: 0.8505 (mp) REVERT: D 145 ILE cc_start: 0.8580 (OUTLIER) cc_final: 0.8237 (mt) REVERT: D 157 MET cc_start: 0.8487 (mtp) cc_final: 0.8269 (mtp) REVERT: D 209 MET cc_start: 0.8471 (tpp) cc_final: 0.8237 (tpt) REVERT: D 376 GLU cc_start: 0.7937 (tp30) cc_final: 0.7547 (tp30) outliers start: 65 outliers final: 42 residues processed: 260 average time/residue: 0.1007 time to fit residues: 38.8359 Evaluate side-chains 258 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 206 time to evaluate : 0.291 ------------------------------------------------------------------------------- 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 145 ILE Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 283 LYS Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 71 MET Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 182 TYR Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 361 ILE Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain C residue 7 ASN Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 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 145 ILE 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 397 LEU Chi-restraints excluded: chain D residue 16 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 59 optimal weight: 1.9990 chunk 91 optimal weight: 4.9990 chunk 88 optimal weight: 0.6980 chunk 50 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 95 optimal weight: 0.4980 chunk 133 optimal weight: 2.9990 chunk 16 optimal weight: 8.9990 chunk 115 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 chunk 112 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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 B 173 GLN C 7 ASN C 173 GLN D 7 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.163804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.126086 restraints weight = 14340.768| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 2.17 r_work: 0.3303 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.2438 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= 0.124 Angle : 0.495 9.101 16660 Z= 0.252 Chirality : 0.036 0.214 1984 Planarity : 0.003 0.025 2008 Dihedral : 4.255 50.809 1740 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 4.85 % Allowed : 27.12 % Favored : 68.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.53 (0.22), residues: 1472 helix: 2.49 (0.14), residues: 1228 sheet: -1.57 (0.68), residues: 40 loop : -3.05 (0.36), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 367 TYR 0.010 0.001 TYR B 214 PHE 0.010 0.001 PHE C 192 TRP 0.006 0.001 TRP B 328 HIS 0.003 0.001 HIS D 189 Details of bonding type rmsd covalent geometry : bond 0.00281 (12304) covalent geometry : angle 0.49536 (16660) hydrogen bonds : bond 0.03719 ( 976) hydrogen bonds : angle 3.42408 ( 2928) *********************** 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 292 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 228 time to evaluate : 0.466 Fit side-chains REVERT: A 145 ILE cc_start: 0.8691 (OUTLIER) cc_final: 0.8183 (mp) REVERT: A 324 ASN cc_start: 0.6983 (p0) cc_final: 0.6598 (m-40) REVERT: A 376 GLU cc_start: 0.7916 (tp30) cc_final: 0.7505 (tp30) REVERT: B 25 LYS cc_start: 0.8006 (mmmm) cc_final: 0.7691 (mmtt) REVERT: B 145 ILE cc_start: 0.8699 (OUTLIER) cc_final: 0.8351 (mt) REVERT: B 157 MET cc_start: 0.8525 (mtp) cc_final: 0.7764 (mtp) REVERT: B 161 MET cc_start: 0.6233 (OUTLIER) cc_final: 0.5876 (pmt) REVERT: B 182 TYR cc_start: 0.8587 (OUTLIER) cc_final: 0.8275 (m-80) REVERT: B 324 ASN cc_start: 0.7060 (p0) cc_final: 0.6660 (m110) REVERT: C 145 ILE cc_start: 0.8672 (OUTLIER) cc_final: 0.8384 (mt) REVERT: C 157 MET cc_start: 0.8334 (mtp) cc_final: 0.7582 (mtp) REVERT: C 161 MET cc_start: 0.6191 (OUTLIER) cc_final: 0.5844 (pmt) REVERT: C 171 ASN cc_start: 0.7594 (t0) cc_final: 0.7377 (t0) REVERT: C 182 TYR cc_start: 0.8594 (OUTLIER) cc_final: 0.8314 (m-80) REVERT: C 209 MET cc_start: 0.8283 (tpp) cc_final: 0.8004 (tpt) REVERT: C 376 GLU cc_start: 0.7882 (tp30) cc_final: 0.7481 (tp30) REVERT: D 145 ILE cc_start: 0.8697 (OUTLIER) cc_final: 0.8354 (mt) REVERT: D 157 MET cc_start: 0.8597 (mtp) cc_final: 0.7741 (mtp) REVERT: D 161 MET cc_start: 0.6084 (OUTLIER) cc_final: 0.5871 (pmt) REVERT: D 209 MET cc_start: 0.8318 (tpp) cc_final: 0.8104 (tpt) REVERT: D 376 GLU cc_start: 0.7899 (tp30) cc_final: 0.7497 (tp30) outliers start: 64 outliers final: 39 residues processed: 271 average time/residue: 0.1026 time to fit residues: 41.0075 Evaluate side-chains 263 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 215 time to evaluate : 0.402 ------------------------------------------------------------------------------- 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 65 SER 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 145 ILE 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 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 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 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 145 ILE Chi-restraints excluded: chain C residue 161 MET Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain C residue 271 ILE Chi-restraints excluded: chain C residue 361 ILE Chi-restraints excluded: chain D residue 7 ASN Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 72 LYS Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 41 optimal weight: 5.9990 chunk 43 optimal weight: 9.9990 chunk 126 optimal weight: 5.9990 chunk 113 optimal weight: 6.9990 chunk 117 optimal weight: 5.9990 chunk 133 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 70 optimal weight: 0.7980 chunk 73 optimal weight: 4.9990 chunk 127 optimal weight: 7.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 ASN B 7 ASN C 7 ASN D 7 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.159339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.121094 restraints weight = 14260.506| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 2.16 r_work: 0.2970 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2820 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.2636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 12304 Z= 0.237 Angle : 0.587 9.401 16660 Z= 0.300 Chirality : 0.040 0.181 1984 Planarity : 0.003 0.030 2008 Dihedral : 4.222 41.056 1736 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 4.24 % Allowed : 28.33 % Favored : 67.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.24 (0.22), residues: 1472 helix: 2.28 (0.14), residues: 1228 sheet: -1.33 (0.72), residues: 40 loop : -3.17 (0.36), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 340 TYR 0.011 0.001 TYR B 56 PHE 0.015 0.002 PHE B 192 TRP 0.008 0.001 TRP B 328 HIS 0.003 0.001 HIS D 189 Details of bonding type rmsd covalent geometry : bond 0.00573 (12304) covalent geometry : angle 0.58689 (16660) hydrogen bonds : bond 0.04511 ( 976) hydrogen bonds : angle 3.65660 ( 2928) *********************** 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 262 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 206 time to evaluate : 0.456 Fit side-chains REVERT: A 7 ASN cc_start: 0.8107 (OUTLIER) cc_final: 0.7781 (p0) REVERT: A 145 ILE cc_start: 0.8680 (OUTLIER) cc_final: 0.8295 (mt) REVERT: A 324 ASN cc_start: 0.6817 (p0) cc_final: 0.6334 (m-40) REVERT: A 376 GLU cc_start: 0.8089 (tp30) cc_final: 0.7661 (tp30) REVERT: B 25 LYS cc_start: 0.7844 (mmmm) cc_final: 0.7500 (mmtt) REVERT: B 145 ILE cc_start: 0.8688 (OUTLIER) cc_final: 0.8293 (mt) REVERT: B 182 TYR cc_start: 0.8775 (OUTLIER) cc_final: 0.8502 (m-80) REVERT: B 324 ASN cc_start: 0.6905 (p0) cc_final: 0.6425 (m-40) REVERT: B 376 GLU cc_start: 0.8042 (tp30) cc_final: 0.7600 (tp30) REVERT: C 145 ILE cc_start: 0.8704 (OUTLIER) cc_final: 0.8320 (mt) REVERT: C 182 TYR cc_start: 0.8800 (OUTLIER) cc_final: 0.8534 (m-80) REVERT: C 209 MET cc_start: 0.8412 (tpp) cc_final: 0.8199 (tpt) REVERT: C 376 GLU cc_start: 0.7978 (tp30) cc_final: 0.7556 (tp30) REVERT: D 145 ILE cc_start: 0.8645 (OUTLIER) cc_final: 0.8275 (mt) REVERT: D 157 MET cc_start: 0.8330 (mtp) cc_final: 0.7463 (mtp) REVERT: D 161 MET cc_start: 0.5972 (OUTLIER) cc_final: 0.5770 (pmt) REVERT: D 209 MET cc_start: 0.8401 (tpp) cc_final: 0.8189 (tpt) outliers start: 56 outliers final: 39 residues processed: 247 average time/residue: 0.0985 time to fit residues: 35.5889 Evaluate side-chains 247 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 200 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ASN Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 283 LYS Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 71 MET Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 182 TYR Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 361 ILE Chi-restraints excluded: chain C residue 7 ASN 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 145 ILE 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 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 138 optimal weight: 0.7980 chunk 14 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 110 optimal weight: 3.9990 chunk 75 optimal weight: 4.9990 chunk 127 optimal weight: 6.9990 chunk 88 optimal weight: 0.9980 chunk 117 optimal weight: 2.9990 chunk 87 optimal weight: 6.9990 chunk 123 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 ASN B 7 ASN C 7 ASN C 278 HIS D 7 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.161905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.123931 restraints weight = 14312.783| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 2.18 r_work: 0.3169 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.2618 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= 0.154 Angle : 0.552 11.302 16660 Z= 0.276 Chirality : 0.039 0.342 1984 Planarity : 0.003 0.024 2008 Dihedral : 4.041 36.943 1736 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 4.77 % Allowed : 28.11 % Favored : 67.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.34 (0.22), residues: 1472 helix: 2.35 (0.14), residues: 1228 sheet: -1.35 (0.71), residues: 40 loop : -3.16 (0.36), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 367 TYR 0.017 0.001 TYR D 214 PHE 0.010 0.001 PHE C 53 TRP 0.006 0.001 TRP B 328 HIS 0.003 0.001 HIS D 189 Details of bonding type rmsd covalent geometry : bond 0.00362 (12304) covalent geometry : angle 0.55184 (16660) hydrogen bonds : bond 0.04010 ( 976) hydrogen bonds : angle 3.55243 ( 2928) *********************** 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 266 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 203 time to evaluate : 0.506 Fit side-chains REVERT: A 145 ILE cc_start: 0.8730 (OUTLIER) cc_final: 0.8337 (mt) REVERT: A 324 ASN cc_start: 0.6998 (p0) cc_final: 0.6618 (m-40) REVERT: A 376 GLU cc_start: 0.7977 (tp30) cc_final: 0.7548 (tp30) REVERT: B 145 ILE cc_start: 0.8755 (OUTLIER) cc_final: 0.8404 (mt) REVERT: B 157 MET cc_start: 0.8530 (mtp) cc_final: 0.7798 (mtp) REVERT: B 161 MET cc_start: 0.6248 (OUTLIER) cc_final: 0.5893 (pmt) REVERT: B 182 TYR cc_start: 0.8677 (OUTLIER) cc_final: 0.8402 (m-80) REVERT: B 376 GLU cc_start: 0.7954 (tp30) cc_final: 0.7514 (tp30) REVERT: C 145 ILE cc_start: 0.8749 (OUTLIER) cc_final: 0.8420 (mt) REVERT: C 157 MET cc_start: 0.8396 (mtp) cc_final: 0.7627 (mtp) REVERT: C 161 MET cc_start: 0.6211 (OUTLIER) cc_final: 0.5858 (pmt) REVERT: C 182 TYR cc_start: 0.8667 (OUTLIER) cc_final: 0.8406 (m-80) REVERT: C 209 MET cc_start: 0.8304 (tpp) cc_final: 0.8090 (tpt) REVERT: C 376 GLU cc_start: 0.7887 (tp30) cc_final: 0.7462 (tp30) REVERT: D 145 ILE cc_start: 0.8737 (OUTLIER) cc_final: 0.8381 (mt) REVERT: D 157 MET cc_start: 0.8576 (mtp) cc_final: 0.7711 (mtp) REVERT: D 161 MET cc_start: 0.6103 (OUTLIER) cc_final: 0.5871 (pmt) REVERT: D 209 MET cc_start: 0.8341 (tpp) cc_final: 0.8127 (tpt) outliers start: 63 outliers final: 43 residues processed: 247 average time/residue: 0.1055 time to fit residues: 38.1182 Evaluate side-chains 249 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 197 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 SER 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 145 ILE 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 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 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 296 VAL Chi-restraints excluded: chain B residue 361 ILE Chi-restraints excluded: chain C residue 7 ASN 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 145 ILE 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 7 ASN Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 65 SER 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 93 optimal weight: 0.9990 chunk 41 optimal weight: 7.9990 chunk 31 optimal weight: 0.8980 chunk 145 optimal weight: 3.9990 chunk 134 optimal weight: 3.9990 chunk 87 optimal weight: 6.9990 chunk 140 optimal weight: 2.9990 chunk 116 optimal weight: 0.9990 chunk 108 optimal weight: 0.5980 chunk 54 optimal weight: 3.9990 chunk 81 optimal weight: 4.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- 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 278 HIS D 7 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.162275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.124284 restraints weight = 14223.009| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 2.16 r_work: 0.3158 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3006 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.2629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.159 12304 Z= 0.218 Angle : 1.024 59.200 16660 Z= 0.607 Chirality : 0.041 0.466 1984 Planarity : 0.005 0.149 2008 Dihedral : 4.116 36.872 1736 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 4.17 % Allowed : 28.79 % Favored : 67.05 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.34 (0.22), residues: 1472 helix: 2.36 (0.14), residues: 1228 sheet: -1.36 (0.71), residues: 40 loop : -3.20 (0.36), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 367 TYR 0.013 0.001 TYR D 214 PHE 0.011 0.001 PHE B 192 TRP 0.005 0.001 TRP B 328 HIS 0.003 0.001 HIS C 278 Details of bonding type rmsd covalent geometry : bond 0.00478 (12304) covalent geometry : angle 1.02369 (16660) hydrogen bonds : bond 0.04006 ( 976) hydrogen bonds : angle 3.56856 ( 2928) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 201 time to evaluate : 0.472 Fit side-chains REVERT: A 145 ILE cc_start: 0.8718 (OUTLIER) cc_final: 0.8320 (mt) REVERT: A 324 ASN cc_start: 0.6937 (p0) cc_final: 0.6492 (m-40) REVERT: A 376 GLU cc_start: 0.8076 (tp30) cc_final: 0.7645 (tp30) REVERT: B 145 ILE cc_start: 0.8751 (OUTLIER) cc_final: 0.8390 (mt) REVERT: B 157 MET cc_start: 0.8369 (mtp) cc_final: 0.7654 (mtp) REVERT: B 161 MET cc_start: 0.6223 (OUTLIER) cc_final: 0.5892 (pmt) REVERT: B 182 TYR cc_start: 0.8733 (OUTLIER) cc_final: 0.8438 (m-80) REVERT: B 324 ASN cc_start: 0.6981 (p0) cc_final: 0.6508 (m110) REVERT: B 376 GLU cc_start: 0.8026 (tp30) cc_final: 0.7586 (tp30) REVERT: C 145 ILE cc_start: 0.8741 (OUTLIER) cc_final: 0.8412 (mt) REVERT: C 157 MET cc_start: 0.8249 (mtp) cc_final: 0.7478 (mtp) REVERT: C 161 MET cc_start: 0.6171 (OUTLIER) cc_final: 0.5850 (pmt) REVERT: C 182 TYR cc_start: 0.8715 (OUTLIER) cc_final: 0.8431 (m-80) REVERT: C 209 MET cc_start: 0.8355 (tpp) cc_final: 0.8144 (tpt) REVERT: C 376 GLU cc_start: 0.7961 (tp30) cc_final: 0.7532 (tp30) REVERT: D 145 ILE cc_start: 0.8729 (OUTLIER) cc_final: 0.8363 (mt) REVERT: D 157 MET cc_start: 0.8418 (mtp) cc_final: 0.7547 (mtp) REVERT: D 161 MET cc_start: 0.6052 (OUTLIER) cc_final: 0.5848 (pmt) REVERT: D 209 MET cc_start: 0.8411 (tpp) cc_final: 0.8196 (tpt) REVERT: D 324 ASN cc_start: 0.6854 (p0) cc_final: 0.6411 (m-40) outliers start: 55 outliers final: 43 residues processed: 240 average time/residue: 0.0942 time to fit residues: 33.7838 Evaluate side-chains 252 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 200 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 65 SER 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 145 ILE 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 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 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 296 VAL Chi-restraints excluded: chain B residue 361 ILE Chi-restraints excluded: chain C residue 7 ASN 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 145 ILE 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 7 ASN Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 65 SER 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 16 optimal weight: 10.0000 chunk 123 optimal weight: 0.9990 chunk 62 optimal weight: 3.9990 chunk 72 optimal weight: 0.9980 chunk 114 optimal weight: 5.9990 chunk 116 optimal weight: 0.0020 chunk 124 optimal weight: 1.9990 chunk 66 optimal weight: 0.5980 chunk 117 optimal weight: 6.9990 chunk 86 optimal weight: 4.9990 chunk 35 optimal weight: 0.9990 overall best weight: 0.7192 ------------------------------------------------------------------------------- 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 C 278 HIS D 7 ASN D 278 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.164095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.126342 restraints weight = 14197.239| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 2.18 r_work: 0.3140 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.2591 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= 0.119 Angle : 0.552 11.722 16660 Z= 0.270 Chirality : 0.039 0.356 1984 Planarity : 0.003 0.025 2008 Dihedral : 3.903 30.212 1736 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 4.09 % Allowed : 29.02 % Favored : 66.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.51 (0.21), residues: 1472 helix: 2.49 (0.14), residues: 1224 sheet: -1.41 (0.69), residues: 40 loop : -3.09 (0.36), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 367 TYR 0.015 0.001 TYR D 214 PHE 0.010 0.001 PHE C 53 TRP 0.006 0.001 TRP B 328 HIS 0.003 0.001 HIS D 189 Details of bonding type rmsd covalent geometry : bond 0.00265 (12304) covalent geometry : angle 0.55229 (16660) hydrogen bonds : bond 0.03760 ( 976) hydrogen bonds : angle 3.49846 ( 2928) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2643.21 seconds wall clock time: 46 minutes 29.23 seconds (2789.23 seconds total)