Starting phenix.real_space_refine on Sat Aug 8 15:07:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9sru_55156/08_2026/9sru_55156.cif Found real_map, /net/cci-nas-00/data/ceres_data/9sru_55156/08_2026/9sru_55156.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9sru_55156/08_2026/9sru_55156.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9sru_55156/08_2026/9sru_55156.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9sru_55156/08_2026/9sru_55156.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9sru_55156/08_2026/9sru_55156.map" } resolution = 2.47 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.021 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: 7 Type Number sf(0) Gaussians Zn 4 6.06 5 P 108 5.49 5 S 52 5.16 5 C 8806 2.51 5 N 2556 2.21 5 O 2940 1.98 5 H 13734 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 28200 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 6187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 6187 Classifications: {'peptide': 399} Link IDs: {'PTRANS': 14, 'TRANS': 384} Chain: "B" Number of atoms: 6187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 6187 Classifications: {'peptide': 399} Link IDs: {'PTRANS': 14, 'TRANS': 384} Chain: "C" Number of atoms: 6187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 6187 Classifications: {'peptide': 399} Link IDs: {'PTRANS': 14, 'TRANS': 384} Chain: "D" Number of atoms: 6187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 6187 Classifications: {'peptide': 399} Link IDs: {'PTRANS': 14, 'TRANS': 384} Chain: "E" Number of atoms: 861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 861 Classifications: {'DNA': 27} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 26} Chain: "F" Number of atoms: 863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 863 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain: "G" Number of atoms: 863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 863 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain: "H" Number of atoms: 861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 861 Classifications: {'DNA': 27} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 26} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 3943 SG CYS A 257 98.607 88.327 22.375 1.00 25.66 S ATOM 3974 SG CYS A 259 102.000 87.001 21.344 1.00 18.39 S ATOM 4029 SG CYS A 264 100.145 85.339 24.246 1.00 13.35 S ATOM 10130 SG CYS B 257 111.276 69.401 45.429 1.00 31.94 S ATOM 10161 SG CYS B 259 109.293 72.093 47.264 1.00 31.74 S ATOM 10216 SG CYS B 264 108.665 71.452 43.545 1.00 10.14 S ATOM 16317 SG CYS C 257 77.748 54.437 22.557 1.00 31.94 S ATOM 16348 SG CYS C 259 74.327 55.510 21.256 1.00 31.74 S ATOM 16403 SG CYS C 264 75.964 57.422 24.136 1.00 10.14 S ATOM 22504 SG CYS D 257 64.976 73.226 45.665 1.00 25.66 S ATOM 22535 SG CYS D 259 67.109 70.479 47.161 1.00 18.39 S ATOM 22590 SG CYS D 264 67.457 71.305 43.442 1.00 13.35 S Time building chain proxies: 4.74, per 1000 atoms: 0.17 Number of scatterers: 28200 At special positions: 0 Unit cell: (179.082, 145.328, 95.6352, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 4 29.99 S 52 16.00 P 108 15.00 O 2940 8.00 N 2556 7.00 C 8806 6.00 H 13734 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.55 Conformation dependent library (CDL) restraints added in 763.9 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 501 " pdb="ZN ZN A 501 " - pdb=" ND1 HIS A 247 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 259 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 257 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 264 " pdb=" ZN B 501 " pdb="ZN ZN B 501 " - pdb=" ND1 HIS B 247 " pdb="ZN ZN B 501 " - pdb=" SG CYS B 259 " pdb="ZN ZN B 501 " - pdb=" SG CYS B 264 " pdb="ZN ZN B 501 " - pdb=" SG CYS B 257 " pdb=" ZN C 501 " pdb="ZN ZN C 501 " - pdb=" ND1 HIS C 247 " pdb="ZN ZN C 501 " - pdb=" SG CYS C 259 " pdb="ZN ZN C 501 " - pdb=" SG CYS C 264 " pdb="ZN ZN C 501 " - pdb=" SG CYS C 257 " pdb=" ZN D 501 " pdb="ZN ZN D 501 " - pdb=" ND1 HIS D 247 " pdb="ZN ZN D 501 " - pdb=" SG CYS D 257 " pdb="ZN ZN D 501 " - pdb=" SG CYS D 259 " pdb="ZN ZN D 501 " - pdb=" SG CYS D 264 " Number of angles added : 12 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2952 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 16 sheets defined 49.0% alpha, 14.8% beta 40 base pairs and 92 stacking pairs defined. Time for finding SS restraints: 4.33 Creating SS restraints... Processing helix chain 'A' and resid 9 through 28 removed outlier: 3.593A pdb=" N ILE A 13 " --> pdb=" O HIS A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 41 Processing helix chain 'A' and resid 43 through 57 Processing helix chain 'A' and resid 123 through 139 Processing helix chain 'A' and resid 179 through 187 Processing helix chain 'A' and resid 194 through 207 Processing helix chain 'A' and resid 244 through 248 Processing helix chain 'A' and resid 265 through 270 Processing helix chain 'A' and resid 270 through 283 Processing helix chain 'A' and resid 296 through 306 Processing helix chain 'A' and resid 308 through 334 removed outlier: 3.516A pdb=" N ASP A 313 " --> pdb=" O LEU A 309 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ILE A 325 " --> pdb=" O HIS A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 346 Processing helix chain 'A' and resid 347 through 363 Proline residue: A 353 - end of helix Processing helix chain 'A' and resid 364 through 369 Processing helix chain 'A' and resid 385 through 396 removed outlier: 3.624A pdb=" N LEU A 389 " --> pdb=" O ALA A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 404 Processing helix chain 'B' and resid 9 through 28 removed outlier: 3.798A pdb=" N ILE B 13 " --> pdb=" O HIS B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 32 through 41 Processing helix chain 'B' and resid 43 through 57 Processing helix chain 'B' and resid 123 through 139 Processing helix chain 'B' and resid 180 through 187 Processing helix chain 'B' and resid 195 through 207 Processing helix chain 'B' and resid 244 through 248 Processing helix chain 'B' and resid 265 through 270 removed outlier: 3.522A pdb=" N SER B 270 " --> pdb=" O GLU B 266 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 283 Processing helix chain 'B' and resid 296 through 307 Processing helix chain 'B' and resid 308 through 334 removed outlier: 3.731A pdb=" N ILE B 325 " --> pdb=" O HIS B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 346 Processing helix chain 'B' and resid 347 through 363 Proline residue: B 353 - end of helix Processing helix chain 'B' and resid 364 through 369 Processing helix chain 'B' and resid 385 through 396 removed outlier: 3.842A pdb=" N LEU B 389 " --> pdb=" O ALA B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 397 through 404 removed outlier: 3.534A pdb=" N ARG B 402 " --> pdb=" O SER B 398 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 28 removed outlier: 3.799A pdb=" N ILE C 13 " --> pdb=" O HIS C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 32 through 41 Processing helix chain 'C' and resid 43 through 57 Processing helix chain 'C' and resid 123 through 139 Processing helix chain 'C' and resid 180 through 187 Processing helix chain 'C' and resid 195 through 207 Processing helix chain 'C' and resid 244 through 248 Processing helix chain 'C' and resid 265 through 270 removed outlier: 3.522A pdb=" N SER C 270 " --> pdb=" O GLU C 266 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 283 Processing helix chain 'C' and resid 296 through 307 Processing helix chain 'C' and resid 308 through 334 removed outlier: 3.860A pdb=" N ILE C 325 " --> pdb=" O HIS C 321 " (cutoff:3.500A) Processing helix chain 'C' and resid 342 through 346 Processing helix chain 'C' and resid 347 through 363 Proline residue: C 353 - end of helix Processing helix chain 'C' and resid 364 through 369 Processing helix chain 'C' and resid 385 through 396 removed outlier: 3.841A pdb=" N LEU C 389 " --> pdb=" O ALA C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 397 through 404 removed outlier: 3.533A pdb=" N ARG C 402 " --> pdb=" O SER C 398 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 28 removed outlier: 3.593A pdb=" N ILE D 13 " --> pdb=" O HIS D 9 " (cutoff:3.500A) Processing helix chain 'D' and resid 32 through 41 Processing helix chain 'D' and resid 43 through 57 Processing helix chain 'D' and resid 123 through 139 Processing helix chain 'D' and resid 179 through 187 Processing helix chain 'D' and resid 194 through 207 Processing helix chain 'D' and resid 244 through 248 Processing helix chain 'D' and resid 265 through 270 Processing helix chain 'D' and resid 270 through 283 removed outlier: 4.020A pdb=" N ASN D 283 " --> pdb=" O GLN D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 296 through 306 Processing helix chain 'D' and resid 308 through 334 removed outlier: 3.686A pdb=" N ILE D 325 " --> pdb=" O HIS D 321 " (cutoff:3.500A) Processing helix chain 'D' and resid 342 through 346 Processing helix chain 'D' and resid 347 through 363 Proline residue: D 353 - end of helix Processing helix chain 'D' and resid 364 through 369 Processing helix chain 'D' and resid 385 through 396 removed outlier: 3.624A pdb=" N LEU D 389 " --> pdb=" O ALA D 385 " (cutoff:3.500A) Processing helix chain 'D' and resid 397 through 404 Processing sheet with id=AA1, first strand: chain 'A' and resid 60 through 62 Processing sheet with id=AA2, first strand: chain 'A' and resid 108 through 115 removed outlier: 6.380A pdb=" N LEU A 108 " --> pdb=" O ASP A 103 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N ASP A 103 " --> pdb=" O LEU A 108 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N HIS A 86 " --> pdb=" O LEU A 146 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N SER A 148 " --> pdb=" O HIS A 86 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 156 through 158 removed outlier: 6.782A pdb=" N ILE A 156 " --> pdb=" O HIS A 165 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 233 through 234 removed outlier: 6.065A pdb=" N ILE A 338 " --> pdb=" O GLU A 374 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 60 through 62 Processing sheet with id=AA6, first strand: chain 'B' and resid 108 through 115 removed outlier: 6.466A pdb=" N LEU B 101 " --> pdb=" O VAL B 109 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N GLU B 111 " --> pdb=" O LEU B 99 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N LEU B 99 " --> pdb=" O GLU B 111 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N SER B 113 " --> pdb=" O ILE B 97 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ILE B 97 " --> pdb=" O SER B 113 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N HIS B 86 " --> pdb=" O LEU B 146 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N SER B 148 " --> pdb=" O HIS B 86 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE B 92 " --> pdb=" O THR B 152 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 156 through 158 removed outlier: 6.712A pdb=" N ILE B 156 " --> pdb=" O HIS B 165 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 233 through 234 removed outlier: 5.929A pdb=" N ILE B 338 " --> pdb=" O GLU B 374 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 60 through 62 Processing sheet with id=AB1, first strand: chain 'C' and resid 108 through 115 removed outlier: 6.466A pdb=" N LEU C 101 " --> pdb=" O VAL C 109 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N GLU C 111 " --> pdb=" O LEU C 99 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N LEU C 99 " --> pdb=" O GLU C 111 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N SER C 113 " --> pdb=" O ILE C 97 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ILE C 97 " --> pdb=" O SER C 113 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N HIS C 86 " --> pdb=" O LEU C 146 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N SER C 148 " --> pdb=" O HIS C 86 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE C 92 " --> pdb=" O THR C 152 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 156 through 158 removed outlier: 6.712A pdb=" N ILE C 156 " --> pdb=" O HIS C 165 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 233 through 234 removed outlier: 5.930A pdb=" N ILE C 338 " --> pdb=" O GLU C 374 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 60 through 62 Processing sheet with id=AB5, first strand: chain 'D' and resid 108 through 115 removed outlier: 6.379A pdb=" N LEU D 108 " --> pdb=" O ASP D 103 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N ASP D 103 " --> pdb=" O LEU D 108 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N HIS D 86 " --> pdb=" O LEU D 146 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N SER D 148 " --> pdb=" O HIS D 86 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 156 through 158 removed outlier: 6.781A pdb=" N ILE D 156 " --> pdb=" O HIS D 165 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 233 through 234 removed outlier: 6.064A pdb=" N ILE D 338 " --> pdb=" O GLU D 374 " (cutoff:3.500A) 654 hydrogen bonds defined for protein. 1866 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 88 hydrogen bonds 176 hydrogen bond angles 0 basepair planarities 40 basepair parallelities 92 stacking parallelities Total time for adding SS restraints: 6.47 Time building geometry restraints manager: 3.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 13730 1.02 - 1.22: 66 1.22 - 1.42: 5923 1.42 - 1.61: 8854 1.61 - 1.81: 89 Bond restraints: 28662 Sorted by residual: bond pdb=" SG CYS A 301 " pdb=" HG CYS A 301 " ideal model delta sigma weight residual 1.200 1.341 -0.141 2.00e-02 2.50e+03 4.99e+01 bond pdb=" ND2 ASN A 283 " pdb="HD21 ASN A 283 " ideal model delta sigma weight residual 0.860 0.981 -0.121 2.00e-02 2.50e+03 3.64e+01 bond pdb=" ND2 ASN A 283 " pdb="HD22 ASN A 283 " ideal model delta sigma weight residual 0.860 0.978 -0.118 2.00e-02 2.50e+03 3.45e+01 bond pdb=" NE ARG A 256 " pdb=" HE ARG A 256 " ideal model delta sigma weight residual 0.860 0.970 -0.110 2.00e-02 2.50e+03 3.01e+01 bond pdb=" NE ARG A 281 " pdb=" HE ARG A 281 " ideal model delta sigma weight residual 0.860 0.970 -0.110 2.00e-02 2.50e+03 3.00e+01 ... (remaining 28657 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.27: 47755 2.27 - 4.54: 3909 4.54 - 6.81: 388 6.81 - 9.08: 6 9.08 - 11.36: 2 Bond angle restraints: 52060 Sorted by residual: angle pdb=" CA LYS A 312 " pdb=" C LYS A 312 " pdb=" O LYS A 312 " ideal model delta sigma weight residual 120.82 113.50 7.32 1.05e+00 9.07e-01 4.86e+01 angle pdb=" N LEU A 282 " pdb=" CA LEU A 282 " pdb=" C LEU A 282 " ideal model delta sigma weight residual 112.54 104.80 7.74 1.22e+00 6.72e-01 4.03e+01 angle pdb=" N MET A 286 " pdb=" CA MET A 286 " pdb=" C MET A 286 " ideal model delta sigma weight residual 112.41 104.74 7.67 1.30e+00 5.92e-01 3.48e+01 angle pdb=" N VAL A 250 " pdb=" CA VAL A 250 " pdb=" C VAL A 250 " ideal model delta sigma weight residual 113.43 107.25 6.18 1.09e+00 8.42e-01 3.22e+01 angle pdb=" O LYS A 312 " pdb=" C LYS A 312 " pdb=" N ASP A 313 " ideal model delta sigma weight residual 122.07 127.41 -5.34 1.03e+00 9.43e-01 2.69e+01 ... (remaining 52055 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.40: 11823 32.40 - 64.80: 1149 64.80 - 97.20: 48 97.20 - 129.60: 0 129.60 - 162.00: 6 Dihedral angle restraints: 13026 sinusoidal: 7922 harmonic: 5104 Sorted by residual: dihedral pdb=" C4' DA G 3 " pdb=" C3' DA G 3 " pdb=" O3' DA G 3 " pdb=" P DA G 4 " ideal model delta sinusoidal sigma weight residual 220.00 58.00 162.00 1 3.50e+01 8.16e-04 1.53e+01 dihedral pdb=" C4' DA F 3 " pdb=" C3' DA F 3 " pdb=" O3' DA F 3 " pdb=" P DA F 4 " ideal model delta sinusoidal sigma weight residual 220.00 58.03 161.97 1 3.50e+01 8.16e-04 1.53e+01 dihedral pdb=" C4' DT H 24 " pdb=" C3' DT H 24 " pdb=" O3' DT H 24 " pdb=" P DA H 25 " ideal model delta sinusoidal sigma weight residual 220.00 75.82 144.18 1 3.50e+01 8.16e-04 1.42e+01 ... (remaining 13023 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.119: 2306 0.119 - 0.237: 121 0.237 - 0.356: 1 0.356 - 0.474: 0 0.474 - 0.593: 4 Chirality restraints: 2432 Sorted by residual: chirality pdb=" P DC H 29 " pdb=" OP1 DC H 29 " pdb=" OP2 DC H 29 " pdb=" O5' DC H 29 " both_signs ideal model delta sigma weight residual True 2.34 -2.93 -0.59 2.00e-01 2.50e+01 8.79e+00 chirality pdb=" P DC E 29 " pdb=" OP1 DC E 29 " pdb=" OP2 DC E 29 " pdb=" O5' DC E 29 " both_signs ideal model delta sigma weight residual True 2.34 -2.91 -0.58 2.00e-01 2.50e+01 8.31e+00 chirality pdb=" P DT H 28 " pdb=" OP1 DT H 28 " pdb=" OP2 DT H 28 " pdb=" O5' DT H 28 " both_signs ideal model delta sigma weight residual True 2.34 -2.84 -0.50 2.00e-01 2.50e+01 6.29e+00 ... (remaining 2429 not shown) Planarity restraints: 3884 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 283 " 0.155 2.00e-02 2.50e+03 4.82e-01 3.48e+03 pdb=" CG ASN A 283 " -0.013 2.00e-02 2.50e+03 pdb=" OD1 ASN A 283 " -0.154 2.00e-02 2.50e+03 pdb=" ND2 ASN A 283 " -0.002 2.00e-02 2.50e+03 pdb="HD21 ASN A 283 " 0.827 2.00e-02 2.50e+03 pdb="HD22 ASN A 283 " -0.813 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN B 249 " 0.244 2.00e-02 2.50e+03 3.21e-01 1.54e+03 pdb=" CD GLN B 249 " -0.017 2.00e-02 2.50e+03 pdb=" OE1 GLN B 249 " -0.238 2.00e-02 2.50e+03 pdb=" NE2 GLN B 249 " -0.002 2.00e-02 2.50e+03 pdb="HE21 GLN B 249 " -0.494 2.00e-02 2.50e+03 pdb="HE22 GLN B 249 " 0.507 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN D 284 " 0.224 2.00e-02 2.50e+03 2.60e-01 1.01e+03 pdb=" CD GLN D 284 " -0.015 2.00e-02 2.50e+03 pdb=" OE1 GLN D 284 " -0.214 2.00e-02 2.50e+03 pdb=" NE2 GLN D 284 " -0.007 2.00e-02 2.50e+03 pdb="HE21 GLN D 284 " 0.399 2.00e-02 2.50e+03 pdb="HE22 GLN D 284 " -0.387 2.00e-02 2.50e+03 ... (remaining 3881 not shown) Histogram of nonbonded interaction distances: 1.43 - 2.06: 419 2.06 - 2.70: 43074 2.70 - 3.33: 80249 3.33 - 3.97: 108506 3.97 - 4.60: 166551 Nonbonded interactions: 398799 Sorted by model distance: nonbonded pdb=" O SER A 105 " pdb=" HG SER A 106 " model vdw 1.431 2.450 nonbonded pdb=" O SER D 105 " pdb=" HG SER D 106 " model vdw 1.431 2.450 nonbonded pdb=" HG SER A 46 " pdb=" OP2 DT F 18 " model vdw 1.497 2.450 nonbonded pdb=" HG SER D 46 " pdb=" OP2 DT G 18 " model vdw 1.497 2.450 nonbonded pdb=" HZ3 LYS C 337 " pdb=" OE2 GLU C 374 " model vdw 1.513 2.450 ... (remaining 398794 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'H' } ncs_group { reference = chain 'F' selection = chain 'G' } 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=0.00 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.210 Extract box with map and model: 0.560 Check model and map are aligned: 0.070 Set scattering table: 0.040 Process input model: 35.560 Find NCS groups from input model: 0.370 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: 0.010 Load rotamer database and sin/cos tables:6.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 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 : 0.006 0.067 14944 Z= 0.416 Angle : 0.734 8.994 20702 Z= 0.545 Chirality : 0.055 0.593 2432 Planarity : 0.005 0.054 2284 Dihedral : 22.262 162.001 5864 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 0.30 % Allowed : 22.01 % Favored : 77.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.22), residues: 1588 helix: 0.54 (0.21), residues: 676 sheet: 0.28 (0.30), residues: 272 loop : -0.82 (0.27), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 256 TYR 0.018 0.001 TYR B 253 PHE 0.007 0.001 PHE A 169 TRP 0.002 0.001 TRP C 85 HIS 0.014 0.001 HIS B 321 Details of bonding type rmsd/Z covalent geometry : bond 0.00555 / 0.42 (14928) covalent geometry : angle 0.73320 / 0.55 (20690) hydrogen bonds : bond 0.14992 / 10.17 ( 742) hydrogen bonds : angle 6.83287 / 5.10 ( 2042) metal coordination : bond 0.01788 / 1.18 ( 16) metal coordination : angle 1.54116 / 0.81 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 439 time to evaluate : 0.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 ARG cc_start: 0.7852 (ttp80) cc_final: 0.7510 (ttp-170) REVERT: A 52 ARG cc_start: 0.7408 (ttm-80) cc_final: 0.7181 (ttm-80) REVERT: A 293 GLN cc_start: 0.7080 (tt0) cc_final: 0.6571 (tt0) REVERT: C 87 TYR cc_start: 0.8443 (p90) cc_final: 0.8030 (p90) REVERT: C 289 MET cc_start: 0.7448 (mtt) cc_final: 0.7248 (mtt) REVERT: C 357 ASP cc_start: 0.8611 (m-30) cc_final: 0.8334 (m-30) outliers start: 4 outliers final: 1 residues processed: 440 average time/residue: 1.4721 time to fit residues: 703.2763 Evaluate side-chains 365 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 364 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 137 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 1.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 27 GLN A 283 ASN A 361 GLN B 41 GLN B 223 ASN B 284 GLN B 291 HIS B 370 HIS C 161 ASN C 361 GLN C 370 HIS D 114 GLN D 361 GLN D 369 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.115792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.100453 restraints weight = 56618.995| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 1.35 r_work: 0.3347 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3229 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.2273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 14944 Z= 0.270 Angle : 0.686 6.086 20702 Z= 0.382 Chirality : 0.047 0.220 2432 Planarity : 0.006 0.075 2284 Dihedral : 22.400 159.731 2954 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 2.17 % Allowed : 22.16 % Favored : 75.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.21), residues: 1588 helix: 1.16 (0.20), residues: 656 sheet: 0.27 (0.30), residues: 276 loop : -1.07 (0.25), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 94 TYR 0.012 0.002 TYR A 253 PHE 0.015 0.002 PHE D 352 TRP 0.007 0.001 TRP C 199 HIS 0.010 0.002 HIS B 262 Details of bonding type rmsd/Z covalent geometry : bond 0.00592 / 0.27 (14928) covalent geometry : angle 0.68541 / 0.38 (20690) hydrogen bonds : bond 0.06067 / 4.16 ( 742) hydrogen bonds : angle 5.14393 / 3.85 ( 2042) metal coordination : bond 0.02506 / 1.65 ( 16) metal coordination : angle 1.56508 / 1.02 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 401 time to evaluate : 0.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 ASP cc_start: 0.7641 (m-30) cc_final: 0.7356 (t0) REVERT: B 175 GLU cc_start: 0.8601 (mp0) cc_final: 0.8371 (mm-30) REVERT: B 289 MET cc_start: 0.8195 (mtp) cc_final: 0.7988 (mtt) REVERT: B 315 ILE cc_start: 0.8688 (OUTLIER) cc_final: 0.8456 (mp) REVERT: D 54 MET cc_start: 0.8505 (mtm) cc_final: 0.8225 (mtm) outliers start: 29 outliers final: 10 residues processed: 414 average time/residue: 1.4533 time to fit residues: 651.9047 Evaluate side-chains 409 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 398 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain B residue 12 GLN Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 391 LYS Chi-restraints excluded: chain D residue 76 VAL Chi-restraints excluded: chain D residue 346 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 96 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 161 optimal weight: 5.9990 chunk 145 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 65 optimal weight: 0.6980 chunk 134 optimal weight: 1.9990 chunk 45 optimal weight: 7.9990 chunk 69 optimal weight: 0.8980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 27 GLN A 361 GLN B 291 HIS B 361 GLN C 134 GLN C 161 ASN C 284 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.114924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.099739 restraints weight = 56283.076| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 1.34 r_work: 0.3334 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3215 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.2845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 14944 Z= 0.254 Angle : 0.606 5.172 20702 Z= 0.350 Chirality : 0.045 0.240 2432 Planarity : 0.006 0.072 2284 Dihedral : 22.435 157.891 2952 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 2.17 % Allowed : 21.11 % Favored : 76.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.21), residues: 1588 helix: 1.23 (0.20), residues: 656 sheet: 0.26 (0.30), residues: 276 loop : -1.20 (0.25), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 94 TYR 0.012 0.002 TYR C 87 PHE 0.013 0.002 PHE C 98 TRP 0.007 0.001 TRP C 199 HIS 0.007 0.001 HIS B 262 Details of bonding type rmsd/Z covalent geometry : bond 0.00564 / 0.25 (14928) covalent geometry : angle 0.60563 / 0.35 (20690) hydrogen bonds : bond 0.05787 / 3.98 ( 742) hydrogen bonds : angle 4.99155 / 3.72 ( 2042) metal coordination : bond 0.02042 / 1.34 ( 16) metal coordination : angle 1.41555 / 0.90 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 404 time to evaluate : 0.800 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 103 ASP cc_start: 0.7600 (m-30) cc_final: 0.7300 (t0) REVERT: A 133 ASP cc_start: 0.8018 (m-30) cc_final: 0.7766 (m-30) REVERT: B 158 ASP cc_start: 0.8359 (t0) cc_final: 0.8120 (t0) REVERT: B 175 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.8313 (mm-30) REVERT: B 315 ILE cc_start: 0.8721 (OUTLIER) cc_final: 0.8469 (mp) REVERT: D 54 MET cc_start: 0.8537 (mtm) cc_final: 0.8307 (mtm) REVERT: D 113 SER cc_start: 0.8553 (t) cc_final: 0.8206 (p) REVERT: D 183 GLU cc_start: 0.7210 (tp30) cc_final: 0.7003 (tp30) outliers start: 29 outliers final: 12 residues processed: 415 average time/residue: 1.4583 time to fit residues: 656.6092 Evaluate side-chains 412 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 398 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 166 ARG Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 273 SER Chi-restraints excluded: chain C residue 391 LYS Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 268 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 58 optimal weight: 1.9990 chunk 159 optimal weight: 6.9990 chunk 89 optimal weight: 1.9990 chunk 160 optimal weight: 4.9990 chunk 136 optimal weight: 0.9980 chunk 114 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 102 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 46 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 27 GLN A 161 ASN A 361 GLN B 41 GLN B 291 HIS C 161 ASN C 361 GLN D 302 GLN D 369 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.115661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.100673 restraints weight = 55993.102| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 1.33 r_work: 0.3350 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3230 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.3023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14944 Z= 0.165 Angle : 0.569 5.170 20702 Z= 0.329 Chirality : 0.043 0.220 2432 Planarity : 0.005 0.050 2284 Dihedral : 22.422 156.889 2952 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 1.65 % Allowed : 21.71 % Favored : 76.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.21), residues: 1588 helix: 1.17 (0.20), residues: 684 sheet: 0.22 (0.30), residues: 276 loop : -1.25 (0.25), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 360 TYR 0.010 0.001 TYR C 87 PHE 0.010 0.001 PHE A 98 TRP 0.004 0.001 TRP C 199 HIS 0.004 0.001 HIS C 247 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.17 (14928) covalent geometry : angle 0.56819 / 0.33 (20690) hydrogen bonds : bond 0.04907 / 3.39 ( 742) hydrogen bonds : angle 4.81136 / 3.56 ( 2042) metal coordination : bond 0.01570 / 1.01 ( 16) metal coordination : angle 1.26624 / 0.79 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 403 time to evaluate : 0.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 ASP cc_start: 0.7570 (m-30) cc_final: 0.7276 (t0) REVERT: A 133 ASP cc_start: 0.8096 (m-30) cc_final: 0.7822 (m-30) REVERT: A 158 ASP cc_start: 0.8113 (t0) cc_final: 0.7912 (t70) REVERT: B 158 ASP cc_start: 0.8355 (t0) cc_final: 0.8110 (t0) REVERT: B 175 GLU cc_start: 0.8526 (mp0) cc_final: 0.8314 (mm-30) REVERT: B 315 ILE cc_start: 0.8729 (OUTLIER) cc_final: 0.8486 (mp) REVERT: C 361 GLN cc_start: 0.7958 (mt0) cc_final: 0.7716 (mt0) REVERT: D 183 GLU cc_start: 0.7213 (tp30) cc_final: 0.7003 (tp30) outliers start: 22 outliers final: 12 residues processed: 410 average time/residue: 1.4924 time to fit residues: 663.2429 Evaluate side-chains 415 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 402 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 312 LYS Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 166 ARG Chi-restraints excluded: chain B residue 256 ARG Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 166 ARG Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 268 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 58 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 chunk 118 optimal weight: 0.9980 chunk 143 optimal weight: 0.0870 chunk 75 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 147 optimal weight: 0.7980 overall best weight: 0.7558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 27 GLN A 161 ASN A 279 GLN A 361 GLN B 291 HIS D 161 ASN D 302 GLN D 369 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.115766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.100783 restraints weight = 56207.032| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 1.34 r_work: 0.3352 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3233 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.3158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14944 Z= 0.160 Angle : 0.557 5.126 20702 Z= 0.322 Chirality : 0.042 0.219 2432 Planarity : 0.005 0.073 2284 Dihedral : 22.394 156.101 2952 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 1.57 % Allowed : 21.78 % Favored : 76.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.21), residues: 1588 helix: 1.29 (0.20), residues: 684 sheet: 0.16 (0.30), residues: 276 loop : -1.24 (0.25), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 360 TYR 0.009 0.001 TYR A 87 PHE 0.009 0.001 PHE A 98 TRP 0.004 0.001 TRP C 199 HIS 0.004 0.001 HIS C 247 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.16 (14928) covalent geometry : angle 0.55619 / 0.32 (20690) hydrogen bonds : bond 0.04718 / 3.26 ( 742) hydrogen bonds : angle 4.71766 / 3.49 ( 2042) metal coordination : bond 0.01539 / 1.00 ( 16) metal coordination : angle 1.18921 / 0.75 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 409 time to evaluate : 0.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 ASP cc_start: 0.7564 (m-30) cc_final: 0.7275 (t0) REVERT: A 133 ASP cc_start: 0.8069 (m-30) cc_final: 0.7794 (m-30) REVERT: B 175 GLU cc_start: 0.8514 (mp0) cc_final: 0.8293 (mm-30) REVERT: B 315 ILE cc_start: 0.8735 (OUTLIER) cc_final: 0.8478 (mp) REVERT: D 120 ASP cc_start: 0.8086 (t0) cc_final: 0.7866 (m-30) REVERT: D 392 ASP cc_start: 0.8059 (t70) cc_final: 0.7816 (t0) outliers start: 21 outliers final: 13 residues processed: 414 average time/residue: 1.4883 time to fit residues: 667.8622 Evaluate side-chains 396 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 382 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 166 ARG Chi-restraints excluded: chain B residue 256 ARG Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 166 ARG Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 161 ASN Chi-restraints excluded: chain D residue 268 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 51 optimal weight: 2.9990 chunk 143 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 chunk 146 optimal weight: 0.6980 chunk 72 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 161 optimal weight: 4.9990 chunk 84 optimal weight: 3.9990 chunk 123 optimal weight: 3.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 27 GLN A 161 ASN B 161 ASN C 361 GLN D 140 GLN D 161 ASN D 302 GLN D 369 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.114593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.099640 restraints weight = 56204.087| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 1.34 r_work: 0.3331 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3211 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.3326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 14944 Z= 0.258 Angle : 0.600 5.489 20702 Z= 0.343 Chirality : 0.045 0.228 2432 Planarity : 0.005 0.068 2284 Dihedral : 22.368 155.548 2952 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.42 % Allowed : 23.13 % Favored : 75.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.21), residues: 1588 helix: 1.07 (0.20), residues: 692 sheet: 0.18 (0.30), residues: 276 loop : -1.26 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 360 TYR 0.013 0.002 TYR D 87 PHE 0.013 0.002 PHE A 98 TRP 0.008 0.001 TRP C 199 HIS 0.006 0.001 HIS B 262 Details of bonding type rmsd/Z covalent geometry : bond 0.00578 / 0.26 (14928) covalent geometry : angle 0.59964 / 0.34 (20690) hydrogen bonds : bond 0.05262 / 3.64 ( 742) hydrogen bonds : angle 4.81756 / 3.55 ( 2042) metal coordination : bond 0.01836 / 1.22 ( 16) metal coordination : angle 1.18813 / 0.77 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 390 time to evaluate : 0.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 ASP cc_start: 0.7600 (m-30) cc_final: 0.7309 (t0) REVERT: A 133 ASP cc_start: 0.8096 (m-30) cc_final: 0.7824 (m-30) REVERT: B 175 GLU cc_start: 0.8534 (mp0) cc_final: 0.8300 (mm-30) REVERT: B 183 GLU cc_start: 0.7528 (tp30) cc_final: 0.7228 (tp30) REVERT: B 315 ILE cc_start: 0.8748 (OUTLIER) cc_final: 0.8490 (mp) outliers start: 19 outliers final: 12 residues processed: 397 average time/residue: 1.4342 time to fit residues: 616.7504 Evaluate side-chains 399 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 386 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 166 ARG Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 112 GLU Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 166 ARG Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 106 SER Chi-restraints excluded: chain D residue 268 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 17 optimal weight: 0.6980 chunk 153 optimal weight: 1.9990 chunk 149 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 127 optimal weight: 0.8980 chunk 148 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 125 optimal weight: 1.9990 chunk 85 optimal weight: 0.5980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 27 GLN A 161 ASN B 161 ASN D 140 GLN D 302 GLN D 369 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.115352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.100462 restraints weight = 56107.206| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 1.34 r_work: 0.3347 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3227 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.3436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14944 Z= 0.159 Angle : 0.565 5.383 20702 Z= 0.325 Chirality : 0.043 0.216 2432 Planarity : 0.005 0.082 2284 Dihedral : 22.352 154.731 2952 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 1.42 % Allowed : 23.35 % Favored : 75.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.21), residues: 1588 helix: 1.25 (0.20), residues: 692 sheet: 0.14 (0.30), residues: 276 loop : -1.25 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 360 TYR 0.013 0.001 TYR C 87 PHE 0.010 0.001 PHE A 98 TRP 0.003 0.001 TRP C 199 HIS 0.004 0.001 HIS C 247 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.16 (14928) covalent geometry : angle 0.56482 / 0.33 (20690) hydrogen bonds : bond 0.04726 / 3.27 ( 742) hydrogen bonds : angle 4.69293 / 3.47 ( 2042) metal coordination : bond 0.01463 / 0.95 ( 16) metal coordination : angle 1.14557 / 0.72 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 385 time to evaluate : 0.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 ASP cc_start: 0.7603 (m-30) cc_final: 0.7304 (t0) REVERT: A 133 ASP cc_start: 0.8036 (m-30) cc_final: 0.7743 (m-30) REVERT: A 361 GLN cc_start: 0.8160 (OUTLIER) cc_final: 0.7811 (mt0) REVERT: B 94 ARG cc_start: 0.7509 (tmt-80) cc_final: 0.7192 (tmt-80) REVERT: B 315 ILE cc_start: 0.8726 (OUTLIER) cc_final: 0.8489 (mp) outliers start: 19 outliers final: 10 residues processed: 391 average time/residue: 1.5595 time to fit residues: 660.0427 Evaluate side-chains 395 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 383 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 361 GLN Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 166 ARG Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 107 LYS Chi-restraints excluded: chain D residue 268 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 73 optimal weight: 0.1980 chunk 104 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 11 optimal weight: 0.0370 chunk 3 optimal weight: 2.9990 chunk 161 optimal weight: 5.9990 chunk 43 optimal weight: 1.9990 overall best weight: 1.2464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 27 GLN A 161 ASN B 161 ASN D 140 GLN D 302 GLN D 369 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.114687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.099811 restraints weight = 55980.253| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 1.34 r_work: 0.3334 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.3214 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.3565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 14944 Z= 0.226 Angle : 0.598 8.118 20702 Z= 0.339 Chirality : 0.044 0.221 2432 Planarity : 0.006 0.086 2284 Dihedral : 22.317 154.100 2952 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 1.27 % Allowed : 23.58 % Favored : 75.15 % 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 are not related in a simple way. whole: 0.06 (0.21), residues: 1588 helix: 1.18 (0.20), residues: 692 sheet: 0.14 (0.30), residues: 276 loop : -1.31 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 360 TYR 0.023 0.002 TYR C 87 PHE 0.011 0.002 PHE D 352 TRP 0.006 0.001 TRP C 199 HIS 0.007 0.001 HIS A 291 Details of bonding type rmsd/Z covalent geometry : bond 0.00503 / 0.23 (14928) covalent geometry : angle 0.59730 / 0.34 (20690) hydrogen bonds : bond 0.05104 / 3.53 ( 742) hydrogen bonds : angle 4.75130 / 3.50 ( 2042) metal coordination : bond 0.01652 / 1.09 ( 16) metal coordination : angle 1.21615 / 0.78 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 387 time to evaluate : 0.735 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 133 ASP cc_start: 0.8033 (m-30) cc_final: 0.7740 (m-30) REVERT: A 361 GLN cc_start: 0.8133 (OUTLIER) cc_final: 0.7776 (mt0) REVERT: B 94 ARG cc_start: 0.7513 (tmt-80) cc_final: 0.7209 (tmt-80) REVERT: B 183 GLU cc_start: 0.7506 (tp30) cc_final: 0.7231 (tp30) REVERT: B 315 ILE cc_start: 0.8718 (OUTLIER) cc_final: 0.8480 (mp) REVERT: C 23 ARG cc_start: 0.8081 (ttp80) cc_final: 0.7867 (ttp-170) outliers start: 17 outliers final: 14 residues processed: 393 average time/residue: 1.4463 time to fit residues: 615.5119 Evaluate side-chains 402 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 386 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 313 ASP Chi-restraints excluded: chain A residue 361 GLN Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 161 ASN Chi-restraints excluded: chain B residue 166 ARG Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 384 MET Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 107 LYS Chi-restraints excluded: chain D residue 268 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 49 optimal weight: 0.9990 chunk 162 optimal weight: 5.9990 chunk 136 optimal weight: 0.9980 chunk 76 optimal weight: 2.9990 chunk 132 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 135 optimal weight: 0.8980 chunk 95 optimal weight: 0.0870 chunk 15 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 overall best weight: 0.7962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 27 GLN A 140 GLN A 161 ASN A 185 HIS C 302 GLN D 140 GLN D 302 GLN D 369 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.115156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.100326 restraints weight = 55860.383| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 1.33 r_work: 0.3344 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3224 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.3613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 14944 Z= 0.165 Angle : 0.574 5.472 20702 Z= 0.330 Chirality : 0.043 0.217 2432 Planarity : 0.006 0.085 2284 Dihedral : 22.301 153.529 2952 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 1.20 % Allowed : 23.65 % Favored : 75.15 % 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 are not related in a simple way. whole: 0.16 (0.21), residues: 1588 helix: 1.29 (0.20), residues: 692 sheet: 0.10 (0.30), residues: 276 loop : -1.24 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 360 TYR 0.021 0.001 TYR C 87 PHE 0.009 0.001 PHE C 98 TRP 0.004 0.001 TRP C 199 HIS 0.006 0.001 HIS B 370 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.16 (14928) covalent geometry : angle 0.57303 / 0.33 (20690) hydrogen bonds : bond 0.04760 / 3.29 ( 742) hydrogen bonds : angle 4.68861 / 3.45 ( 2042) metal coordination : bond 0.01441 / 0.94 ( 16) metal coordination : angle 1.16417 / 0.72 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 384 time to evaluate : 0.766 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 ASP cc_start: 0.7601 (m-30) cc_final: 0.7341 (t0) REVERT: A 133 ASP cc_start: 0.8002 (m-30) cc_final: 0.7700 (m-30) REVERT: B 94 ARG cc_start: 0.7529 (tmt-80) cc_final: 0.7248 (tmt-80) REVERT: B 175 GLU cc_start: 0.8502 (mp0) cc_final: 0.8262 (mm-30) REVERT: B 183 GLU cc_start: 0.7495 (tp30) cc_final: 0.7222 (tp30) REVERT: B 315 ILE cc_start: 0.8695 (OUTLIER) cc_final: 0.8448 (mp) REVERT: C 23 ARG cc_start: 0.8078 (ttp80) cc_final: 0.7857 (ttp-170) outliers start: 16 outliers final: 11 residues processed: 390 average time/residue: 1.4523 time to fit residues: 613.5451 Evaluate side-chains 392 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 380 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 324 ARG Chi-restraints excluded: chain B residue 384 MET Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 107 LYS Chi-restraints excluded: chain D residue 268 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 21 optimal weight: 1.9990 chunk 150 optimal weight: 0.9980 chunk 136 optimal weight: 0.9980 chunk 109 optimal weight: 1.9990 chunk 139 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 55 optimal weight: 0.0970 chunk 44 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 chunk 91 optimal weight: 0.4980 chunk 126 optimal weight: 2.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 27 GLN B 370 HIS C 302 GLN D 140 GLN D 302 GLN D 369 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.115047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.100210 restraints weight = 55755.524| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 1.34 r_work: 0.3342 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3222 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.3663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 14944 Z= 0.177 Angle : 0.572 5.781 20702 Z= 0.329 Chirality : 0.043 0.217 2432 Planarity : 0.006 0.092 2284 Dihedral : 22.273 152.966 2952 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 0.97 % Allowed : 24.18 % Favored : 74.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.21), residues: 1588 helix: 1.31 (0.20), residues: 692 sheet: 0.12 (0.30), residues: 276 loop : -1.26 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 360 TYR 0.025 0.001 TYR C 87 PHE 0.011 0.001 PHE A 206 TRP 0.005 0.001 TRP C 199 HIS 0.009 0.001 HIS B 370 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.18 (14928) covalent geometry : angle 0.57183 / 0.33 (20690) hydrogen bonds : bond 0.04761 / 3.29 ( 742) hydrogen bonds : angle 4.67902 / 3.44 ( 2042) metal coordination : bond 0.01424 / 0.95 ( 16) metal coordination : angle 1.13626 / 0.73 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 386 time to evaluate : 0.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 ASP cc_start: 0.8016 (m-30) cc_final: 0.7707 (m-30) REVERT: B 94 ARG cc_start: 0.7541 (tmt-80) cc_final: 0.7280 (tmt-80) REVERT: B 175 GLU cc_start: 0.8503 (mp0) cc_final: 0.8258 (mm-30) REVERT: C 23 ARG cc_start: 0.8073 (ttp80) cc_final: 0.7851 (ttp-170) outliers start: 13 outliers final: 10 residues processed: 391 average time/residue: 1.6338 time to fit residues: 691.3390 Evaluate side-chains 392 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 382 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 384 MET Chi-restraints excluded: chain C residue 112 GLU Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 107 LYS Chi-restraints excluded: chain D residue 268 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 94 optimal weight: 0.0980 chunk 137 optimal weight: 0.6980 chunk 83 optimal weight: 0.6980 chunk 36 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 4 optimal weight: 0.5980 chunk 17 optimal weight: 0.2980 chunk 52 optimal weight: 2.9990 chunk 63 optimal weight: 0.0980 chunk 98 optimal weight: 1.9990 chunk 160 optimal weight: 5.9990 overall best weight: 0.3580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 27 GLN A 161 ASN C 302 GLN D 302 GLN D 369 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.116223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.101403 restraints weight = 56164.187| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 1.35 r_work: 0.3361 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3241 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.3695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 14944 Z= 0.121 Angle : 0.551 8.569 20702 Z= 0.317 Chirality : 0.042 0.219 2432 Planarity : 0.006 0.093 2284 Dihedral : 22.252 152.185 2952 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 0.82 % Allowed : 23.88 % Favored : 75.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.21), residues: 1588 helix: 1.52 (0.20), residues: 688 sheet: 0.08 (0.30), residues: 276 loop : -1.19 (0.25), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 360 TYR 0.014 0.001 TYR C 87 PHE 0.009 0.001 PHE A 206 TRP 0.002 0.000 TRP C 199 HIS 0.004 0.001 HIS B 262 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.12 (14928) covalent geometry : angle 0.55056 / 0.32 (20690) hydrogen bonds : bond 0.04204 / 2.91 ( 742) hydrogen bonds : angle 4.54620 / 3.35 ( 2042) metal coordination : bond 0.01263 / 0.82 ( 16) metal coordination : angle 1.08786 / 0.71 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13767.86 seconds wall clock time: 232 minutes 16.93 seconds (13936.93 seconds total)