Starting phenix.real_space_refine on Wed Sep 17 06:26:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fdy_50333/09_2025/9fdy_50333.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fdy_50333/09_2025/9fdy_50333.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9fdy_50333/09_2025/9fdy_50333.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fdy_50333/09_2025/9fdy_50333.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9fdy_50333/09_2025/9fdy_50333.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fdy_50333/09_2025/9fdy_50333.map" } resolution = 3.4 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= 0.000 sd= 0.030 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 60 5.16 5 C 3881 2.51 5 N 1037 2.21 5 O 1141 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 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: 6119 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 896 Classifications: {'peptide': 112} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 102} Chain: "B" Number of atoms: 897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 897 Classifications: {'peptide': 112} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 102} Chain: "C" Number of atoms: 2606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2606 Classifications: {'peptide': 330} Link IDs: {'PCIS': 2, 'PTRANS': 22, 'TRANS': 305} Chain: "D" Number of atoms: 852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 852 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 100} Chain: "E" Number of atoms: 868 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 868 Classifications: {'peptide': 109} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 102} Time building chain proxies: 1.71, per 1000 atoms: 0.28 Number of scatterers: 6119 At special positions: 0 Unit cell: (76.443, 86.574, 145.518, 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 60 16.00 O 1141 8.00 N 1037 7.00 C 3881 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=23, symmetry=0 Simple disulfide: pdb=" SG CYS A 7 " - pdb=" SG CYS A 16 " distance=2.03 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 78 " distance=2.03 Simple disulfide: pdb=" SG CYS A 44 " - pdb=" SG CYS A 109 " distance=2.03 Simple disulfide: pdb=" SG CYS A 48 " - pdb=" SG CYS A 111 " distance=2.03 Simple disulfide: pdb=" SG CYS A 77 " - pdb=" SG CYS B 77 " distance=2.03 Simple disulfide: pdb=" SG CYS B 7 " - pdb=" SG CYS B 16 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 78 " distance=2.03 Simple disulfide: pdb=" SG CYS B 44 " - pdb=" SG CYS B 109 " distance=2.03 Simple disulfide: pdb=" SG CYS B 48 " - pdb=" SG CYS B 111 " distance=2.03 Simple disulfide: pdb=" SG CYS C 4 " - pdb=" SG CYS C 197 " distance=2.03 Simple disulfide: pdb=" SG CYS C 28 " - pdb=" SG CYS C 173 " distance=2.03 Simple disulfide: pdb=" SG CYS D 14 " - pdb=" SG CYS D 47 " distance=2.03 Simple disulfide: pdb=" SG CYS D 17 " - pdb=" SG CYS D 34 " distance=2.03 Simple disulfide: pdb=" SG CYS D 24 " - pdb=" SG CYS D 30 " distance=2.03 Simple disulfide: pdb=" SG CYS D 40 " - pdb=" SG CYS D 64 " distance=2.03 Simple disulfide: pdb=" SG CYS D 84 " - pdb=" SG CYS D 99 " distance=2.03 Simple disulfide: pdb=" SG CYS D 101 " - pdb=" SG CYS D 106 " distance=2.03 Simple disulfide: pdb=" SG CYS E 14 " - pdb=" SG CYS E 47 " distance=2.03 Simple disulfide: pdb=" SG CYS E 17 " - pdb=" SG CYS E 34 " distance=2.03 Simple disulfide: pdb=" SG CYS E 24 " - pdb=" SG CYS E 30 " distance=2.03 Simple disulfide: pdb=" SG CYS E 40 " - pdb=" SG CYS E 64 " distance=2.03 Simple disulfide: pdb=" SG CYS E 84 " - pdb=" SG CYS E 99 " distance=2.03 Simple disulfide: pdb=" SG CYS E 101 " - pdb=" SG CYS E 106 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.51 Conformation dependent library (CDL) restraints added in 356.0 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1484 Finding SS restraints... Secondary structure from input PDB file: 11 helices and 14 sheets defined 12.1% alpha, 34.5% 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 3 through 10 removed outlier: 3.762A pdb=" N SER A 10 " --> pdb=" O TYR A 6 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 69 removed outlier: 3.580A pdb=" N LYS A 60 " --> pdb=" O THR A 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 10 Processing helix chain 'B' and resid 56 through 69 Processing helix chain 'C' and resid 117 through 120 Processing helix chain 'C' and resid 132 through 145 Processing helix chain 'C' and resid 280 through 284 Processing helix chain 'C' and resid 299 through 311 removed outlier: 3.905A pdb=" N MET C 304 " --> pdb=" O GLN C 300 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 81 removed outlier: 4.543A pdb=" N ALA D 80 " --> pdb=" O GLU D 77 " (cutoff:3.500A) Processing helix chain 'E' and resid 70 through 74 removed outlier: 4.304A pdb=" N ASP E 73 " --> pdb=" O PRO E 70 " (cutoff:3.500A) Processing helix chain 'E' and resid 105 through 107 No H-bonds generated for 'chain 'E' and resid 105 through 107' Processing sheet with id=AA1, first strand: chain 'A' and resid 16 through 18 Processing sheet with id=AA2, first strand: chain 'A' and resid 21 through 23 Processing sheet with id=AA3, first strand: chain 'A' and resid 95 through 112 removed outlier: 7.102A pdb=" N LYS A 97 " --> pdb=" O VAL A 92 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N VAL A 92 " --> pdb=" O LYS A 97 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N GLU A 99 " --> pdb=" O TYR A 90 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N TYR A 90 " --> pdb=" O GLU A 99 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N LEU A 101 " --> pdb=" O ILE A 88 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N ILE A 88 " --> pdb=" O LEU A 101 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N ASN A 103 " --> pdb=" O LEU A 86 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N LEU A 86 " --> pdb=" O ASN A 103 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N ALA A 82 " --> pdb=" O ARG A 107 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N CYS A 109 " --> pdb=" O PRO A 80 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N CYS A 111 " --> pdb=" O CYS A 78 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N CYS A 78 " --> pdb=" O CYS A 111 " (cutoff:3.500A) removed outlier: 15.446A pdb=" N THR D 37 " --> pdb=" O PRO A 87 " (cutoff:3.500A) removed outlier: 9.897A pdb=" N VAL A 89 " --> pdb=" O THR D 37 " (cutoff:3.500A) removed outlier: 10.045A pdb=" N ILE D 39 " --> pdb=" O VAL A 89 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N TYR A 91 " --> pdb=" O ILE D 39 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 2 through 3 removed outlier: 4.394A pdb=" N LEU B 2 " --> pdb=" O CYS B 109 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N CYS B 109 " --> pdb=" O LEU B 2 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N LYS B 97 " --> pdb=" O VAL B 92 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N VAL B 92 " --> pdb=" O LYS B 97 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N GLU B 99 " --> pdb=" O TYR B 90 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N TYR B 90 " --> pdb=" O GLU B 99 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N LEU B 101 " --> pdb=" O ILE B 88 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N ILE B 88 " --> pdb=" O LEU B 101 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N ASN B 103 " --> pdb=" O LEU B 86 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N LEU B 86 " --> pdb=" O ASN B 103 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ALA B 82 " --> pdb=" O ARG B 107 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N CYS B 109 " --> pdb=" O PRO B 80 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N CYS B 111 " --> pdb=" O CYS B 78 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N CYS B 78 " --> pdb=" O CYS B 111 " (cutoff:3.500A) removed outlier: 15.246A pdb=" N THR E 37 " --> pdb=" O PRO B 87 " (cutoff:3.500A) removed outlier: 9.545A pdb=" N VAL B 89 " --> pdb=" O THR E 37 " (cutoff:3.500A) removed outlier: 9.302A pdb=" N ILE E 39 " --> pdb=" O VAL B 89 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N TYR B 91 " --> pdb=" O ILE E 39 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 16 through 18 Processing sheet with id=AA6, first strand: chain 'B' and resid 21 through 23 Processing sheet with id=AA7, first strand: chain 'C' and resid 7 through 8 removed outlier: 6.855A pdb=" N VAL C 323 " --> pdb=" O ILE C 214 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N VAL C 241 " --> pdb=" O LYS C 265 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N ASN C 267 " --> pdb=" O VAL C 241 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N LYS C 243 " --> pdb=" O ASN C 267 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N LYS C 269 " --> pdb=" O LYS C 243 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N LEU C 245 " --> pdb=" O LYS C 269 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N ILE C 271 " --> pdb=" O LEU C 245 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N LEU C 247 " --> pdb=" O ILE C 271 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N THR C 287 " --> pdb=" O VAL C 264 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N GLY C 266 " --> pdb=" O THR C 287 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N THR C 289 " --> pdb=" O GLY C 266 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N LEU C 268 " --> pdb=" O THR C 289 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N LEU C 291 " --> pdb=" O LEU C 268 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N VAL C 270 " --> pdb=" O LEU C 291 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 91 through 92 Processing sheet with id=AA9, first strand: chain 'C' and resid 91 through 92 removed outlier: 8.396A pdb=" N ILE C 159 " --> pdb=" O GLU C 58 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N THR C 60 " --> pdb=" O ILE C 159 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N ILE C 161 " --> pdb=" O THR C 60 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N HIS C 62 " --> pdb=" O ILE C 161 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N VAL C 163 " --> pdb=" O HIS C 62 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ASN C 64 " --> pdb=" O VAL C 163 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ASN C 158 " --> pdb=" O GLU C 187 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA C 186 " --> pdb=" O THR C 23 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N THR C 23 " --> pdb=" O ALA C 186 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LYS C 192 " --> pdb=" O ALA C 17 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N ALA C 17 " --> pdb=" O LYS C 192 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU C 18 " --> pdb=" O ARG C 326 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N ILE C 229 " --> pdb=" O PHE C 327 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N LEU C 329 " --> pdb=" O ILE C 229 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ASP C 231 " --> pdb=" O LEU C 329 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N LEU C 331 " --> pdb=" O ASP C 231 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N ARG C 233 " --> pdb=" O LEU C 331 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N TRP C 257 " --> pdb=" O GLY C 277 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 26 through 29 removed outlier: 6.186A pdb=" N GLU C 39 " --> pdb=" O VAL C 77 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N LEU C 79 " --> pdb=" O GLU C 39 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N HIS C 41 " --> pdb=" O LEU C 79 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N ASN C 81 " --> pdb=" O HIS C 41 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N LEU C 43 " --> pdb=" O ASN C 81 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N ILE C 76 " --> pdb=" O LEU C 102 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N LEU C 104 " --> pdb=" O ILE C 76 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N PHE C 78 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N SER C 106 " --> pdb=" O PHE C 78 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N LEU C 80 " --> pdb=" O SER C 106 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ARG C 101 " --> pdb=" O GLU C 123 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N GLU C 125 " --> pdb=" O ARG C 101 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N PHE C 103 " --> pdb=" O GLU C 125 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N ARG C 127 " --> pdb=" O PHE C 103 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N VAL C 105 " --> pdb=" O ARG C 127 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 17 through 20 removed outlier: 4.981A pdb=" N ASP D 18 " --> pdb=" O THR D 62 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N THR D 62 " --> pdb=" O ASP D 18 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 29 through 31 Processing sheet with id=AB4, first strand: chain 'E' and resid 20 through 21 removed outlier: 4.629A pdb=" N PHE E 96 " --> pdb=" O LYS E 89 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 29 through 31 162 hydrogen bonds defined for protein. 405 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: 0.95 Time building geometry restraints manager: 0.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1981 1.34 - 1.46: 1342 1.46 - 1.58: 2877 1.58 - 1.70: 0 1.70 - 1.82: 73 Bond restraints: 6273 Sorted by residual: bond pdb=" N ASP E 66 " pdb=" CA ASP E 66 " ideal model delta sigma weight residual 1.458 1.483 -0.026 1.64e-02 3.72e+03 2.46e+00 bond pdb=" N ILE A 51 " pdb=" CA ILE A 51 " ideal model delta sigma weight residual 1.474 1.457 0.018 1.57e-02 4.06e+03 1.29e+00 bond pdb=" C ASP E 66 " pdb=" N PRO E 67 " ideal model delta sigma weight residual 1.335 1.349 -0.014 1.28e-02 6.10e+03 1.26e+00 bond pdb=" N ILE B 51 " pdb=" CA ILE B 51 " ideal model delta sigma weight residual 1.474 1.457 0.017 1.57e-02 4.06e+03 1.19e+00 bond pdb=" CA ASN E 107 " pdb=" C ASN E 107 " ideal model delta sigma weight residual 1.523 1.508 0.015 1.41e-02 5.03e+03 1.08e+00 ... (remaining 6268 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.05: 8053 1.05 - 2.09: 366 2.09 - 3.14: 86 3.14 - 4.19: 8 4.19 - 5.23: 2 Bond angle restraints: 8515 Sorted by residual: angle pdb=" N ASN E 26 " pdb=" CA ASN E 26 " pdb=" CB ASN E 26 " ideal model delta sigma weight residual 113.65 110.50 3.15 1.47e+00 4.63e-01 4.59e+00 angle pdb=" CA ILE B 51 " pdb=" C ILE B 51 " pdb=" O ILE B 51 " ideal model delta sigma weight residual 122.63 120.82 1.81 8.70e-01 1.32e+00 4.35e+00 angle pdb=" N ILE A 51 " pdb=" CA ILE A 51 " pdb=" C ILE A 51 " ideal model delta sigma weight residual 106.21 108.43 -2.22 1.07e+00 8.73e-01 4.30e+00 angle pdb=" C ALA C 186 " pdb=" N GLU C 187 " pdb=" CA GLU C 187 " ideal model delta sigma weight residual 123.00 120.11 2.89 1.41e+00 5.03e-01 4.19e+00 angle pdb=" CA ILE A 51 " pdb=" C ILE A 51 " pdb=" O ILE A 51 " ideal model delta sigma weight residual 122.63 120.86 1.77 8.70e-01 1.32e+00 4.13e+00 ... (remaining 8510 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.10: 3645 16.10 - 32.19: 209 32.19 - 48.29: 33 48.29 - 64.38: 14 64.38 - 80.48: 1 Dihedral angle restraints: 3902 sinusoidal: 1626 harmonic: 2276 Sorted by residual: dihedral pdb=" CA VAL E 63 " pdb=" C VAL E 63 " pdb=" N CYS E 64 " pdb=" CA CYS E 64 " ideal model delta harmonic sigma weight residual 180.00 161.93 18.07 0 5.00e+00 4.00e-02 1.31e+01 dihedral pdb=" N CYS B 16 " pdb=" CA CYS B 16 " pdb=" CB CYS B 16 " pdb=" SG CYS B 16 " ideal model delta sinusoidal sigma weight residual -60.00 -119.83 59.83 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" N CYS A 16 " pdb=" CA CYS A 16 " pdb=" CB CYS A 16 " pdb=" SG CYS A 16 " ideal model delta sinusoidal sigma weight residual -60.00 -118.88 58.88 3 1.50e+01 4.44e-03 9.47e+00 ... (remaining 3899 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 492 0.026 - 0.052: 260 0.052 - 0.078: 75 0.078 - 0.103: 74 0.103 - 0.129: 33 Chirality restraints: 934 Sorted by residual: chirality pdb=" CA ILE C 159 " pdb=" N ILE C 159 " pdb=" C ILE C 159 " pdb=" CB ILE C 159 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.17e-01 chirality pdb=" CA ILE E 58 " pdb=" N ILE E 58 " pdb=" C ILE E 58 " pdb=" CB ILE E 58 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.96e-01 chirality pdb=" CA VAL E 48 " pdb=" N VAL E 48 " pdb=" C VAL E 48 " pdb=" CB VAL E 48 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 3.92e-01 ... (remaining 931 not shown) Planarity restraints: 1103 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 86 " 0.030 5.00e-02 4.00e+02 4.59e-02 3.37e+00 pdb=" N PRO B 87 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO B 87 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 87 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS B 48 " -0.023 5.00e-02 4.00e+02 3.50e-02 1.96e+00 pdb=" N PRO B 49 " 0.061 5.00e-02 4.00e+02 pdb=" CA PRO B 49 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 49 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN C 190 " -0.020 5.00e-02 4.00e+02 3.00e-02 1.44e+00 pdb=" N PRO C 191 " 0.052 5.00e-02 4.00e+02 pdb=" CA PRO C 191 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO C 191 " -0.017 5.00e-02 4.00e+02 ... (remaining 1100 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 180 2.71 - 3.26: 5864 3.26 - 3.80: 9575 3.80 - 4.35: 12041 4.35 - 4.90: 20820 Nonbonded interactions: 48480 Sorted by model distance: nonbonded pdb=" OD1 ASP A 3 " pdb=" OG SER A 108 " model vdw 2.162 3.040 nonbonded pdb=" O ALA A 72 " pdb=" OG SER A 73 " model vdw 2.240 3.040 nonbonded pdb=" O LEU E 13 " pdb=" N GLU E 105 " model vdw 2.252 3.120 nonbonded pdb=" NE2 HIS C 13 " pdb=" OG1 THR C 319 " model vdw 2.264 3.120 nonbonded pdb=" NZ LYS C 74 " pdb=" OE2 GLU C 165 " model vdw 2.316 3.120 ... (remaining 48475 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 1 through 111 or (resid 112 and (name N or name CA or name \ C or name O or name CB or name OG )))) } ncs_group { reference = chain 'D' selection = (chain 'E' and resid 10 through 116) } 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=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: 1.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 7.660 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 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 0.036 6296 Z= 0.167 Angle : 0.535 5.232 8561 Z= 0.300 Chirality : 0.044 0.129 934 Planarity : 0.004 0.046 1103 Dihedral : 10.682 80.477 2349 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 2.56 % Allowed : 7.68 % Favored : 89.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: -0.50 (0.31), residues: 760 helix: 1.26 (0.61), residues: 79 sheet: -0.58 (0.30), residues: 304 loop : -0.32 (0.32), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 107 TYR 0.006 0.001 TYR A 39 PHE 0.009 0.001 PHE B 43 TRP 0.008 0.001 TRP C 257 HIS 0.003 0.001 HIS C 62 Details of bonding type rmsd covalent geometry : bond 0.00360 ( 6273) covalent geometry : angle 0.53493 ( 8515) SS BOND : bond 0.00275 ( 23) SS BOND : angle 0.59920 ( 46) hydrogen bonds : bond 0.14181 ( 160) hydrogen bonds : angle 6.29593 ( 405) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 209 time to evaluate : 0.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.8668 (mmm) cc_final: 0.8033 (tpp) REVERT: A 105 ILE cc_start: 0.8903 (mt) cc_final: 0.8592 (mp) REVERT: B 60 LYS cc_start: 0.8656 (mtpm) cc_final: 0.8372 (mttt) REVERT: C 113 PHE cc_start: 0.8195 (m-80) cc_final: 0.7947 (m-80) REVERT: C 132 GLU cc_start: 0.8777 (tp30) cc_final: 0.8416 (tt0) REVERT: C 195 GLU cc_start: 0.8162 (mt-10) cc_final: 0.7653 (mm-30) REVERT: C 231 ASP cc_start: 0.8010 (m-30) cc_final: 0.7406 (m-30) REVERT: C 251 CYS cc_start: 0.8309 (t) cc_final: 0.8055 (t) REVERT: C 263 ASP cc_start: 0.8211 (m-30) cc_final: 0.7926 (t0) REVERT: E 21 PHE cc_start: 0.7822 (m-80) cc_final: 0.7471 (m-80) REVERT: E 45 GLU cc_start: 0.7146 (mt-10) cc_final: 0.6704 (mp0) REVERT: E 63 VAL cc_start: 0.8939 (m) cc_final: 0.8737 (m) REVERT: E 91 LYS cc_start: 0.7592 (tppt) cc_final: 0.7178 (tptt) REVERT: E 97 PHE cc_start: 0.7633 (m-80) cc_final: 0.6844 (m-80) outliers start: 18 outliers final: 8 residues processed: 221 average time/residue: 0.0975 time to fit residues: 27.1997 Evaluate side-chains 168 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 160 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 CYS Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 77 CYS Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 184 TYR Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 221 TYR Chi-restraints excluded: chain D residue 84 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 0.0050 chunk 61 optimal weight: 0.0270 chunk 45 optimal weight: 10.0000 chunk 74 optimal weight: 1.9990 overall best weight: 0.3652 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 5 ASN ** C 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 204 HIS C 302 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.184640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.120262 restraints weight = 7911.168| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 3.78 r_work: 0.3290 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7172 moved from start: 0.2299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6296 Z= 0.122 Angle : 0.575 8.047 8561 Z= 0.290 Chirality : 0.045 0.144 934 Planarity : 0.004 0.058 1103 Dihedral : 6.314 57.406 835 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 4.69 % Allowed : 14.37 % Favored : 80.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: -0.46 (0.31), residues: 760 helix: 1.27 (0.62), residues: 81 sheet: -0.75 (0.31), residues: 277 loop : -0.17 (0.31), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 233 TYR 0.010 0.001 TYR A 50 PHE 0.016 0.001 PHE A 8 TRP 0.009 0.001 TRP C 257 HIS 0.002 0.001 HIS C 13 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 6273) covalent geometry : angle 0.56964 ( 8515) SS BOND : bond 0.00364 ( 23) SS BOND : angle 1.21078 ( 46) hydrogen bonds : bond 0.03363 ( 160) hydrogen bonds : angle 5.65178 ( 405) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 164 time to evaluate : 0.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 GLU cc_start: 0.7777 (tp30) cc_final: 0.7403 (mm-30) REVERT: A 104 MET cc_start: 0.8847 (mmm) cc_final: 0.7836 (mmm) REVERT: A 105 ILE cc_start: 0.8778 (mt) cc_final: 0.8433 (mp) REVERT: B 60 LYS cc_start: 0.8348 (mtpm) cc_final: 0.8003 (mttm) REVERT: B 102 SER cc_start: 0.8965 (OUTLIER) cc_final: 0.8616 (m) REVERT: C 113 PHE cc_start: 0.8227 (m-80) cc_final: 0.7943 (m-80) REVERT: C 132 GLU cc_start: 0.8935 (tp30) cc_final: 0.8305 (tt0) REVERT: C 195 GLU cc_start: 0.8515 (mt-10) cc_final: 0.7764 (mm-30) REVERT: C 231 ASP cc_start: 0.8263 (m-30) cc_final: 0.7502 (m-30) REVERT: C 251 CYS cc_start: 0.8674 (t) cc_final: 0.8334 (t) REVERT: C 263 ASP cc_start: 0.8709 (m-30) cc_final: 0.8090 (t0) REVERT: C 283 GLU cc_start: 0.7813 (OUTLIER) cc_final: 0.7296 (mp0) REVERT: D 31 MET cc_start: 0.7776 (tpp) cc_final: 0.7367 (tpt) REVERT: E 21 PHE cc_start: 0.8391 (m-80) cc_final: 0.8093 (m-80) REVERT: E 28 LYS cc_start: 0.8707 (ptmm) cc_final: 0.8048 (ttpt) REVERT: E 91 LYS cc_start: 0.7372 (tppt) cc_final: 0.6887 (tptt) REVERT: E 97 PHE cc_start: 0.7706 (m-80) cc_final: 0.6666 (m-80) outliers start: 33 outliers final: 16 residues processed: 182 average time/residue: 0.0805 time to fit residues: 19.3113 Evaluate side-chains 166 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 148 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 CYS Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 184 TYR Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 221 TYR Chi-restraints excluded: chain C residue 283 GLU Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain D residue 84 CYS Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 61 GLU Chi-restraints excluded: chain E residue 75 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 27 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 71 optimal weight: 4.9990 chunk 51 optimal weight: 0.0030 chunk 18 optimal weight: 7.9990 chunk 5 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 chunk 4 optimal weight: 0.0270 chunk 45 optimal weight: 5.9990 chunk 26 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 overall best weight: 1.1452 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 ASN B 5 ASN ** C 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 135 HIS C 204 HIS ** D 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 72 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.179330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.115330 restraints weight = 7921.307| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 3.71 r_work: 0.3242 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7264 moved from start: 0.2649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6296 Z= 0.177 Angle : 0.579 10.473 8561 Z= 0.289 Chirality : 0.045 0.138 934 Planarity : 0.004 0.048 1103 Dihedral : 6.173 59.117 834 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 4.84 % Allowed : 15.08 % Favored : 80.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: -0.48 (0.31), residues: 760 helix: 1.10 (0.62), residues: 81 sheet: -0.71 (0.32), residues: 278 loop : -0.19 (0.31), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 326 TYR 0.012 0.001 TYR A 50 PHE 0.015 0.001 PHE A 8 TRP 0.005 0.001 TRP A 52 HIS 0.008 0.001 HIS A 34 Details of bonding type rmsd covalent geometry : bond 0.00417 ( 6273) covalent geometry : angle 0.57480 ( 8515) SS BOND : bond 0.00541 ( 23) SS BOND : angle 1.15497 ( 46) hydrogen bonds : bond 0.03189 ( 160) hydrogen bonds : angle 5.59611 ( 405) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 144 time to evaluate : 0.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 ASP cc_start: 0.7791 (p0) cc_final: 0.7269 (p0) REVERT: A 5 ASN cc_start: 0.9427 (m-40) cc_final: 0.9029 (p0) REVERT: A 81 GLN cc_start: 0.7755 (mt0) cc_final: 0.7201 (mt0) REVERT: A 99 GLU cc_start: 0.7849 (tp30) cc_final: 0.7445 (mm-30) REVERT: A 105 ILE cc_start: 0.8849 (mt) cc_final: 0.8519 (mp) REVERT: B 13 LYS cc_start: 0.8085 (tppt) cc_final: 0.7773 (mttp) REVERT: B 60 LYS cc_start: 0.8408 (mtpm) cc_final: 0.8073 (mttt) REVERT: C 23 THR cc_start: 0.8825 (m) cc_final: 0.8491 (p) REVERT: C 77 VAL cc_start: 0.9153 (t) cc_final: 0.8789 (m) REVERT: C 132 GLU cc_start: 0.8953 (tp30) cc_final: 0.8380 (tt0) REVERT: C 195 GLU cc_start: 0.8472 (mt-10) cc_final: 0.7782 (mm-30) REVERT: C 231 ASP cc_start: 0.8301 (m-30) cc_final: 0.7627 (m-30) REVERT: C 263 ASP cc_start: 0.8716 (m-30) cc_final: 0.8101 (t0) REVERT: C 283 GLU cc_start: 0.7866 (OUTLIER) cc_final: 0.7354 (mp0) REVERT: C 320 MET cc_start: 0.8963 (ttp) cc_final: 0.8623 (tmm) REVERT: E 21 PHE cc_start: 0.8401 (m-80) cc_final: 0.8160 (m-80) REVERT: E 28 LYS cc_start: 0.8747 (ptmm) cc_final: 0.8146 (ttpp) REVERT: E 98 MET cc_start: 0.8680 (ttp) cc_final: 0.8412 (ttt) outliers start: 34 outliers final: 22 residues processed: 165 average time/residue: 0.0834 time to fit residues: 17.9890 Evaluate side-chains 161 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 138 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 CYS Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 184 TYR Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 221 TYR Chi-restraints excluded: chain C residue 227 ASP Chi-restraints excluded: chain C residue 283 GLU Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain D residue 84 CYS Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 75 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 10 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 41 optimal weight: 3.9990 chunk 24 optimal weight: 0.2980 chunk 46 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 chunk 40 optimal weight: 0.9990 chunk 16 optimal weight: 0.5980 chunk 28 optimal weight: 0.7980 chunk 6 optimal weight: 0.7980 chunk 67 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 5 ASN ** C 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 204 HIS ** D 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.181301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.116014 restraints weight = 8008.192| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 3.86 r_work: 0.3253 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7241 moved from start: 0.2951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6296 Z= 0.125 Angle : 0.539 6.748 8561 Z= 0.271 Chirality : 0.044 0.134 934 Planarity : 0.004 0.038 1103 Dihedral : 6.162 59.919 834 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 4.55 % Allowed : 16.64 % Favored : 78.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: -0.56 (0.31), residues: 760 helix: 0.98 (0.62), residues: 81 sheet: -0.78 (0.31), residues: 280 loop : -0.21 (0.31), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 52 TYR 0.009 0.001 TYR B 58 PHE 0.012 0.001 PHE E 97 TRP 0.007 0.001 TRP C 257 HIS 0.009 0.001 HIS A 34 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 6273) covalent geometry : angle 0.53435 ( 8515) SS BOND : bond 0.00381 ( 23) SS BOND : angle 1.09050 ( 46) hydrogen bonds : bond 0.02900 ( 160) hydrogen bonds : angle 5.37205 ( 405) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 143 time to evaluate : 0.208 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 VAL cc_start: 0.8321 (OUTLIER) cc_final: 0.8008 (m) REVERT: A 39 TYR cc_start: 0.8744 (p90) cc_final: 0.8216 (p90) REVERT: A 81 GLN cc_start: 0.7771 (mt0) cc_final: 0.7155 (mt0) REVERT: A 99 GLU cc_start: 0.7764 (tp30) cc_final: 0.7192 (mm-30) REVERT: A 104 MET cc_start: 0.8227 (tpp) cc_final: 0.7744 (tpp) REVERT: A 105 ILE cc_start: 0.8819 (mt) cc_final: 0.8492 (mp) REVERT: B 13 LYS cc_start: 0.8004 (tppt) cc_final: 0.7746 (mttp) REVERT: B 15 CYS cc_start: 0.6867 (OUTLIER) cc_final: 0.6047 (t) REVERT: B 60 LYS cc_start: 0.8313 (mtpm) cc_final: 0.7971 (mttt) REVERT: C 23 THR cc_start: 0.8822 (m) cc_final: 0.8538 (p) REVERT: C 77 VAL cc_start: 0.9185 (t) cc_final: 0.8871 (m) REVERT: C 132 GLU cc_start: 0.8952 (tp30) cc_final: 0.8328 (tt0) REVERT: C 195 GLU cc_start: 0.8494 (mt-10) cc_final: 0.7801 (mm-30) REVERT: C 231 ASP cc_start: 0.8365 (m-30) cc_final: 0.7659 (m-30) REVERT: C 263 ASP cc_start: 0.8697 (m-30) cc_final: 0.8050 (t0) REVERT: C 283 GLU cc_start: 0.7880 (OUTLIER) cc_final: 0.7345 (mp0) REVERT: C 320 MET cc_start: 0.8943 (ttp) cc_final: 0.8589 (tmm) REVERT: D 31 MET cc_start: 0.8045 (mmm) cc_final: 0.7600 (tpt) REVERT: E 28 LYS cc_start: 0.8750 (ptmm) cc_final: 0.8169 (ttpp) REVERT: E 78 ASP cc_start: 0.7496 (t0) cc_final: 0.7158 (t0) REVERT: E 96 PHE cc_start: 0.6848 (t80) cc_final: 0.6581 (t80) REVERT: E 97 PHE cc_start: 0.7758 (m-80) cc_final: 0.7213 (m-80) REVERT: E 98 MET cc_start: 0.8491 (ttp) cc_final: 0.8124 (ttt) outliers start: 32 outliers final: 24 residues processed: 165 average time/residue: 0.0791 time to fit residues: 17.2546 Evaluate side-chains 164 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 137 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 CYS Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 102 SER Chi-restraints excluded: chain B residue 15 CYS Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 66 ILE Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 184 TYR Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 197 CYS Chi-restraints excluded: chain C residue 221 TYR Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 283 GLU Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain D residue 84 CYS Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 111 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 46 optimal weight: 4.9990 chunk 54 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 41 optimal weight: 4.9990 chunk 42 optimal weight: 0.6980 chunk 47 optimal weight: 0.9990 chunk 45 optimal weight: 4.9990 chunk 55 optimal weight: 7.9990 chunk 43 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 5 ASN ** C 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 204 HIS ** D 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 72 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.179552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.115581 restraints weight = 8103.824| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 3.74 r_work: 0.3248 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7268 moved from start: 0.3112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6296 Z= 0.144 Angle : 0.547 10.374 8561 Z= 0.273 Chirality : 0.044 0.137 934 Planarity : 0.004 0.037 1103 Dihedral : 6.064 58.919 834 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 5.12 % Allowed : 16.36 % Favored : 78.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: -0.62 (0.31), residues: 760 helix: 0.67 (0.59), residues: 87 sheet: -0.74 (0.31), residues: 298 loop : -0.22 (0.32), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 330 TYR 0.010 0.001 TYR A 90 PHE 0.025 0.001 PHE C 113 TRP 0.005 0.001 TRP C 257 HIS 0.011 0.001 HIS A 34 Details of bonding type rmsd covalent geometry : bond 0.00341 ( 6273) covalent geometry : angle 0.54265 ( 8515) SS BOND : bond 0.00335 ( 23) SS BOND : angle 1.06875 ( 46) hydrogen bonds : bond 0.02873 ( 160) hydrogen bonds : angle 5.29012 ( 405) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 136 time to evaluate : 0.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 TYR cc_start: 0.8674 (p90) cc_final: 0.8453 (p90) REVERT: A 81 GLN cc_start: 0.7800 (mt0) cc_final: 0.7179 (mt0) REVERT: A 99 GLU cc_start: 0.7641 (tp30) cc_final: 0.7097 (mm-30) REVERT: A 105 ILE cc_start: 0.8818 (mt) cc_final: 0.8491 (mp) REVERT: B 13 LYS cc_start: 0.8078 (tppt) cc_final: 0.7839 (mttp) REVERT: B 15 CYS cc_start: 0.6942 (OUTLIER) cc_final: 0.6177 (t) REVERT: B 60 LYS cc_start: 0.8314 (mtpm) cc_final: 0.7947 (mttt) REVERT: C 23 THR cc_start: 0.8820 (m) cc_final: 0.8567 (p) REVERT: C 77 VAL cc_start: 0.9178 (t) cc_final: 0.8826 (m) REVERT: C 132 GLU cc_start: 0.8945 (tp30) cc_final: 0.8318 (tt0) REVERT: C 195 GLU cc_start: 0.8523 (mt-10) cc_final: 0.7878 (mm-30) REVERT: C 231 ASP cc_start: 0.8394 (m-30) cc_final: 0.7722 (m-30) REVERT: C 263 ASP cc_start: 0.8632 (m-30) cc_final: 0.8030 (t0) REVERT: C 283 GLU cc_start: 0.7935 (OUTLIER) cc_final: 0.7416 (mp0) REVERT: C 320 MET cc_start: 0.8926 (ttp) cc_final: 0.8580 (tmm) REVERT: D 98 MET cc_start: 0.8458 (ppp) cc_final: 0.7538 (ttp) REVERT: E 28 LYS cc_start: 0.8817 (ptmm) cc_final: 0.8261 (ttpp) REVERT: E 74 PHE cc_start: 0.8568 (m-80) cc_final: 0.8269 (m-80) REVERT: E 97 PHE cc_start: 0.7764 (m-80) cc_final: 0.7169 (m-80) REVERT: E 98 MET cc_start: 0.8405 (ttp) cc_final: 0.8139 (ttt) outliers start: 36 outliers final: 26 residues processed: 162 average time/residue: 0.0775 time to fit residues: 16.7799 Evaluate side-chains 161 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 133 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ASN Chi-restraints excluded: chain A residue 16 CYS Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 102 SER Chi-restraints excluded: chain B residue 15 CYS Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 66 ILE Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 184 TYR Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 221 TYR Chi-restraints excluded: chain C residue 227 ASP Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 283 GLU Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain D residue 84 CYS Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 111 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 53 optimal weight: 4.9990 chunk 35 optimal weight: 0.7980 chunk 27 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 73 optimal weight: 10.0000 chunk 37 optimal weight: 0.8980 chunk 55 optimal weight: 10.0000 chunk 25 optimal weight: 3.9990 chunk 38 optimal weight: 0.0270 chunk 3 optimal weight: 4.9990 overall best weight: 1.7442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 5 ASN ** C 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 135 HIS C 204 HIS C 333 ASN ** D 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 72 HIS ** E 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.176670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.110553 restraints weight = 8136.750| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 3.91 r_work: 0.3187 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7385 moved from start: 0.3250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 6296 Z= 0.243 Angle : 0.619 6.717 8561 Z= 0.315 Chirality : 0.046 0.212 934 Planarity : 0.004 0.042 1103 Dihedral : 6.259 57.491 834 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 5.26 % Allowed : 17.35 % Favored : 77.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: -0.89 (0.31), residues: 760 helix: 0.54 (0.59), residues: 87 sheet: -0.90 (0.30), residues: 312 loop : -0.40 (0.32), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 326 TYR 0.011 0.002 TYR B 58 PHE 0.023 0.002 PHE C 113 TRP 0.006 0.001 TRP A 52 HIS 0.008 0.001 HIS A 34 Details of bonding type rmsd covalent geometry : bond 0.00573 ( 6273) covalent geometry : angle 0.61213 ( 8515) SS BOND : bond 0.00481 ( 23) SS BOND : angle 1.41176 ( 46) hydrogen bonds : bond 0.03230 ( 160) hydrogen bonds : angle 5.53421 ( 405) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 141 time to evaluate : 0.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 GLN cc_start: 0.7859 (mt0) cc_final: 0.7253 (mt0) REVERT: A 105 ILE cc_start: 0.8832 (mt) cc_final: 0.8495 (mp) REVERT: B 15 CYS cc_start: 0.7029 (OUTLIER) cc_final: 0.6291 (t) REVERT: B 60 LYS cc_start: 0.8471 (mtpm) cc_final: 0.8115 (mttt) REVERT: C 23 THR cc_start: 0.8849 (m) cc_final: 0.8609 (p) REVERT: C 77 VAL cc_start: 0.9209 (t) cc_final: 0.8842 (m) REVERT: C 132 GLU cc_start: 0.8954 (tp30) cc_final: 0.8366 (tt0) REVERT: C 195 GLU cc_start: 0.8631 (mt-10) cc_final: 0.7964 (mm-30) REVERT: C 231 ASP cc_start: 0.8399 (m-30) cc_final: 0.7803 (m-30) REVERT: C 256 ASN cc_start: 0.9103 (t0) cc_final: 0.8831 (t0) REVERT: C 263 ASP cc_start: 0.8684 (m-30) cc_final: 0.8027 (t0) REVERT: C 283 GLU cc_start: 0.7984 (OUTLIER) cc_final: 0.7443 (mp0) REVERT: C 320 MET cc_start: 0.9001 (ttp) cc_final: 0.8659 (tmm) REVERT: D 31 MET cc_start: 0.8115 (mmm) cc_final: 0.7650 (tpt) REVERT: D 98 MET cc_start: 0.8426 (ppp) cc_final: 0.7721 (ttt) REVERT: E 28 LYS cc_start: 0.8835 (ptmm) cc_final: 0.8289 (ttpp) REVERT: E 45 GLU cc_start: 0.7436 (mt-10) cc_final: 0.6686 (mt-10) REVERT: E 74 PHE cc_start: 0.8644 (m-80) cc_final: 0.8439 (m-80) REVERT: E 78 ASP cc_start: 0.7274 (t0) cc_final: 0.6978 (t0) REVERT: E 97 PHE cc_start: 0.7704 (m-80) cc_final: 0.6992 (m-80) outliers start: 37 outliers final: 29 residues processed: 164 average time/residue: 0.0726 time to fit residues: 15.8066 Evaluate side-chains 171 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 140 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ASN Chi-restraints excluded: chain A residue 16 CYS Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain B residue 15 CYS Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 66 ILE Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 184 TYR Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 221 TYR Chi-restraints excluded: chain C residue 227 ASP Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 283 GLU Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 309 ASP Chi-restraints excluded: chain D residue 84 CYS Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 111 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 23 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 52 optimal weight: 0.5980 chunk 61 optimal weight: 0.4980 chunk 12 optimal weight: 0.7980 chunk 19 optimal weight: 0.4980 chunk 17 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 21 optimal weight: 0.5980 chunk 4 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 5 ASN B 67 GLN ** C 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 135 HIS C 204 HIS D 27 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.180066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.115007 restraints weight = 8057.113| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 3.90 r_work: 0.3246 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 moved from start: 0.3392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6296 Z= 0.122 Angle : 0.558 7.578 8561 Z= 0.280 Chirality : 0.045 0.171 934 Planarity : 0.004 0.044 1103 Dihedral : 6.014 57.523 834 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 4.69 % Allowed : 17.78 % Favored : 77.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: -0.80 (0.31), residues: 760 helix: 0.60 (0.58), residues: 87 sheet: -0.86 (0.30), residues: 311 loop : -0.32 (0.32), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 52 TYR 0.025 0.001 TYR A 39 PHE 0.024 0.001 PHE C 113 TRP 0.009 0.001 TRP C 257 HIS 0.006 0.001 HIS A 34 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 6273) covalent geometry : angle 0.55201 ( 8515) SS BOND : bond 0.00276 ( 23) SS BOND : angle 1.20078 ( 46) hydrogen bonds : bond 0.02822 ( 160) hydrogen bonds : angle 5.18366 ( 405) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 149 time to evaluate : 0.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 GLN cc_start: 0.7802 (mt0) cc_final: 0.7187 (mt0) REVERT: A 99 GLU cc_start: 0.7491 (mm-30) cc_final: 0.6935 (mm-30) REVERT: A 105 ILE cc_start: 0.8774 (mt) cc_final: 0.8468 (mp) REVERT: B 15 CYS cc_start: 0.6946 (OUTLIER) cc_final: 0.6418 (t) REVERT: B 60 LYS cc_start: 0.8339 (mtpm) cc_final: 0.7959 (mttt) REVERT: C 23 THR cc_start: 0.8842 (m) cc_final: 0.8632 (p) REVERT: C 77 VAL cc_start: 0.9192 (t) cc_final: 0.8866 (m) REVERT: C 132 GLU cc_start: 0.8938 (tp30) cc_final: 0.8385 (tt0) REVERT: C 195 GLU cc_start: 0.8579 (mt-10) cc_final: 0.7935 (mm-30) REVERT: C 231 ASP cc_start: 0.8356 (m-30) cc_final: 0.7706 (m-30) REVERT: C 263 ASP cc_start: 0.8577 (m-30) cc_final: 0.7978 (t0) REVERT: C 283 GLU cc_start: 0.8001 (OUTLIER) cc_final: 0.7428 (mp0) REVERT: C 320 MET cc_start: 0.8938 (ttp) cc_final: 0.8615 (tmm) REVERT: D 107 ASN cc_start: 0.8348 (p0) cc_final: 0.8070 (p0) REVERT: E 28 LYS cc_start: 0.8814 (ptmm) cc_final: 0.8318 (ttpt) REVERT: E 45 GLU cc_start: 0.7311 (mt-10) cc_final: 0.6563 (mt-10) REVERT: E 74 PHE cc_start: 0.8655 (m-80) cc_final: 0.8431 (m-80) REVERT: E 78 ASP cc_start: 0.7079 (t0) cc_final: 0.6756 (t0) REVERT: E 97 PHE cc_start: 0.7626 (m-80) cc_final: 0.7053 (m-80) outliers start: 33 outliers final: 24 residues processed: 171 average time/residue: 0.0712 time to fit residues: 16.2591 Evaluate side-chains 165 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 139 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 CYS Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain B residue 15 CYS Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 19 MET Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 184 TYR Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 221 TYR Chi-restraints excluded: chain C residue 227 ASP Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 283 GLU Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain D residue 84 CYS Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 111 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 9 optimal weight: 9.9990 chunk 70 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 chunk 0 optimal weight: 7.9990 chunk 46 optimal weight: 4.9990 chunk 72 optimal weight: 3.9990 chunk 60 optimal weight: 40.0000 chunk 62 optimal weight: 9.9990 chunk 19 optimal weight: 0.8980 chunk 49 optimal weight: 3.9990 chunk 58 optimal weight: 4.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 5 ASN ** B 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 81 ASN C 135 HIS ** C 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.174309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.108069 restraints weight = 8366.035| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 3.93 r_work: 0.3148 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.3533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.060 6296 Z= 0.338 Angle : 0.714 8.347 8561 Z= 0.369 Chirality : 0.049 0.166 934 Planarity : 0.005 0.049 1103 Dihedral : 6.446 58.285 834 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 5.26 % Allowed : 17.07 % Favored : 77.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: -1.08 (0.31), residues: 760 helix: 0.41 (0.58), residues: 87 sheet: -1.16 (0.30), residues: 313 loop : -0.39 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 326 TYR 0.013 0.002 TYR B 58 PHE 0.022 0.002 PHE C 113 TRP 0.008 0.001 TRP B 32 HIS 0.006 0.001 HIS A 34 Details of bonding type rmsd covalent geometry : bond 0.00798 ( 6273) covalent geometry : angle 0.70048 ( 8515) SS BOND : bond 0.00662 ( 23) SS BOND : angle 2.03546 ( 46) hydrogen bonds : bond 0.03574 ( 160) hydrogen bonds : angle 5.64961 ( 405) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 139 time to evaluate : 0.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 GLN cc_start: 0.7975 (mt0) cc_final: 0.7152 (mt0) REVERT: A 99 GLU cc_start: 0.7747 (mm-30) cc_final: 0.7157 (mm-30) REVERT: A 105 ILE cc_start: 0.8777 (mt) cc_final: 0.8482 (mp) REVERT: B 13 LYS cc_start: 0.8414 (tptp) cc_final: 0.7994 (mttp) REVERT: B 15 CYS cc_start: 0.7284 (OUTLIER) cc_final: 0.6736 (t) REVERT: C 23 THR cc_start: 0.8924 (m) cc_final: 0.8700 (p) REVERT: C 132 GLU cc_start: 0.8956 (tp30) cc_final: 0.8362 (tt0) REVERT: C 195 GLU cc_start: 0.8719 (mt-10) cc_final: 0.7956 (mm-30) REVERT: C 231 ASP cc_start: 0.8400 (m-30) cc_final: 0.7836 (m-30) REVERT: C 263 ASP cc_start: 0.8686 (m-30) cc_final: 0.7934 (t0) REVERT: C 283 GLU cc_start: 0.8039 (OUTLIER) cc_final: 0.7452 (mp0) REVERT: C 320 MET cc_start: 0.9038 (ttp) cc_final: 0.8715 (tmm) REVERT: D 107 ASN cc_start: 0.8406 (p0) cc_final: 0.8122 (p0) REVERT: E 28 LYS cc_start: 0.8886 (ptmm) cc_final: 0.8415 (ttpt) REVERT: E 74 PHE cc_start: 0.8622 (m-80) cc_final: 0.8379 (m-80) REVERT: E 78 ASP cc_start: 0.7032 (t0) cc_final: 0.6567 (t0) REVERT: E 97 PHE cc_start: 0.7604 (m-80) cc_final: 0.7099 (m-80) REVERT: E 98 MET cc_start: 0.8632 (ttt) cc_final: 0.8408 (ttt) outliers start: 37 outliers final: 30 residues processed: 164 average time/residue: 0.0793 time to fit residues: 17.1157 Evaluate side-chains 163 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 131 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ASN Chi-restraints excluded: chain A residue 12 GLU Chi-restraints excluded: chain A residue 16 CYS Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain B residue 15 CYS Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 19 MET Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 184 TYR Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 221 TYR Chi-restraints excluded: chain C residue 227 ASP Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 283 GLU Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain D residue 84 CYS Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 111 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 30 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 50 optimal weight: 0.9980 chunk 29 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 chunk 45 optimal weight: 5.9990 chunk 2 optimal weight: 0.7980 chunk 43 optimal weight: 0.6980 chunk 34 optimal weight: 0.9990 chunk 28 optimal weight: 0.6980 chunk 31 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 5 ASN ** C 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 135 HIS C 256 ASN ** D 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.179375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.115676 restraints weight = 8314.818| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 3.75 r_work: 0.3284 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.3706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 6296 Z= 0.156 Angle : 0.659 10.510 8561 Z= 0.332 Chirality : 0.047 0.170 934 Planarity : 0.004 0.043 1103 Dihedral : 6.333 55.232 834 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 4.69 % Allowed : 18.35 % Favored : 76.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -0.99 (0.31), residues: 760 helix: 0.53 (0.58), residues: 87 sheet: -0.99 (0.29), residues: 318 loop : -0.44 (0.33), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 52 TYR 0.011 0.001 TYR B 58 PHE 0.025 0.001 PHE C 113 TRP 0.006 0.001 TRP C 257 HIS 0.006 0.001 HIS A 34 Details of bonding type rmsd covalent geometry : bond 0.00379 ( 6273) covalent geometry : angle 0.63825 ( 8515) SS BOND : bond 0.00335 ( 23) SS BOND : angle 2.33557 ( 46) hydrogen bonds : bond 0.03249 ( 160) hydrogen bonds : angle 5.57071 ( 405) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 138 time to evaluate : 0.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 GLN cc_start: 0.7785 (mt0) cc_final: 0.7049 (mt0) REVERT: A 99 GLU cc_start: 0.7519 (mm-30) cc_final: 0.6928 (mm-30) REVERT: A 104 MET cc_start: 0.8278 (tpp) cc_final: 0.8041 (tpp) REVERT: A 105 ILE cc_start: 0.8841 (mt) cc_final: 0.8535 (mp) REVERT: B 13 LYS cc_start: 0.8357 (tptp) cc_final: 0.8005 (mttp) REVERT: B 15 CYS cc_start: 0.7182 (OUTLIER) cc_final: 0.6678 (t) REVERT: C 132 GLU cc_start: 0.8945 (tp30) cc_final: 0.8449 (tt0) REVERT: C 195 GLU cc_start: 0.8671 (mt-10) cc_final: 0.7987 (mm-30) REVERT: C 231 ASP cc_start: 0.8251 (m-30) cc_final: 0.7702 (m-30) REVERT: C 256 ASN cc_start: 0.9041 (OUTLIER) cc_final: 0.8804 (t0) REVERT: C 263 ASP cc_start: 0.8471 (m-30) cc_final: 0.7794 (t0) REVERT: C 283 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.7515 (mp0) REVERT: C 320 MET cc_start: 0.8874 (ttp) cc_final: 0.8593 (tmm) REVERT: D 27 GLN cc_start: 0.8084 (pt0) cc_final: 0.7831 (pm20) REVERT: D 31 MET cc_start: 0.8168 (mmm) cc_final: 0.7945 (tmm) REVERT: D 107 ASN cc_start: 0.8471 (p0) cc_final: 0.8195 (p0) REVERT: E 28 LYS cc_start: 0.8817 (ptmm) cc_final: 0.8339 (ttpp) REVERT: E 45 GLU cc_start: 0.7576 (mt-10) cc_final: 0.7158 (mp0) REVERT: E 78 ASP cc_start: 0.7077 (t0) cc_final: 0.6716 (t0) REVERT: E 97 PHE cc_start: 0.7574 (m-80) cc_final: 0.6993 (m-80) outliers start: 33 outliers final: 29 residues processed: 161 average time/residue: 0.0807 time to fit residues: 17.2463 Evaluate side-chains 166 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 134 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ASN Chi-restraints excluded: chain A residue 12 GLU Chi-restraints excluded: chain A residue 16 CYS Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain B residue 15 CYS Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 19 MET Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 184 TYR Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 221 TYR Chi-restraints excluded: chain C residue 227 ASP Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 256 ASN Chi-restraints excluded: chain C residue 283 GLU Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain D residue 84 CYS Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 99 CYS Chi-restraints excluded: chain E residue 111 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 63 optimal weight: 9.9990 chunk 66 optimal weight: 0.5980 chunk 5 optimal weight: 0.8980 chunk 31 optimal weight: 0.8980 chunk 4 optimal weight: 4.9990 chunk 19 optimal weight: 0.5980 chunk 58 optimal weight: 9.9990 chunk 3 optimal weight: 0.9980 chunk 67 optimal weight: 3.9990 chunk 61 optimal weight: 10.0000 chunk 50 optimal weight: 8.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 5 ASN ** C 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 135 HIS C 256 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.179716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.116420 restraints weight = 8329.266| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 3.73 r_work: 0.3291 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.3831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6296 Z= 0.149 Angle : 0.652 8.768 8561 Z= 0.329 Chirality : 0.046 0.144 934 Planarity : 0.004 0.041 1103 Dihedral : 6.216 55.663 834 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 4.27 % Allowed : 19.77 % Favored : 75.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: -1.03 (0.30), residues: 760 helix: 0.57 (0.58), residues: 87 sheet: -1.09 (0.30), residues: 300 loop : -0.47 (0.31), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 52 TYR 0.010 0.001 TYR B 58 PHE 0.025 0.001 PHE C 113 TRP 0.005 0.001 TRP C 257 HIS 0.006 0.001 HIS A 34 Details of bonding type rmsd covalent geometry : bond 0.00356 ( 6273) covalent geometry : angle 0.63957 ( 8515) SS BOND : bond 0.00311 ( 23) SS BOND : angle 1.82792 ( 46) hydrogen bonds : bond 0.03233 ( 160) hydrogen bonds : angle 5.53292 ( 405) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 135 time to evaluate : 0.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 GLN cc_start: 0.7797 (mt0) cc_final: 0.7051 (mt0) REVERT: A 99 GLU cc_start: 0.7499 (mm-30) cc_final: 0.6903 (mm-30) REVERT: A 104 MET cc_start: 0.8312 (tpp) cc_final: 0.8082 (tpp) REVERT: A 105 ILE cc_start: 0.8859 (mt) cc_final: 0.8565 (mp) REVERT: B 15 CYS cc_start: 0.7191 (OUTLIER) cc_final: 0.6698 (t) REVERT: C 132 GLU cc_start: 0.8946 (tp30) cc_final: 0.8452 (tt0) REVERT: C 195 GLU cc_start: 0.8653 (mt-10) cc_final: 0.7997 (mm-30) REVERT: C 231 ASP cc_start: 0.8209 (m-30) cc_final: 0.7673 (m-30) REVERT: C 263 ASP cc_start: 0.8400 (m-30) cc_final: 0.7724 (t0) REVERT: C 283 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7521 (mp0) REVERT: C 320 MET cc_start: 0.8842 (ttp) cc_final: 0.8578 (tmm) REVERT: D 27 GLN cc_start: 0.8025 (pt0) cc_final: 0.7782 (pm20) REVERT: D 31 MET cc_start: 0.8162 (mmm) cc_final: 0.7781 (tpt) REVERT: D 98 MET cc_start: 0.8387 (ppp) cc_final: 0.7752 (ttp) REVERT: D 107 ASN cc_start: 0.8478 (p0) cc_final: 0.8202 (p0) REVERT: E 28 LYS cc_start: 0.8826 (ptmm) cc_final: 0.8446 (ttpt) REVERT: E 45 GLU cc_start: 0.7426 (mt-10) cc_final: 0.7053 (mp0) REVERT: E 78 ASP cc_start: 0.7050 (t0) cc_final: 0.6812 (t0) REVERT: E 97 PHE cc_start: 0.7673 (m-80) cc_final: 0.7114 (m-80) outliers start: 30 outliers final: 26 residues processed: 156 average time/residue: 0.0841 time to fit residues: 17.3487 Evaluate side-chains 162 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 134 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 GLU Chi-restraints excluded: chain A residue 16 CYS Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain B residue 15 CYS Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 19 MET Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 184 TYR Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 221 TYR Chi-restraints excluded: chain C residue 227 ASP Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 256 ASN Chi-restraints excluded: chain C residue 283 GLU Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain D residue 84 CYS Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 99 CYS Chi-restraints excluded: chain E residue 111 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 22 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 50 optimal weight: 4.9990 chunk 62 optimal weight: 5.9990 chunk 69 optimal weight: 0.7980 chunk 43 optimal weight: 0.0870 chunk 42 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 71 optimal weight: 0.0670 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 5 ASN ** C 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 135 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.180865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.118124 restraints weight = 8253.407| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 3.72 r_work: 0.3307 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 moved from start: 0.3901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6296 Z= 0.129 Angle : 0.636 8.393 8561 Z= 0.319 Chirality : 0.046 0.135 934 Planarity : 0.004 0.038 1103 Dihedral : 6.161 56.056 834 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 3.98 % Allowed : 19.91 % Favored : 76.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: -1.04 (0.30), residues: 760 helix: 0.61 (0.58), residues: 87 sheet: -1.09 (0.29), residues: 302 loop : -0.48 (0.32), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 52 TYR 0.011 0.001 TYR C 312 PHE 0.025 0.001 PHE C 113 TRP 0.005 0.001 TRP C 139 HIS 0.007 0.001 HIS A 34 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 6273) covalent geometry : angle 0.62579 ( 8515) SS BOND : bond 0.00274 ( 23) SS BOND : angle 1.66252 ( 46) hydrogen bonds : bond 0.03130 ( 160) hydrogen bonds : angle 5.46612 ( 405) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1939.10 seconds wall clock time: 33 minutes 51.48 seconds (2031.48 seconds total)