Starting phenix.real_space_refine on Tue Mar 3 22:28:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wuj_32837/03_2026/7wuj_32837.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wuj_32837/03_2026/7wuj_32837.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wuj_32837/03_2026/7wuj_32837.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wuj_32837/03_2026/7wuj_32837.map" model { file = "/net/cci-nas-00/data/ceres_data/7wuj_32837/03_2026/7wuj_32837.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wuj_32837/03_2026/7wuj_32837.cif" } resolution = 3.3 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= 0.014 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 683 atoms to isotropic. 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 57 5.16 5 C 5545 2.51 5 N 1461 2.21 5 O 1537 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8600 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1655 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 77} Link IDs: {'PTRANS': 4, 'TRANS': 228} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 279 Unresolved non-hydrogen angles: 347 Unresolved non-hydrogen dihedrals: 223 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLU:plan': 10, 'GLN:plan1': 2, 'ASP:plan': 16, 'ARG:plan': 9, 'TYR:plan': 3, 'HIS:plan': 1, 'ASN:plan1': 4} Unresolved non-hydrogen planarities: 179 Chain: "B" Number of atoms: 2318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2318 Classifications: {'peptide': 334} Incomplete info: {'truncation_to_alanine': 66} Link IDs: {'PTRANS': 5, 'TRANS': 328} Unresolved non-hydrogen bonds: 250 Unresolved non-hydrogen angles: 312 Unresolved non-hydrogen dihedrals: 193 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ARG:plan': 13, 'GLN:plan1': 4, 'GLU:plan': 7, 'ASP:plan': 22, 'ASN:plan1': 5, 'TYR:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 203 Chain: "E" Number of atoms: 1995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 1995 Classifications: {'peptide': 267} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PTRANS': 5, 'TRANS': 261} Chain breaks: 3 Unresolved non-hydrogen bonds: 163 Unresolved non-hydrogen angles: 199 Unresolved non-hydrogen dihedrals: 138 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'ASP:plan': 4, 'GLU:plan': 3, 'GLN:plan1': 2, 'HIS:plan': 1, 'ARG:plan': 3, 'TYR:plan': 1, 'PHE:plan': 3} Unresolved non-hydrogen planarities: 77 Chain: "S" Number of atoms: 1574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1574 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PTRANS': 9, 'TRANS': 212} Chain breaks: 3 Unresolved non-hydrogen bonds: 137 Unresolved non-hydrogen angles: 167 Unresolved non-hydrogen dihedrals: 109 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 6, 'ASP:plan': 4, 'ARG:plan': 4, 'ASN:plan1': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 88 Chain: "Y" Number of atoms: 363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 363 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 58 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 3, 'GLU:plan': 6, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 50 Chain: "N" Number of atoms: 695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 695 Classifications: {'peptide': 97} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain breaks: 4 Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 83 Unresolved non-hydrogen dihedrals: 59 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 4, 'PHE:plan': 2, 'ARG:plan': 2, 'ASP:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 48 Time building chain proxies: 2.16, per 1000 atoms: 0.25 Number of scatterers: 8600 At special positions: 0 Unit cell: (94.5, 120, 112.5, 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 57 16.00 O 1537 8.00 N 1461 7.00 C 5545 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS E2809 " - pdb=" SG CYS E2886 " distance=2.04 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.03 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " distance=2.04 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.02 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: 0.65 Conformation dependent library (CDL) restraints added in 270.8 milliseconds 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2262 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 16 sheets defined 31.6% alpha, 17.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 13 through 39 removed outlier: 3.659A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 64 removed outlier: 3.757A pdb=" N LYS A 58 " --> pdb=" O SER A 54 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ARG A 61 " --> pdb=" O VAL A 57 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N HIS A 64 " --> pdb=" O MET A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 239 Processing helix chain 'A' and resid 267 through 278 Processing helix chain 'A' and resid 296 through 302 Processing helix chain 'A' and resid 312 through 316 removed outlier: 3.888A pdb=" N ALA A 316 " --> pdb=" O PRO A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 347 removed outlier: 3.540A pdb=" N ASP A 343 " --> pdb=" O TYR A 339 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE A 345 " --> pdb=" O ILE A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 removed outlier: 3.559A pdb=" N ASP A 378 " --> pdb=" O ARG A 374 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASP A 381 " --> pdb=" O ASN A 377 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ILE A 382 " --> pdb=" O ASP A 378 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ARG A 385 " --> pdb=" O ASP A 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 25 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'E' and resid 2723 through 2727 removed outlier: 3.584A pdb=" N VAL E2726 " --> pdb=" O HIS E2723 " (cutoff:3.500A) Processing helix chain 'E' and resid 2739 through 2758 removed outlier: 3.748A pdb=" N ILE E2756 " --> pdb=" O GLY E2752 " (cutoff:3.500A) Processing helix chain 'E' and resid 2758 through 2763 Processing helix chain 'E' and resid 2769 through 2773 removed outlier: 3.555A pdb=" N ARG E2772 " --> pdb=" O HIS E2769 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LYS E2773 " --> pdb=" O LYS E2770 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 2769 through 2773' Processing helix chain 'E' and resid 2774 through 2803 removed outlier: 3.691A pdb=" N ILE E2781 " --> pdb=" O ALA E2777 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA E2786 " --> pdb=" O ASN E2782 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N SER E2798 " --> pdb=" O PHE E2794 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N TRP E2799 " --> pdb=" O LEU E2795 " (cutoff:3.500A) Processing helix chain 'E' and resid 2805 through 2838 removed outlier: 3.529A pdb=" N ALA E2812 " --> pdb=" O VAL E2808 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N HIS E2817 " --> pdb=" O ALA E2813 " (cutoff:3.500A) Processing helix chain 'E' and resid 2848 through 2858 removed outlier: 3.535A pdb=" N VAL E2856 " --> pdb=" O LYS E2852 " (cutoff:3.500A) Processing helix chain 'E' and resid 2859 through 2872 removed outlier: 3.562A pdb=" N ALA E2866 " --> pdb=" O ALA E2862 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER E2870 " --> pdb=" O ALA E2866 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL E2871 " --> pdb=" O ILE E2867 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LYS E2872 " --> pdb=" O THR E2868 " (cutoff:3.500A) Processing helix chain 'E' and resid 2873 through 2877 removed outlier: 3.730A pdb=" N TYR E2876 " --> pdb=" O LYS E2873 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLY E2877 " --> pdb=" O ASP E2874 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 2873 through 2877' Processing helix chain 'E' and resid 2891 through 2896 Processing helix chain 'E' and resid 2898 through 2925 removed outlier: 3.556A pdb=" N MET E2908 " --> pdb=" O LEU E2904 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N VAL E2916 " --> pdb=" O MET E2912 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N SER E2922 " --> pdb=" O VAL E2918 " (cutoff:3.500A) Processing helix chain 'E' and resid 2935 through 2943 Processing helix chain 'E' and resid 2951 through 2953 No H-bonds generated for 'chain 'E' and resid 2951 through 2953' Processing helix chain 'E' and resid 2954 through 2960 removed outlier: 3.894A pdb=" N PHE E2958 " --> pdb=" O GLY E2954 " (cutoff:3.500A) Processing helix chain 'E' and resid 2965 through 2975 removed outlier: 3.823A pdb=" N TYR E2969 " --> pdb=" O ASN E2965 " (cutoff:3.500A) Processing helix chain 'E' and resid 2977 through 2987 Processing helix chain 'E' and resid 2992 through 2998 Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'Y' and resid 9 through 14 Processing helix chain 'Y' and resid 16 through 21 removed outlier: 4.030A pdb=" N MET Y 21 " --> pdb=" O GLU Y 17 " (cutoff:3.500A) Processing helix chain 'Y' and resid 29 through 44 removed outlier: 3.529A pdb=" N CYS Y 41 " --> pdb=" O LEU Y 37 " (cutoff:3.500A) Processing helix chain 'N' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 213 removed outlier: 3.688A pdb=" N ASP A 223 " --> pdb=" O PHE A 208 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N VAL A 224 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 8.335A pdb=" N LEU A 45 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 9.139A pdb=" N ALA A 243 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 248 through 249 Processing sheet with id=AA3, first strand: chain 'B' and resid 49 through 50 removed outlier: 3.772A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.687A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 5.235A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 148 through 153 removed outlier: 3.706A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 191 through 192 removed outlier: 3.510A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 235 removed outlier: 4.602A pdb=" N ALA B 240 " --> pdb=" O PHE B 235 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 275 Processing sheet with id=AB1, first strand: chain 'S' and resid 19 through 23 Processing sheet with id=AB2, first strand: chain 'S' and resid 59 through 60 removed outlier: 6.428A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL S 97 " --> pdb=" O HIS S 35 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N PHE S 110 " --> pdb=" O ARG S 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 92 through 94 Processing sheet with id=AB4, first strand: chain 'S' and resid 159 through 160 Processing sheet with id=AB5, first strand: chain 'S' and resid 185 through 189 removed outlier: 6.292A pdb=" N TRP S 176 " --> pdb=" O LEU S 188 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'N' and resid 3 through 5 removed outlier: 3.559A pdb=" N MET N 83 " --> pdb=" O LEU N 18 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'N' and resid 36 through 39 removed outlier: 4.321A pdb=" N VAL N 93 " --> pdb=" O GLN N 39 " (cutoff:3.500A) 349 hydrogen bonds defined for protein. 984 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: 1.51 Time building geometry restraints manager: 0.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2118 1.33 - 1.45: 2025 1.45 - 1.58: 4562 1.58 - 1.70: 0 1.70 - 1.82: 80 Bond restraints: 8785 Sorted by residual: bond pdb=" C GLN N 13 " pdb=" N PRO N 14 " ideal model delta sigma weight residual 1.330 1.372 -0.042 1.22e-02 6.72e+03 1.18e+01 bond pdb=" C THR E2825 " pdb=" O THR E2825 " ideal model delta sigma weight residual 1.237 1.208 0.028 1.19e-02 7.06e+03 5.65e+00 bond pdb=" C SER E2823 " pdb=" O SER E2823 " ideal model delta sigma weight residual 1.237 1.210 0.027 1.17e-02 7.31e+03 5.18e+00 bond pdb=" C MET E2834 " pdb=" O MET E2834 " ideal model delta sigma weight residual 1.237 1.210 0.026 1.17e-02 7.31e+03 5.03e+00 bond pdb=" CG LEU B 318 " pdb=" CD2 LEU B 318 " ideal model delta sigma weight residual 1.521 1.449 0.072 3.30e-02 9.18e+02 4.79e+00 ... (remaining 8780 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.81: 11164 1.81 - 3.62: 680 3.62 - 5.43: 109 5.43 - 7.24: 27 7.24 - 9.05: 11 Bond angle restraints: 11991 Sorted by residual: angle pdb=" C ARG A 231 " pdb=" N ARG A 232 " pdb=" CA ARG A 232 " ideal model delta sigma weight residual 120.38 127.47 -7.09 1.37e+00 5.33e-01 2.68e+01 angle pdb=" C ASN S 194 " pdb=" N LEU S 195 " pdb=" CA LEU S 195 " ideal model delta sigma weight residual 122.09 114.94 7.15 1.48e+00 4.57e-01 2.33e+01 angle pdb=" C ASP B 195 " pdb=" N THR B 196 " pdb=" CA THR B 196 " ideal model delta sigma weight residual 121.54 130.59 -9.05 1.91e+00 2.74e-01 2.24e+01 angle pdb=" C HIS B 142 " pdb=" N THR B 143 " pdb=" CA THR B 143 " ideal model delta sigma weight residual 122.46 129.01 -6.55 1.41e+00 5.03e-01 2.16e+01 angle pdb=" N HIS E2833 " pdb=" CA HIS E2833 " pdb=" C HIS E2833 " ideal model delta sigma weight residual 111.69 106.13 5.56 1.23e+00 6.61e-01 2.04e+01 ... (remaining 11986 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.72: 4593 17.72 - 35.45: 381 35.45 - 53.17: 64 53.17 - 70.89: 8 70.89 - 88.61: 3 Dihedral angle restraints: 5049 sinusoidal: 1552 harmonic: 3497 Sorted by residual: dihedral pdb=" CB CYS E2809 " pdb=" SG CYS E2809 " pdb=" SG CYS E2886 " pdb=" CB CYS E2886 " ideal model delta sinusoidal sigma weight residual 93.00 24.63 68.37 1 1.00e+01 1.00e-02 6.06e+01 dihedral pdb=" CA TRP B 82 " pdb=" C TRP B 82 " pdb=" N ASP B 83 " pdb=" CA ASP B 83 " ideal model delta harmonic sigma weight residual 180.00 153.45 26.55 0 5.00e+00 4.00e-02 2.82e+01 dihedral pdb=" CA GLY B 141 " pdb=" C GLY B 141 " pdb=" N HIS B 142 " pdb=" CA HIS B 142 " ideal model delta harmonic sigma weight residual 180.00 154.81 25.19 0 5.00e+00 4.00e-02 2.54e+01 ... (remaining 5046 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 981 0.051 - 0.102: 335 0.102 - 0.152: 91 0.152 - 0.203: 22 0.203 - 0.254: 5 Chirality restraints: 1434 Sorted by residual: chirality pdb=" CA THR E2825 " pdb=" N THR E2825 " pdb=" C THR E2825 " pdb=" CB THR E2825 " both_signs ideal model delta sigma weight residual False 2.53 2.27 0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" CA ASN S 194 " pdb=" N ASN S 194 " pdb=" C ASN S 194 " pdb=" CB ASN S 194 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" CA SER S 193 " pdb=" N SER S 193 " pdb=" C SER S 193 " pdb=" CB SER S 193 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.52e+00 ... (remaining 1431 not shown) Planarity restraints: 1496 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR S 235 " 0.051 5.00e-02 4.00e+02 7.70e-02 9.50e+00 pdb=" N PRO S 236 " -0.133 5.00e-02 4.00e+02 pdb=" CA PRO S 236 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO S 236 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE E2860 " 0.039 5.00e-02 4.00e+02 5.88e-02 5.53e+00 pdb=" N PRO E2861 " -0.102 5.00e-02 4.00e+02 pdb=" CA PRO E2861 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO E2861 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR E2775 " 0.039 5.00e-02 4.00e+02 5.82e-02 5.43e+00 pdb=" N PRO E2776 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO E2776 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO E2776 " 0.033 5.00e-02 4.00e+02 ... (remaining 1493 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1495 2.76 - 3.29: 8341 3.29 - 3.83: 15476 3.83 - 4.36: 18801 4.36 - 4.90: 30914 Nonbonded interactions: 75027 Sorted by model distance: nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.219 3.040 nonbonded pdb=" OH TYR E2765 " pdb=" O HIS E2986 " model vdw 2.223 3.040 nonbonded pdb=" O ASN E2782 " pdb=" CD1 TRP E2826 " model vdw 2.224 3.260 nonbonded pdb=" O ILE S 100 " pdb=" OG SER S 105 " model vdw 2.248 3.040 nonbonded pdb=" O ASN E2782 " pdb=" NE1 TRP E2826 " model vdw 2.264 3.120 ... (remaining 75022 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.450 Find NCS groups from input model: 0.040 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: 11.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7054 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 : 0.007 0.072 8790 Z= 0.330 Angle : 1.006 9.048 12001 Z= 0.590 Chirality : 0.057 0.254 1434 Planarity : 0.006 0.077 1496 Dihedral : 13.922 88.614 2772 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 18.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 0.51 % Allowed : 10.49 % Favored : 89.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.30 (0.21), residues: 1171 helix: -4.00 (0.15), residues: 347 sheet: -2.71 (0.29), residues: 262 loop : -1.98 (0.25), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 314 TYR 0.036 0.003 TYR S 235 PHE 0.029 0.003 PHE B 235 TRP 0.019 0.003 TRP A 234 HIS 0.024 0.003 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00716 ( 8785) covalent geometry : angle 1.00433 (11991) SS BOND : bond 0.00735 ( 5) SS BOND : angle 2.00730 ( 10) hydrogen bonds : bond 0.28143 ( 349) hydrogen bonds : angle 11.13856 ( 984) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 258 time to evaluate : 0.256 Fit side-chains revert: symmetry clash REVERT: A 21 GLU cc_start: 0.7161 (tp30) cc_final: 0.6901 (tp30) REVERT: A 28 LYS cc_start: 0.7829 (ttmm) cc_final: 0.7511 (mtpp) REVERT: A 342 ARG cc_start: 0.8184 (tmm-80) cc_final: 0.7980 (tmm-80) REVERT: A 381 ASP cc_start: 0.8127 (t0) cc_final: 0.7782 (t70) REVERT: B 45 MET cc_start: 0.6625 (ttm) cc_final: 0.6377 (ttm) REVERT: B 264 TYR cc_start: 0.7393 (m-80) cc_final: 0.6844 (m-80) REVERT: E 2943 MET cc_start: 0.5221 (ttt) cc_final: 0.4939 (ttp) REVERT: E 2975 ASN cc_start: 0.8659 (m-40) cc_final: 0.8428 (m110) REVERT: S 21 SER cc_start: 0.7566 (t) cc_final: 0.7174 (t) REVERT: S 47 TRP cc_start: 0.7429 (t60) cc_final: 0.6988 (t60) REVERT: Y 21 MET cc_start: 0.6330 (ptt) cc_final: 0.6086 (ptt) REVERT: Y 41 CYS cc_start: 0.6650 (m) cc_final: 0.5391 (m) REVERT: N 34 MET cc_start: 0.6551 (mtm) cc_final: 0.6112 (mtm) REVERT: N 117 TYR cc_start: 0.4054 (p90) cc_final: 0.3597 (p90) outliers start: 4 outliers final: 1 residues processed: 262 average time/residue: 0.0923 time to fit residues: 33.0944 Evaluate side-chains 211 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 210 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 2809 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 0.0770 chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 3.9990 chunk 113 optimal weight: 9.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.6980 chunk 117 optimal weight: 20.0000 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN B 110 ASN B 119 ASN B 220 GLN B 259 GLN ** B 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E2782 ASN E2833 HIS E2919 GLN ** E2978 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E2996 GLN S 179 GLN N 3 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.193617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.163549 restraints weight = 9582.559| |-----------------------------------------------------------------------------| r_work (start): 0.3904 rms_B_bonded: 1.86 r_work: 0.3789 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3657 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7116 moved from start: 0.2135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8790 Z= 0.137 Angle : 0.615 9.474 12001 Z= 0.334 Chirality : 0.044 0.240 1434 Planarity : 0.005 0.056 1496 Dihedral : 5.747 22.694 1269 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 15.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 2.05 % Allowed : 16.88 % Favored : 81.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.20 (0.23), residues: 1171 helix: -2.28 (0.22), residues: 363 sheet: -2.57 (0.28), residues: 267 loop : -1.56 (0.27), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG S 38 TYR 0.029 0.002 TYR S 235 PHE 0.017 0.002 PHE B 199 TRP 0.019 0.002 TRP B 82 HIS 0.004 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 8785) covalent geometry : angle 0.61285 (11991) SS BOND : bond 0.00357 ( 5) SS BOND : angle 1.96143 ( 10) hydrogen bonds : bond 0.04499 ( 349) hydrogen bonds : angle 6.74743 ( 984) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 236 time to evaluate : 0.307 Fit side-chains REVERT: A 381 ASP cc_start: 0.8704 (t0) cc_final: 0.8178 (t70) REVERT: B 45 MET cc_start: 0.6609 (ttm) cc_final: 0.6284 (ttm) REVERT: B 161 SER cc_start: 0.8426 (p) cc_final: 0.8057 (p) REVERT: E 2975 ASN cc_start: 0.8915 (m-40) cc_final: 0.8649 (m-40) REVERT: Y 21 MET cc_start: 0.6364 (ptt) cc_final: 0.6118 (ptt) REVERT: N 5 GLN cc_start: 0.6676 (mp10) cc_final: 0.6319 (mp10) REVERT: N 34 MET cc_start: 0.7139 (mtm) cc_final: 0.6646 (mtm) REVERT: N 117 TYR cc_start: 0.4369 (p90) cc_final: 0.3986 (p90) outliers start: 16 outliers final: 9 residues processed: 248 average time/residue: 0.0853 time to fit residues: 29.7049 Evaluate side-chains 215 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 206 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain E residue 2758 LEU Chi-restraints excluded: chain E residue 2781 ILE Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 84 THR Chi-restraints excluded: chain S residue 224 VAL Chi-restraints excluded: chain N residue 2 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 66 optimal weight: 4.9990 chunk 32 optimal weight: 0.5980 chunk 102 optimal weight: 1.9990 chunk 16 optimal weight: 8.9990 chunk 33 optimal weight: 0.8980 chunk 42 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 94 optimal weight: 7.9990 chunk 111 optimal weight: 5.9990 chunk 50 optimal weight: 0.3980 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS ** B 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2978 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2986 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.188805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.157427 restraints weight = 9612.998| |-----------------------------------------------------------------------------| r_work (start): 0.3830 rms_B_bonded: 1.87 r_work: 0.3715 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3579 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7199 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8790 Z= 0.177 Angle : 0.617 8.495 12001 Z= 0.332 Chirality : 0.044 0.262 1434 Planarity : 0.004 0.053 1496 Dihedral : 5.501 22.153 1268 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 16.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 3.58 % Allowed : 19.57 % Favored : 76.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.57 (0.23), residues: 1171 helix: -1.33 (0.24), residues: 363 sheet: -2.58 (0.29), residues: 264 loop : -1.33 (0.27), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 251 TYR 0.029 0.002 TYR S 235 PHE 0.029 0.002 PHE B 241 TRP 0.015 0.002 TRP B 82 HIS 0.006 0.001 HIS E2986 Details of bonding type rmsd covalent geometry : bond 0.00396 ( 8785) covalent geometry : angle 0.61402 (11991) SS BOND : bond 0.00358 ( 5) SS BOND : angle 2.28687 ( 10) hydrogen bonds : bond 0.04450 ( 349) hydrogen bonds : angle 6.14506 ( 984) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 218 time to evaluate : 0.200 Fit side-chains REVERT: A 381 ASP cc_start: 0.8700 (t0) cc_final: 0.8191 (t70) REVERT: B 45 MET cc_start: 0.6783 (ttm) cc_final: 0.6507 (ttm) REVERT: B 161 SER cc_start: 0.7884 (p) cc_final: 0.7645 (p) REVERT: B 253 PHE cc_start: 0.8322 (m-80) cc_final: 0.7720 (m-10) REVERT: E 2912 MET cc_start: 0.8160 (mmm) cc_final: 0.7941 (tpp) REVERT: E 2975 ASN cc_start: 0.8981 (m-40) cc_final: 0.8711 (m-40) REVERT: S 18 ARG cc_start: 0.7032 (OUTLIER) cc_final: 0.6630 (ttm-80) REVERT: S 137 ASP cc_start: 0.6265 (p0) cc_final: 0.6060 (p0) REVERT: Y 21 MET cc_start: 0.6184 (ptt) cc_final: 0.5864 (ptt) REVERT: N 117 TYR cc_start: 0.4817 (p90) cc_final: 0.4506 (p90) outliers start: 28 outliers final: 18 residues processed: 237 average time/residue: 0.0857 time to fit residues: 28.5294 Evaluate side-chains 222 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 203 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 290 PHE Chi-restraints excluded: chain A residue 311 TYR Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 180 PHE Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain E residue 2758 LEU Chi-restraints excluded: chain E residue 2765 TYR Chi-restraints excluded: chain E residue 2917 LEU Chi-restraints excluded: chain S residue 18 ARG Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 84 THR Chi-restraints excluded: chain S residue 178 LEU Chi-restraints excluded: chain S residue 224 VAL Chi-restraints excluded: chain N residue 2 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 11 optimal weight: 3.9990 chunk 107 optimal weight: 8.9990 chunk 82 optimal weight: 0.4980 chunk 68 optimal weight: 6.9990 chunk 20 optimal weight: 8.9990 chunk 14 optimal weight: 20.0000 chunk 45 optimal weight: 4.9990 chunk 31 optimal weight: 0.9990 chunk 72 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2978 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2986 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.188595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.157505 restraints weight = 9860.588| |-----------------------------------------------------------------------------| r_work (start): 0.3825 rms_B_bonded: 1.88 r_work: 0.3714 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3579 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7198 moved from start: 0.2698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 8790 Z= 0.179 Angle : 0.615 8.665 12001 Z= 0.329 Chirality : 0.044 0.246 1434 Planarity : 0.004 0.050 1496 Dihedral : 5.363 23.513 1268 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 16.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 4.35 % Allowed : 21.36 % Favored : 74.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.19 (0.24), residues: 1171 helix: -0.81 (0.25), residues: 365 sheet: -2.46 (0.29), residues: 262 loop : -1.21 (0.28), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 52 TYR 0.029 0.002 TYR S 235 PHE 0.019 0.002 PHE A 345 TRP 0.015 0.002 TRP B 82 HIS 0.005 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00404 ( 8785) covalent geometry : angle 0.61250 (11991) SS BOND : bond 0.00327 ( 5) SS BOND : angle 2.15610 ( 10) hydrogen bonds : bond 0.04232 ( 349) hydrogen bonds : angle 5.94497 ( 984) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 215 time to evaluate : 0.307 Fit side-chains REVERT: A 232 ARG cc_start: 0.8552 (ttm110) cc_final: 0.7819 (ttm170) REVERT: A 381 ASP cc_start: 0.8796 (t0) cc_final: 0.8341 (t70) REVERT: B 45 MET cc_start: 0.6934 (ttm) cc_final: 0.6655 (ttm) REVERT: B 159 THR cc_start: 0.8337 (m) cc_final: 0.7880 (p) REVERT: B 253 PHE cc_start: 0.8278 (m-80) cc_final: 0.7688 (m-10) REVERT: B 264 TYR cc_start: 0.7850 (m-80) cc_final: 0.7033 (m-80) REVERT: E 2912 MET cc_start: 0.8119 (mmm) cc_final: 0.7898 (tpp) REVERT: E 2970 LEU cc_start: 0.7848 (OUTLIER) cc_final: 0.7523 (mt) REVERT: E 2975 ASN cc_start: 0.8999 (m-40) cc_final: 0.8625 (m110) REVERT: S 47 TRP cc_start: 0.7584 (t60) cc_final: 0.7226 (t60) REVERT: Y 21 MET cc_start: 0.6156 (ptt) cc_final: 0.5804 (ptt) REVERT: N 117 TYR cc_start: 0.4863 (p90) cc_final: 0.4421 (p90) outliers start: 34 outliers final: 25 residues processed: 235 average time/residue: 0.0864 time to fit residues: 28.2948 Evaluate side-chains 224 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 198 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 290 PHE Chi-restraints excluded: chain A residue 311 TYR Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 180 PHE Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain E residue 2758 LEU Chi-restraints excluded: chain E residue 2765 TYR Chi-restraints excluded: chain E residue 2781 ILE Chi-restraints excluded: chain E residue 2871 VAL Chi-restraints excluded: chain E residue 2917 LEU Chi-restraints excluded: chain E residue 2944 SER Chi-restraints excluded: chain E residue 2970 LEU Chi-restraints excluded: chain S residue 21 SER Chi-restraints excluded: chain S residue 84 THR Chi-restraints excluded: chain S residue 178 LEU Chi-restraints excluded: chain S residue 210 THR Chi-restraints excluded: chain S residue 224 VAL Chi-restraints excluded: chain Y residue 16 VAL Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 93 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 9 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 64 optimal weight: 7.9990 chunk 12 optimal weight: 1.9990 chunk 113 optimal weight: 10.0000 chunk 104 optimal weight: 0.0270 chunk 3 optimal weight: 0.9980 overall best weight: 0.9040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2978 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.194121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.163738 restraints weight = 9637.004| |-----------------------------------------------------------------------------| r_work (start): 0.3893 rms_B_bonded: 1.86 r_work: 0.3781 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3645 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7152 moved from start: 0.3000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8790 Z= 0.135 Angle : 0.579 7.450 12001 Z= 0.309 Chirality : 0.043 0.186 1434 Planarity : 0.004 0.050 1496 Dihedral : 5.091 20.717 1268 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 14.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 4.73 % Allowed : 21.61 % Favored : 73.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.85 (0.24), residues: 1171 helix: -0.28 (0.27), residues: 365 sheet: -2.35 (0.29), residues: 259 loop : -1.17 (0.28), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 52 TYR 0.021 0.002 TYR S 235 PHE 0.019 0.002 PHE B 199 TRP 0.016 0.002 TRP B 82 HIS 0.006 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 8785) covalent geometry : angle 0.57599 (11991) SS BOND : bond 0.00394 ( 5) SS BOND : angle 2.03555 ( 10) hydrogen bonds : bond 0.03788 ( 349) hydrogen bonds : angle 5.65984 ( 984) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 223 time to evaluate : 0.251 Fit side-chains REVERT: A 232 ARG cc_start: 0.8550 (ttm110) cc_final: 0.8171 (ttm170) REVERT: A 381 ASP cc_start: 0.8849 (t0) cc_final: 0.8379 (t70) REVERT: B 45 MET cc_start: 0.6803 (ttm) cc_final: 0.6487 (ttm) REVERT: B 159 THR cc_start: 0.8277 (OUTLIER) cc_final: 0.7872 (p) REVERT: B 249 THR cc_start: 0.7388 (p) cc_final: 0.7001 (p) REVERT: B 253 PHE cc_start: 0.8068 (m-80) cc_final: 0.7573 (m-10) REVERT: E 2851 LEU cc_start: 0.6755 (tt) cc_final: 0.5736 (mm) REVERT: E 2895 TYR cc_start: 0.6695 (m-10) cc_final: 0.6480 (m-80) REVERT: E 2912 MET cc_start: 0.8062 (mmm) cc_final: 0.7476 (tpp) REVERT: E 2975 ASN cc_start: 0.8966 (m-40) cc_final: 0.8624 (m110) REVERT: S 47 TRP cc_start: 0.7382 (t60) cc_final: 0.6980 (t60) REVERT: S 98 ARG cc_start: 0.8298 (ttp-170) cc_final: 0.7551 (ttp-170) REVERT: Y 21 MET cc_start: 0.6069 (ptt) cc_final: 0.5747 (ptt) REVERT: N 117 TYR cc_start: 0.5107 (p90) cc_final: 0.4693 (p90) outliers start: 37 outliers final: 26 residues processed: 244 average time/residue: 0.0861 time to fit residues: 29.3092 Evaluate side-chains 227 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 200 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 311 TYR Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 180 PHE Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain E residue 2758 LEU Chi-restraints excluded: chain E residue 2765 TYR Chi-restraints excluded: chain E residue 2827 MET Chi-restraints excluded: chain E residue 2871 VAL Chi-restraints excluded: chain E residue 2917 LEU Chi-restraints excluded: chain S residue 18 ARG Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 84 THR Chi-restraints excluded: chain S residue 178 LEU Chi-restraints excluded: chain S residue 213 THR Chi-restraints excluded: chain S residue 224 VAL Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain Y residue 16 VAL Chi-restraints excluded: chain Y residue 31 SER Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 93 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 115 optimal weight: 5.9990 chunk 43 optimal weight: 1.9990 chunk 78 optimal weight: 4.9990 chunk 84 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 101 optimal weight: 3.9990 chunk 81 optimal weight: 0.0270 chunk 18 optimal weight: 0.8980 chunk 113 optimal weight: 9.9990 chunk 12 optimal weight: 5.9990 chunk 9 optimal weight: 0.5980 overall best weight: 0.9042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 110 ASN ** B 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E2817 HIS ** E2978 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 = 0.4221 r_free = 0.4221 target = 0.195177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.164887 restraints weight = 9568.889| |-----------------------------------------------------------------------------| r_work (start): 0.3905 rms_B_bonded: 1.84 r_work: 0.3794 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3659 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7111 moved from start: 0.3206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8790 Z= 0.138 Angle : 0.584 8.526 12001 Z= 0.310 Chirality : 0.044 0.291 1434 Planarity : 0.004 0.049 1496 Dihedral : 5.022 21.154 1268 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 15.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 5.12 % Allowed : 21.99 % Favored : 72.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.64 (0.25), residues: 1171 helix: 0.06 (0.27), residues: 362 sheet: -2.20 (0.30), residues: 255 loop : -1.21 (0.27), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 251 TYR 0.020 0.002 TYR S 235 PHE 0.019 0.002 PHE E2902 TRP 0.015 0.002 TRP B 82 HIS 0.006 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 8785) covalent geometry : angle 0.58112 (11991) SS BOND : bond 0.00448 ( 5) SS BOND : angle 1.96347 ( 10) hydrogen bonds : bond 0.03785 ( 349) hydrogen bonds : angle 5.52256 ( 984) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 212 time to evaluate : 0.333 Fit side-chains revert: symmetry clash REVERT: A 232 ARG cc_start: 0.8492 (OUTLIER) cc_final: 0.7554 (ttm170) REVERT: A 381 ASP cc_start: 0.8755 (t0) cc_final: 0.8232 (t70) REVERT: B 45 MET cc_start: 0.6657 (ttm) cc_final: 0.6352 (ttm) REVERT: B 111 TYR cc_start: 0.7462 (m-80) cc_final: 0.7187 (m-10) REVERT: B 126 LEU cc_start: 0.8369 (OUTLIER) cc_final: 0.8117 (mt) REVERT: B 253 PHE cc_start: 0.8004 (m-80) cc_final: 0.7586 (m-10) REVERT: E 2851 LEU cc_start: 0.6704 (tt) cc_final: 0.5701 (mm) REVERT: E 2895 TYR cc_start: 0.6522 (m-10) cc_final: 0.6298 (m-80) REVERT: E 2943 MET cc_start: 0.6271 (ttp) cc_final: 0.5229 (mmt) REVERT: E 2975 ASN cc_start: 0.9040 (m-40) cc_final: 0.8710 (m110) REVERT: S 20 LEU cc_start: 0.7491 (tp) cc_final: 0.7269 (tp) REVERT: S 47 TRP cc_start: 0.7302 (t60) cc_final: 0.6758 (t60) REVERT: S 98 ARG cc_start: 0.8194 (ttp-170) cc_final: 0.7467 (ttt180) REVERT: Y 21 MET cc_start: 0.6079 (ptt) cc_final: 0.5749 (ptt) REVERT: N 117 TYR cc_start: 0.5077 (p90) cc_final: 0.4533 (p90) outliers start: 40 outliers final: 30 residues processed: 237 average time/residue: 0.0857 time to fit residues: 28.4039 Evaluate side-chains 227 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 195 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 232 ARG Chi-restraints excluded: chain A residue 290 PHE Chi-restraints excluded: chain A residue 311 TYR Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 180 PHE Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain E residue 2758 LEU Chi-restraints excluded: chain E residue 2765 TYR Chi-restraints excluded: chain E residue 2821 LEU Chi-restraints excluded: chain E residue 2871 VAL Chi-restraints excluded: chain E residue 2908 MET Chi-restraints excluded: chain E residue 2917 LEU Chi-restraints excluded: chain S residue 18 ARG Chi-restraints excluded: chain S residue 74 ASP Chi-restraints excluded: chain S residue 84 THR Chi-restraints excluded: chain S residue 178 LEU Chi-restraints excluded: chain S residue 213 THR Chi-restraints excluded: chain S residue 224 VAL Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain S residue 235 TYR Chi-restraints excluded: chain Y residue 16 VAL Chi-restraints excluded: chain Y residue 31 SER Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 93 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 78 optimal weight: 5.9990 chunk 8 optimal weight: 0.9990 chunk 111 optimal weight: 10.0000 chunk 57 optimal weight: 6.9990 chunk 42 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 67 optimal weight: 0.0970 chunk 10 optimal weight: 0.6980 chunk 64 optimal weight: 5.9990 chunk 5 optimal weight: 20.0000 chunk 26 optimal weight: 2.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 GLN B 220 GLN ** B 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2978 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 = 0.4212 r_free = 0.4212 target = 0.194201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.163545 restraints weight = 9694.804| |-----------------------------------------------------------------------------| r_work (start): 0.3890 rms_B_bonded: 1.87 r_work: 0.3782 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3648 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7125 moved from start: 0.3312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8790 Z= 0.152 Angle : 0.608 7.694 12001 Z= 0.321 Chirality : 0.044 0.358 1434 Planarity : 0.004 0.049 1496 Dihedral : 5.012 20.611 1268 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 16.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 6.01 % Allowed : 21.61 % Favored : 72.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.55 (0.25), residues: 1171 helix: 0.16 (0.27), residues: 362 sheet: -2.12 (0.30), residues: 259 loop : -1.17 (0.27), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 68 TYR 0.021 0.002 TYR S 235 PHE 0.022 0.002 PHE E2902 TRP 0.014 0.002 TRP B 82 HIS 0.006 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 8785) covalent geometry : angle 0.60558 (11991) SS BOND : bond 0.00386 ( 5) SS BOND : angle 1.94297 ( 10) hydrogen bonds : bond 0.03827 ( 349) hydrogen bonds : angle 5.51404 ( 984) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 200 time to evaluate : 0.311 Fit side-chains revert: symmetry clash REVERT: A 232 ARG cc_start: 0.8481 (OUTLIER) cc_final: 0.7547 (ttm170) REVERT: A 381 ASP cc_start: 0.8720 (t0) cc_final: 0.8254 (t70) REVERT: B 45 MET cc_start: 0.6677 (ttm) cc_final: 0.6397 (ttm) REVERT: B 68 ARG cc_start: 0.8260 (OUTLIER) cc_final: 0.7864 (ttt-90) REVERT: B 99 TRP cc_start: 0.7757 (m100) cc_final: 0.6923 (m100) REVERT: B 111 TYR cc_start: 0.7437 (m-80) cc_final: 0.7177 (m-10) REVERT: B 126 LEU cc_start: 0.8402 (OUTLIER) cc_final: 0.8155 (mt) REVERT: B 234 PHE cc_start: 0.8551 (OUTLIER) cc_final: 0.7475 (m-80) REVERT: B 253 PHE cc_start: 0.8038 (m-80) cc_final: 0.7619 (m-10) REVERT: E 2851 LEU cc_start: 0.6820 (tt) cc_final: 0.5796 (mm) REVERT: E 2895 TYR cc_start: 0.6784 (m-10) cc_final: 0.6477 (m-80) REVERT: E 2912 MET cc_start: 0.7753 (tpp) cc_final: 0.7032 (tpp) REVERT: E 2943 MET cc_start: 0.6276 (ttp) cc_final: 0.5754 (mtp) REVERT: E 2970 LEU cc_start: 0.7775 (OUTLIER) cc_final: 0.7538 (mt) REVERT: E 2975 ASN cc_start: 0.9059 (m-40) cc_final: 0.8681 (m110) REVERT: S 20 LEU cc_start: 0.7512 (tp) cc_final: 0.7258 (tp) REVERT: S 47 TRP cc_start: 0.7320 (t60) cc_final: 0.6734 (t60) REVERT: S 98 ARG cc_start: 0.8228 (ttp-170) cc_final: 0.7407 (ttp-170) REVERT: Y 21 MET cc_start: 0.6076 (ptt) cc_final: 0.5770 (ptt) outliers start: 47 outliers final: 34 residues processed: 230 average time/residue: 0.0812 time to fit residues: 26.5728 Evaluate side-chains 233 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 194 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASP Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 232 ARG Chi-restraints excluded: chain A residue 290 PHE Chi-restraints excluded: chain A residue 311 TYR Chi-restraints excluded: chain B residue 68 ARG Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 180 PHE Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain E residue 2758 LEU Chi-restraints excluded: chain E residue 2765 TYR Chi-restraints excluded: chain E residue 2781 ILE Chi-restraints excluded: chain E residue 2821 LEU Chi-restraints excluded: chain E residue 2827 MET Chi-restraints excluded: chain E residue 2871 VAL Chi-restraints excluded: chain E residue 2908 MET Chi-restraints excluded: chain E residue 2917 LEU Chi-restraints excluded: chain E residue 2970 LEU Chi-restraints excluded: chain S residue 18 ARG Chi-restraints excluded: chain S residue 74 ASP Chi-restraints excluded: chain S residue 84 THR Chi-restraints excluded: chain S residue 178 LEU Chi-restraints excluded: chain S residue 213 THR Chi-restraints excluded: chain S residue 224 VAL Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain S residue 235 TYR Chi-restraints excluded: chain Y residue 16 VAL Chi-restraints excluded: chain Y residue 31 SER Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 93 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 111 optimal weight: 7.9990 chunk 54 optimal weight: 0.0970 chunk 30 optimal weight: 0.8980 chunk 29 optimal weight: 3.9990 chunk 56 optimal weight: 7.9990 chunk 92 optimal weight: 5.9990 chunk 44 optimal weight: 0.5980 chunk 78 optimal weight: 10.0000 chunk 68 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 8 optimal weight: 0.0770 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN ** B 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2978 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 = 0.4259 r_free = 0.4259 target = 0.198514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.173889 restraints weight = 9496.967| |-----------------------------------------------------------------------------| r_work (start): 0.4022 rms_B_bonded: 1.49 r_work: 0.3901 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3785 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7039 moved from start: 0.3641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8790 Z= 0.121 Angle : 0.583 8.196 12001 Z= 0.308 Chirality : 0.044 0.277 1434 Planarity : 0.004 0.050 1496 Dihedral : 4.824 20.847 1268 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 14.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 4.60 % Allowed : 23.27 % Favored : 72.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.38 (0.25), residues: 1171 helix: 0.42 (0.28), residues: 361 sheet: -1.85 (0.31), residues: 250 loop : -1.28 (0.27), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 68 TYR 0.021 0.001 TYR S 235 PHE 0.021 0.002 PHE A 246 TRP 0.015 0.001 TRP B 82 HIS 0.005 0.001 HIS A 41 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 8785) covalent geometry : angle 0.58082 (11991) SS BOND : bond 0.00396 ( 5) SS BOND : angle 1.91455 ( 10) hydrogen bonds : bond 0.03555 ( 349) hydrogen bonds : angle 5.39303 ( 984) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 207 time to evaluate : 0.312 Fit side-chains REVERT: A 232 ARG cc_start: 0.8396 (OUTLIER) cc_final: 0.7529 (ttm170) REVERT: A 312 PHE cc_start: 0.7789 (m-80) cc_final: 0.7577 (m-10) REVERT: A 342 ARG cc_start: 0.7908 (tmm-80) cc_final: 0.7684 (tmm-80) REVERT: A 381 ASP cc_start: 0.8542 (t0) cc_final: 0.8143 (t70) REVERT: B 45 MET cc_start: 0.6494 (ttm) cc_final: 0.6208 (ttm) REVERT: B 65 THR cc_start: 0.7227 (p) cc_final: 0.6935 (p) REVERT: B 126 LEU cc_start: 0.8276 (OUTLIER) cc_final: 0.7996 (mt) REVERT: B 234 PHE cc_start: 0.8360 (OUTLIER) cc_final: 0.7359 (m-80) REVERT: E 2851 LEU cc_start: 0.6559 (tt) cc_final: 0.5623 (mm) REVERT: E 2895 TYR cc_start: 0.6651 (m-10) cc_final: 0.6332 (m-10) REVERT: E 2975 ASN cc_start: 0.8974 (m-40) cc_final: 0.8631 (m110) REVERT: S 20 LEU cc_start: 0.7208 (tp) cc_final: 0.6996 (tp) REVERT: S 52 SER cc_start: 0.7768 (t) cc_final: 0.7501 (t) REVERT: S 98 ARG cc_start: 0.8063 (ttp-170) cc_final: 0.7376 (ttt180) REVERT: S 235 TYR cc_start: 0.5986 (OUTLIER) cc_final: 0.5699 (t80) REVERT: Y 21 MET cc_start: 0.6131 (ptt) cc_final: 0.5869 (ptt) outliers start: 36 outliers final: 24 residues processed: 229 average time/residue: 0.0855 time to fit residues: 27.5375 Evaluate side-chains 228 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 200 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 232 ARG Chi-restraints excluded: chain A residue 311 TYR Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 180 PHE Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain E residue 2758 LEU Chi-restraints excluded: chain E residue 2821 LEU Chi-restraints excluded: chain E residue 2871 VAL Chi-restraints excluded: chain E residue 2908 MET Chi-restraints excluded: chain S residue 18 ARG Chi-restraints excluded: chain S residue 74 ASP Chi-restraints excluded: chain S residue 84 THR Chi-restraints excluded: chain S residue 178 LEU Chi-restraints excluded: chain S residue 213 THR Chi-restraints excluded: chain S residue 224 VAL Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain S residue 235 TYR Chi-restraints excluded: chain Y residue 16 VAL Chi-restraints excluded: chain Y residue 31 SER Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 93 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 79 optimal weight: 0.9990 chunk 36 optimal weight: 0.0050 chunk 9 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 82 optimal weight: 10.0000 chunk 22 optimal weight: 0.7980 chunk 8 optimal weight: 0.9990 chunk 64 optimal weight: 6.9990 chunk 97 optimal weight: 8.9990 chunk 87 optimal weight: 0.5980 chunk 27 optimal weight: 3.9990 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN ** B 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN E2817 HIS ** E2978 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 = 0.4268 r_free = 0.4268 target = 0.200020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.171593 restraints weight = 9527.892| |-----------------------------------------------------------------------------| r_work (start): 0.3983 rms_B_bonded: 1.71 r_work: 0.3873 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3748 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7072 moved from start: 0.3789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8790 Z= 0.129 Angle : 0.592 8.122 12001 Z= 0.312 Chirality : 0.043 0.234 1434 Planarity : 0.004 0.050 1496 Dihedral : 4.815 20.513 1268 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 14.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 4.22 % Allowed : 24.55 % Favored : 71.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.27 (0.25), residues: 1171 helix: 0.58 (0.28), residues: 360 sheet: -1.85 (0.30), residues: 258 loop : -1.21 (0.27), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 68 TYR 0.022 0.001 TYR S 102 PHE 0.020 0.002 PHE E2902 TRP 0.016 0.002 TRP B 169 HIS 0.003 0.001 HIS A 41 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 8785) covalent geometry : angle 0.59007 (11991) SS BOND : bond 0.00406 ( 5) SS BOND : angle 1.91250 ( 10) hydrogen bonds : bond 0.03561 ( 349) hydrogen bonds : angle 5.37740 ( 984) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 208 time to evaluate : 0.306 Fit side-chains REVERT: A 232 ARG cc_start: 0.8440 (OUTLIER) cc_final: 0.7556 (ttm170) REVERT: A 381 ASP cc_start: 0.8407 (t0) cc_final: 0.7996 (t70) REVERT: B 52 ARG cc_start: 0.7164 (mtp85) cc_final: 0.6925 (mtp85) REVERT: B 65 THR cc_start: 0.7365 (p) cc_final: 0.7132 (p) REVERT: B 126 LEU cc_start: 0.8330 (OUTLIER) cc_final: 0.7924 (mt) REVERT: B 222 PHE cc_start: 0.7603 (m-80) cc_final: 0.7327 (m-80) REVERT: B 234 PHE cc_start: 0.8372 (OUTLIER) cc_final: 0.7350 (m-80) REVERT: E 2851 LEU cc_start: 0.6599 (tt) cc_final: 0.5640 (mm) REVERT: E 2895 TYR cc_start: 0.6666 (m-10) cc_final: 0.6395 (m-10) REVERT: E 2943 MET cc_start: 0.6229 (ttp) cc_final: 0.5319 (mmt) REVERT: E 2975 ASN cc_start: 0.8970 (m-40) cc_final: 0.8612 (m110) REVERT: S 20 LEU cc_start: 0.7749 (tp) cc_final: 0.7464 (tp) REVERT: S 52 SER cc_start: 0.7803 (t) cc_final: 0.7496 (t) REVERT: S 98 ARG cc_start: 0.8128 (ttp-170) cc_final: 0.7470 (ttt180) REVERT: S 100 ILE cc_start: 0.8564 (tt) cc_final: 0.8268 (tt) REVERT: S 235 TYR cc_start: 0.6080 (OUTLIER) cc_final: 0.5774 (t80) REVERT: Y 21 MET cc_start: 0.6041 (ptt) cc_final: 0.5756 (ptt) REVERT: N 60 TYR cc_start: 0.7874 (m-80) cc_final: 0.7255 (m-80) outliers start: 33 outliers final: 26 residues processed: 229 average time/residue: 0.0887 time to fit residues: 28.3298 Evaluate side-chains 226 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 196 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 ARG Chi-restraints excluded: chain A residue 311 TYR Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 180 PHE Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain E residue 2758 LEU Chi-restraints excluded: chain E residue 2781 ILE Chi-restraints excluded: chain E residue 2821 LEU Chi-restraints excluded: chain E residue 2871 VAL Chi-restraints excluded: chain E residue 2908 MET Chi-restraints excluded: chain E residue 2917 LEU Chi-restraints excluded: chain E residue 2951 LEU Chi-restraints excluded: chain S residue 18 ARG Chi-restraints excluded: chain S residue 74 ASP Chi-restraints excluded: chain S residue 84 THR Chi-restraints excluded: chain S residue 178 LEU Chi-restraints excluded: chain S residue 213 THR Chi-restraints excluded: chain S residue 224 VAL Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain S residue 235 TYR Chi-restraints excluded: chain Y residue 16 VAL Chi-restraints excluded: chain Y residue 31 SER Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 93 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 44 optimal weight: 7.9990 chunk 109 optimal weight: 9.9990 chunk 115 optimal weight: 6.9990 chunk 2 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 91 optimal weight: 7.9990 chunk 45 optimal weight: 1.9990 chunk 25 optimal weight: 20.0000 chunk 18 optimal weight: 0.9980 chunk 66 optimal weight: 0.8980 chunk 51 optimal weight: 0.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E2817 HIS ** E2978 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2986 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.194266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.164977 restraints weight = 9519.856| |-----------------------------------------------------------------------------| r_work (start): 0.3907 rms_B_bonded: 1.71 r_work: 0.3794 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3666 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7168 moved from start: 0.3710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8790 Z= 0.168 Angle : 0.630 10.343 12001 Z= 0.330 Chirality : 0.044 0.245 1434 Planarity : 0.004 0.049 1496 Dihedral : 5.016 20.380 1268 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 17.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 4.09 % Allowed : 25.06 % Favored : 70.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.32 (0.25), residues: 1171 helix: 0.51 (0.28), residues: 362 sheet: -1.95 (0.30), residues: 267 loop : -1.15 (0.28), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 373 TYR 0.022 0.002 TYR S 102 PHE 0.022 0.002 PHE B 241 TRP 0.019 0.002 TRP B 169 HIS 0.004 0.001 HIS A 387 Details of bonding type rmsd covalent geometry : bond 0.00389 ( 8785) covalent geometry : angle 0.62796 (11991) SS BOND : bond 0.00395 ( 5) SS BOND : angle 1.91012 ( 10) hydrogen bonds : bond 0.03842 ( 349) hydrogen bonds : angle 5.45357 ( 984) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 192 time to evaluate : 0.300 Fit side-chains REVERT: A 230 GLU cc_start: 0.7573 (OUTLIER) cc_final: 0.7168 (mp0) REVERT: A 232 ARG cc_start: 0.8512 (OUTLIER) cc_final: 0.8117 (ttm170) REVERT: A 381 ASP cc_start: 0.8491 (t0) cc_final: 0.8123 (t70) REVERT: B 52 ARG cc_start: 0.7289 (mtp85) cc_final: 0.6942 (mtp85) REVERT: B 111 TYR cc_start: 0.7149 (m-10) cc_final: 0.6437 (m-80) REVERT: B 126 LEU cc_start: 0.8249 (OUTLIER) cc_final: 0.7990 (mt) REVERT: B 220 GLN cc_start: 0.8048 (mt0) cc_final: 0.7508 (tt0) REVERT: B 234 PHE cc_start: 0.8442 (OUTLIER) cc_final: 0.7422 (m-80) REVERT: E 2851 LEU cc_start: 0.6963 (tt) cc_final: 0.5716 (mm) REVERT: E 2855 LEU cc_start: 0.7047 (mm) cc_final: 0.6793 (mm) REVERT: E 2895 TYR cc_start: 0.6873 (m-10) cc_final: 0.6410 (m-80) REVERT: E 2975 ASN cc_start: 0.9012 (m-40) cc_final: 0.8560 (m110) REVERT: S 20 LEU cc_start: 0.7517 (tp) cc_final: 0.7248 (tp) REVERT: S 98 ARG cc_start: 0.8163 (ttp-170) cc_final: 0.7503 (ttt180) REVERT: S 100 ILE cc_start: 0.8578 (tt) cc_final: 0.8323 (tt) REVERT: S 235 TYR cc_start: 0.6138 (OUTLIER) cc_final: 0.5810 (t80) REVERT: Y 21 MET cc_start: 0.6036 (ptt) cc_final: 0.5724 (ptt) outliers start: 32 outliers final: 23 residues processed: 212 average time/residue: 0.0862 time to fit residues: 25.6646 Evaluate side-chains 212 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 184 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 GLU Chi-restraints excluded: chain A residue 232 ARG Chi-restraints excluded: chain A residue 311 TYR Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 180 PHE Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain E residue 2758 LEU Chi-restraints excluded: chain E residue 2781 ILE Chi-restraints excluded: chain E residue 2821 LEU Chi-restraints excluded: chain E residue 2871 VAL Chi-restraints excluded: chain E residue 2908 MET Chi-restraints excluded: chain S residue 18 ARG Chi-restraints excluded: chain S residue 74 ASP Chi-restraints excluded: chain S residue 178 LEU Chi-restraints excluded: chain S residue 213 THR Chi-restraints excluded: chain S residue 224 VAL Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain S residue 235 TYR Chi-restraints excluded: chain Y residue 16 VAL Chi-restraints excluded: chain Y residue 31 SER Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 93 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 112 optimal weight: 10.0000 chunk 40 optimal weight: 8.9990 chunk 24 optimal weight: 5.9990 chunk 106 optimal weight: 9.9990 chunk 100 optimal weight: 2.9990 chunk 95 optimal weight: 0.9980 chunk 71 optimal weight: 8.9990 chunk 46 optimal weight: 0.8980 chunk 2 optimal weight: 0.6980 chunk 107 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN ** B 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E2723 HIS E2817 HIS ** E2978 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2986 HIS ** 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 = 0.4221 r_free = 0.4221 target = 0.194928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.163994 restraints weight = 9585.785| |-----------------------------------------------------------------------------| r_work (start): 0.3892 rms_B_bonded: 1.85 r_work: 0.3783 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3653 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7115 moved from start: 0.3717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8790 Z= 0.164 Angle : 0.631 12.937 12001 Z= 0.330 Chirality : 0.044 0.224 1434 Planarity : 0.004 0.048 1496 Dihedral : 5.035 20.433 1268 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 17.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 4.22 % Allowed : 24.30 % Favored : 71.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.31 (0.25), residues: 1171 helix: 0.55 (0.28), residues: 362 sheet: -1.99 (0.29), residues: 277 loop : -1.12 (0.28), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 68 TYR 0.025 0.002 TYR S 103 PHE 0.023 0.002 PHE B 241 TRP 0.018 0.002 TRP B 169 HIS 0.004 0.001 HIS A 387 Details of bonding type rmsd covalent geometry : bond 0.00382 ( 8785) covalent geometry : angle 0.62819 (11991) SS BOND : bond 0.00507 ( 5) SS BOND : angle 2.07599 ( 10) hydrogen bonds : bond 0.03815 ( 349) hydrogen bonds : angle 5.51757 ( 984) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2433.97 seconds wall clock time: 42 minutes 23.66 seconds (2543.66 seconds total)