Starting phenix.real_space_refine on Sun Apr 7 01:37:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wuj_32837/04_2024/7wuj_32837.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wuj_32837/04_2024/7wuj_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wuj_32837/04_2024/7wuj_32837.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wuj_32837/04_2024/7wuj_32837.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wuj_32837/04_2024/7wuj_32837.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wuj_32837/04_2024/7wuj_32837.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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 Residue "A ARG 385": "NH1" <-> "NH2" Residue "B TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 283": "NH1" <-> "NH2" Residue "S GLU 46": "OE1" <-> "OE2" Residue "N ARG 19": "NH1" <-> "NH2" Residue "N ARG 38": "NH1" <-> "NH2" Residue "N ARG 72": "NH1" <-> "NH2" Residue "N ARG 98": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/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: {'GLN:plan1': 2, 'ASP:plan': 16, 'TYR:plan': 3, 'ASN:plan1': 4, 'HIS:plan': 1, 'GLU:plan': 10, 'ARG:plan': 9} 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: {'GLN:plan1': 4, 'TYR:plan': 1, 'ASN:plan1': 5, 'ASP:plan': 22, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 13} 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: {'GLN:plan1': 2, 'ASP:plan': 4, 'TYR:plan': 1, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 3, 'ARG: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, 'ASN:plan1': 2, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 4} 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, 'GLU:plan': 6, 'ARG:plan': 3, '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, 'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 48 Time building chain proxies: 5.34, per 1000 atoms: 0.62 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 - 3.50 Amino acid : False - 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: 3.67 Conformation dependent library (CDL) restraints added in 2.2 seconds 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: 1.25 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: 3.06 Time building geometry restraints manager: 3.90 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: 99.57 - 106.49: 225 106.49 - 113.42: 4822 113.42 - 120.34: 3122 120.34 - 127.26: 3713 127.26 - 134.19: 109 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 2.440 nonbonded pdb=" OH TYR E2765 " pdb=" O HIS E2986 " model vdw 2.223 2.440 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 2.440 nonbonded pdb=" O ASN E2782 " pdb=" NE1 TRP E2826 " model vdw 2.264 2.520 ... (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 ========== 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: 0.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.000 Extract box with map and model: 1.080 Check model and map are aligned: 0.140 Set scattering table: 0.080 Process input model: 30.350 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.230 ------------------------------------------------------------------------------- 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 8785 Z= 0.474 Angle : 1.004 9.048 11991 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 : 18.92 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.019 0.003 TRP A 234 HIS 0.024 0.003 HIS A 220 PHE 0.029 0.003 PHE B 235 TYR 0.036 0.003 TYR S 235 ARG 0.010 0.001 ARG B 314 *********************** 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 fitting. rotamer outliers: 4 poor density : 258 time to evaluate : 0.935 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: 0.7512 (mtpp) REVERT: A 342 ARG cc_start: 0.8184 (tmm-80) cc_final: 0.7980 (tmm-80) REVERT: A 381 ASP cc_start: 0.8126 (t0) cc_final: 0.7782 (t70) REVERT: B 45 MET cc_start: 0.6625 (ttm) cc_final: 0.6378 (ttm) REVERT: B 264 TYR cc_start: 0.7393 (m-80) cc_final: 0.6792 (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: 0.8427 (m110) REVERT: S 21 SER cc_start: 0.7566 (t) cc_final: 0.7156 (t) REVERT: S 47 TRP cc_start: 0.7429 (t60) cc_final: 0.6987 (t60) REVERT: Y 21 MET cc_start: 0.6329 (ptt) cc_final: 0.6090 (ptt) REVERT: Y 41 CYS cc_start: 0.6650 (m) cc_final: 0.5398 (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: 0.3609 (p90) outliers start: 4 outliers final: 1 residues processed: 262 average time/residue: 0.2109 time to fit residues: 75.2680 Evaluate side-chains 211 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 210 time to evaluate : 0.910 ------------------------------------------------------------------------------- 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 99 optimal weight: 0.8980 chunk 89 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 30 optimal weight: 0.6980 chunk 60 optimal weight: 6.9990 chunk 47 optimal weight: 0.7980 chunk 92 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 56 optimal weight: 6.9990 chunk 68 optimal weight: 0.9980 chunk 107 optimal weight: 10.0000 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E2782 ASN 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7002 moved from start: 0.1992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8785 Z= 0.202 Angle : 0.596 8.871 11991 Z= 0.324 Chirality : 0.044 0.229 1434 Planarity : 0.005 0.056 1496 Dihedral : 5.732 23.108 1269 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 17.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 2.17 % Allowed : 17.77 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.13 (0.23), residues: 1171 helix: -2.26 (0.22), residues: 361 sheet: -2.53 (0.28), residues: 267 loop : -1.50 (0.27), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 82 HIS 0.004 0.001 HIS A 357 PHE 0.017 0.002 PHE B 199 TYR 0.029 0.002 TYR S 235 ARG 0.006 0.001 ARG S 38 *********************** 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 fitting. rotamer outliers: 17 poor density : 235 time to evaluate : 0.872 Fit side-chains REVERT: A 227 GLN cc_start: 0.8056 (mp10) cc_final: 0.7853 (mp10) REVERT: A 381 ASP cc_start: 0.8218 (t0) cc_final: 0.7791 (t70) REVERT: B 45 MET cc_start: 0.6538 (ttm) cc_final: 0.6172 (ttm) REVERT: B 89 LYS cc_start: 0.7776 (mttp) cc_final: 0.7067 (mttp) REVERT: B 189 SER cc_start: 0.7251 (p) cc_final: 0.7021 (t) REVERT: B 313 ASN cc_start: 0.7380 (t0) cc_final: 0.7020 (t0) REVERT: S 47 TRP cc_start: 0.7158 (t60) cc_final: 0.6853 (t60) REVERT: Y 21 MET cc_start: 0.6213 (ptt) cc_final: 0.6009 (ptt) REVERT: N 34 MET cc_start: 0.6311 (mtm) cc_final: 0.5939 (mtm) REVERT: N 117 TYR cc_start: 0.4139 (p90) cc_final: 0.3788 (p90) outliers start: 17 outliers final: 10 residues processed: 247 average time/residue: 0.1980 time to fit residues: 67.9641 Evaluate side-chains 226 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 216 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain B residue 38 ASP 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 78 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 59 optimal weight: 0.6980 chunk 33 optimal weight: 0.0170 chunk 89 optimal weight: 0.9990 chunk 72 optimal weight: 0.0870 chunk 29 optimal weight: 0.8980 chunk 107 optimal weight: 9.9990 chunk 115 optimal weight: 9.9990 chunk 95 optimal weight: 20.0000 chunk 106 optimal weight: 5.9990 chunk 36 optimal weight: 6.9990 chunk 86 optimal weight: 6.9990 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E2782 ASN E2791 ASN E2975 ASN ** E2978 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6939 moved from start: 0.2550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8785 Z= 0.170 Angle : 0.556 8.417 11991 Z= 0.299 Chirality : 0.043 0.246 1434 Planarity : 0.004 0.055 1496 Dihedral : 5.207 22.813 1268 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 17.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 3.45 % Allowed : 20.97 % Favored : 75.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.37 (0.23), residues: 1171 helix: -1.14 (0.25), residues: 365 sheet: -2.39 (0.29), residues: 260 loop : -1.29 (0.27), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.008 0.001 HIS B 142 PHE 0.025 0.002 PHE B 241 TYR 0.026 0.001 TYR S 235 ARG 0.005 0.001 ARG B 52 *********************** 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 264 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 237 time to evaluate : 0.977 Fit side-chains revert: symmetry clash REVERT: A 232 ARG cc_start: 0.8130 (ttm110) cc_final: 0.7555 (ttm170) REVERT: A 381 ASP cc_start: 0.8126 (t0) cc_final: 0.7722 (t70) REVERT: B 45 MET cc_start: 0.6252 (ttm) cc_final: 0.5979 (ttm) REVERT: B 52 ARG cc_start: 0.6976 (mtp85) cc_final: 0.6726 (mtp85) REVERT: B 99 TRP cc_start: 0.7653 (m100) cc_final: 0.7022 (m100) REVERT: B 253 PHE cc_start: 0.7815 (m-80) cc_final: 0.7484 (m-80) REVERT: E 2932 ARG cc_start: 0.4371 (ttp80) cc_final: 0.3693 (ttp80) REVERT: Y 21 MET cc_start: 0.6147 (ptt) cc_final: 0.5889 (ptt) REVERT: N 117 TYR cc_start: 0.4313 (p90) cc_final: 0.4006 (p90) outliers start: 27 outliers final: 16 residues processed: 252 average time/residue: 0.2007 time to fit residues: 70.6617 Evaluate side-chains 218 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 202 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 ASP 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 188 MET Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain E residue 2758 LEU Chi-restraints excluded: chain E residue 2762 VAL Chi-restraints excluded: chain E residue 2917 LEU Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 178 LEU Chi-restraints excluded: chain S residue 224 VAL Chi-restraints excluded: chain S residue 231 GLN Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 35 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 106 optimal weight: 6.9990 chunk 80 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 72 optimal weight: 7.9990 chunk 107 optimal weight: 3.9990 chunk 114 optimal weight: 8.9990 chunk 56 optimal weight: 2.9990 chunk 102 optimal weight: 4.9990 chunk 30 optimal weight: 0.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E2782 ASN E2817 HIS ** E2978 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7121 moved from start: 0.2654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 8785 Z= 0.339 Angle : 0.641 8.937 11991 Z= 0.341 Chirality : 0.045 0.281 1434 Planarity : 0.004 0.049 1496 Dihedral : 5.510 24.837 1268 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 20.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 6.27 % Allowed : 20.72 % Favored : 73.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.14 (0.24), residues: 1171 helix: -0.73 (0.26), residues: 363 sheet: -2.38 (0.29), residues: 268 loop : -1.21 (0.28), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 99 HIS 0.007 0.001 HIS A 387 PHE 0.020 0.002 PHE E2902 TYR 0.030 0.002 TYR S 235 ARG 0.006 0.001 ARG B 49 *********************** 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 263 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 214 time to evaluate : 0.822 Fit side-chains revert: symmetry clash REVERT: A 32 LYS cc_start: 0.8183 (ttmt) cc_final: 0.7847 (mtpt) REVERT: A 381 ASP cc_start: 0.8288 (t0) cc_final: 0.7897 (t70) REVERT: B 45 MET cc_start: 0.6657 (ttm) cc_final: 0.6407 (ttm) REVERT: B 79 LEU cc_start: 0.8477 (OUTLIER) cc_final: 0.7666 (mp) REVERT: B 111 TYR cc_start: 0.7100 (m-80) cc_final: 0.6841 (m-80) REVERT: B 253 PHE cc_start: 0.7901 (m-80) cc_final: 0.7528 (m-80) REVERT: E 2970 LEU cc_start: 0.7892 (OUTLIER) cc_final: 0.7603 (mt) REVERT: S 47 TRP cc_start: 0.7238 (t60) cc_final: 0.6846 (t60) outliers start: 49 outliers final: 39 residues processed: 244 average time/residue: 0.1968 time to fit residues: 67.1083 Evaluate side-chains 241 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 200 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 MET Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain A residue 290 PHE Chi-restraints excluded: chain A residue 311 TYR Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 110 ASN 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 329 THR 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 2795 LEU 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 2944 SER Chi-restraints excluded: chain E residue 2948 LEU Chi-restraints excluded: chain E residue 2970 LEU Chi-restraints excluded: chain S residue 21 SER Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 178 LEU Chi-restraints excluded: chain S residue 224 VAL Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain S residue 231 GLN Chi-restraints excluded: chain S residue 238 THR Chi-restraints excluded: chain Y residue 16 VAL Chi-restraints excluded: chain Y residue 31 SER Chi-restraints excluded: chain Y residue 51 LEU Chi-restraints excluded: chain Y residue 52 THR Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 71 SER 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 94 optimal weight: 9.9990 chunk 64 optimal weight: 6.9990 chunk 1 optimal weight: 0.8980 chunk 84 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 97 optimal weight: 0.9990 chunk 78 optimal weight: 0.2980 chunk 0 optimal weight: 0.9990 chunk 58 optimal weight: 8.9990 chunk 102 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E2782 ASN E2791 ASN ** E2978 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7016 moved from start: 0.2861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8785 Z= 0.213 Angle : 0.577 9.280 11991 Z= 0.308 Chirality : 0.044 0.238 1434 Planarity : 0.004 0.048 1496 Dihedral : 5.171 23.707 1268 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 18.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 5.24 % Allowed : 22.89 % Favored : 71.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.83 (0.24), residues: 1171 helix: -0.32 (0.26), residues: 364 sheet: -2.26 (0.29), residues: 265 loop : -1.13 (0.28), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 82 HIS 0.007 0.001 HIS B 142 PHE 0.020 0.002 PHE B 278 TYR 0.024 0.002 TYR S 103 ARG 0.005 0.001 ARG B 251 *********************** 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 254 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 213 time to evaluate : 1.081 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 232 ARG cc_start: 0.8398 (ttm110) cc_final: 0.7727 (ttm170) REVERT: A 381 ASP cc_start: 0.8297 (t0) cc_final: 0.7887 (t70) REVERT: B 45 MET cc_start: 0.6578 (ttm) cc_final: 0.6281 (ttm) REVERT: B 79 LEU cc_start: 0.8240 (OUTLIER) cc_final: 0.7406 (mp) REVERT: B 253 PHE cc_start: 0.7675 (m-80) cc_final: 0.7419 (m-80) REVERT: E 2855 LEU cc_start: 0.6768 (mm) cc_final: 0.6534 (mm) REVERT: E 2943 MET cc_start: 0.5795 (ttp) cc_final: 0.5392 (mtp) REVERT: S 20 LEU cc_start: 0.7363 (tp) cc_final: 0.7121 (tp) REVERT: S 47 TRP cc_start: 0.7014 (t60) cc_final: 0.6676 (t60) REVERT: S 74 ASP cc_start: 0.6595 (m-30) cc_final: 0.6191 (t0) outliers start: 41 outliers final: 28 residues processed: 236 average time/residue: 0.1994 time to fit residues: 65.6362 Evaluate side-chains 223 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 194 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 MET 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 223 ASP 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 110 ASN 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 2781 ILE Chi-restraints excluded: chain E residue 2821 LEU Chi-restraints excluded: chain E residue 2827 MET Chi-restraints excluded: chain E residue 2908 MET Chi-restraints excluded: chain E residue 2917 LEU Chi-restraints excluded: chain S residue 21 SER Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 178 LEU Chi-restraints excluded: chain S residue 224 VAL Chi-restraints excluded: chain S residue 231 GLN 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 38 optimal weight: 1.9990 chunk 102 optimal weight: 10.0000 chunk 22 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 28 optimal weight: 0.7980 chunk 114 optimal weight: 5.9990 chunk 94 optimal weight: 9.9990 chunk 52 optimal weight: 0.0980 chunk 9 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 59 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E2782 ASN E2791 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6971 moved from start: 0.3116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8785 Z= 0.190 Angle : 0.558 7.715 11991 Z= 0.298 Chirality : 0.043 0.184 1434 Planarity : 0.004 0.048 1496 Dihedral : 4.994 22.993 1268 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 17.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 6.14 % Allowed : 22.38 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.25), residues: 1171 helix: 0.06 (0.27), residues: 364 sheet: -2.13 (0.30), residues: 265 loop : -1.09 (0.28), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 82 HIS 0.005 0.001 HIS B 142 PHE 0.016 0.002 PHE S 68 TYR 0.022 0.002 TYR S 103 ARG 0.006 0.001 ARG B 52 *********************** 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 262 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 214 time to evaluate : 0.995 Fit side-chains REVERT: A 232 ARG cc_start: 0.8312 (OUTLIER) cc_final: 0.8002 (ttm170) REVERT: A 381 ASP cc_start: 0.8291 (t0) cc_final: 0.7884 (t70) REVERT: B 45 MET cc_start: 0.6523 (ttm) cc_final: 0.6249 (ttm) REVERT: B 79 LEU cc_start: 0.8168 (OUTLIER) cc_final: 0.7323 (mp) REVERT: B 234 PHE cc_start: 0.8451 (OUTLIER) cc_final: 0.7498 (m-80) REVERT: B 253 PHE cc_start: 0.7669 (m-80) cc_final: 0.7307 (m-10) REVERT: E 2851 LEU cc_start: 0.6549 (tt) cc_final: 0.5789 (mm) REVERT: E 2943 MET cc_start: 0.5686 (ttp) cc_final: 0.5369 (mtp) REVERT: S 20 LEU cc_start: 0.7319 (tp) cc_final: 0.7071 (tp) REVERT: S 34 MET cc_start: 0.7507 (mmp) cc_final: 0.7214 (mmp) REVERT: S 47 TRP cc_start: 0.6932 (t60) cc_final: 0.6562 (t60) outliers start: 48 outliers final: 37 residues processed: 239 average time/residue: 0.2068 time to fit residues: 69.8295 Evaluate side-chains 241 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 201 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 MET Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 223 ASP 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 79 LEU Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 110 ASN Chi-restraints excluded: chain B residue 146 LEU 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 2827 MET Chi-restraints excluded: chain E residue 2871 VAL Chi-restraints excluded: chain E residue 2890 ASP Chi-restraints excluded: chain E residue 2908 MET Chi-restraints excluded: chain E residue 2917 LEU Chi-restraints excluded: chain E residue 2944 SER Chi-restraints excluded: chain S residue 21 SER Chi-restraints excluded: chain S residue 78 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 231 GLN Chi-restraints excluded: chain Y residue 16 VAL Chi-restraints excluded: chain Y residue 31 SER Chi-restraints excluded: chain Y residue 52 THR 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 110 optimal weight: 6.9990 chunk 12 optimal weight: 0.0980 chunk 65 optimal weight: 4.9990 chunk 83 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 96 optimal weight: 10.0000 chunk 63 optimal weight: 0.7980 chunk 113 optimal weight: 0.0270 chunk 71 optimal weight: 3.9990 chunk 69 optimal weight: 0.5980 chunk 52 optimal weight: 10.0000 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 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E2782 ASN E2833 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6965 moved from start: 0.3281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8785 Z= 0.201 Angle : 0.562 8.043 11991 Z= 0.300 Chirality : 0.043 0.184 1434 Planarity : 0.004 0.048 1496 Dihedral : 4.906 20.902 1268 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 18.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 5.75 % Allowed : 24.04 % Favored : 70.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.25), residues: 1171 helix: 0.28 (0.28), residues: 362 sheet: -2.00 (0.30), residues: 265 loop : -1.10 (0.27), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 82 HIS 0.008 0.001 HIS B 142 PHE 0.017 0.002 PHE B 199 TYR 0.025 0.002 TYR S 103 ARG 0.007 0.001 ARG A 38 *********************** 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 250 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 205 time to evaluate : 0.908 Fit side-chains REVERT: A 232 ARG cc_start: 0.8378 (OUTLIER) cc_final: 0.8149 (ttm170) REVERT: A 381 ASP cc_start: 0.8303 (t0) cc_final: 0.7899 (t70) REVERT: B 45 MET cc_start: 0.6529 (ttm) cc_final: 0.6246 (ttm) REVERT: B 79 LEU cc_start: 0.8176 (OUTLIER) cc_final: 0.7335 (mp) REVERT: B 234 PHE cc_start: 0.8433 (OUTLIER) cc_final: 0.7485 (m-80) REVERT: B 261 LEU cc_start: 0.7542 (OUTLIER) cc_final: 0.7296 (mt) REVERT: E 2851 LEU cc_start: 0.6562 (tt) cc_final: 0.5523 (mm) REVERT: E 2855 LEU cc_start: 0.6884 (mm) cc_final: 0.6647 (mm) REVERT: E 2943 MET cc_start: 0.5699 (ttp) cc_final: 0.5417 (mtp) REVERT: S 20 LEU cc_start: 0.7208 (tp) cc_final: 0.6960 (tp) REVERT: S 47 TRP cc_start: 0.6900 (t60) cc_final: 0.6407 (t60) REVERT: S 98 ARG cc_start: 0.7677 (ttp-170) cc_final: 0.7263 (ttp80) REVERT: N 60 TYR cc_start: 0.7904 (m-80) cc_final: 0.7283 (m-80) outliers start: 45 outliers final: 35 residues processed: 230 average time/residue: 0.1944 time to fit residues: 62.3379 Evaluate side-chains 239 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 200 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 MET Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 223 ASP 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 79 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 110 ASN Chi-restraints excluded: chain B residue 146 LEU 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 261 LEU 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 2827 MET Chi-restraints excluded: chain E residue 2890 ASP Chi-restraints excluded: chain E residue 2908 MET Chi-restraints excluded: chain E residue 2917 LEU Chi-restraints excluded: chain E residue 2944 SER Chi-restraints excluded: chain E residue 2951 LEU Chi-restraints excluded: chain S residue 78 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 231 GLN Chi-restraints excluded: chain Y residue 16 VAL Chi-restraints excluded: chain Y residue 31 SER Chi-restraints excluded: chain Y residue 52 THR 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 70 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 chunk 67 optimal weight: 0.8980 chunk 34 optimal weight: 0.0980 chunk 22 optimal weight: 0.4980 chunk 72 optimal weight: 3.9990 chunk 77 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 chunk 103 optimal weight: 4.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E2782 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6947 moved from start: 0.3401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8785 Z= 0.200 Angle : 0.560 7.377 11991 Z= 0.299 Chirality : 0.043 0.194 1434 Planarity : 0.004 0.048 1496 Dihedral : 4.863 20.920 1268 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 18.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 6.01 % Allowed : 24.30 % Favored : 69.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.25), residues: 1171 helix: 0.46 (0.28), residues: 363 sheet: -1.85 (0.31), residues: 257 loop : -1.09 (0.27), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 82 HIS 0.008 0.001 HIS B 142 PHE 0.019 0.002 PHE E2902 TYR 0.021 0.002 TYR S 235 ARG 0.007 0.001 ARG A 38 *********************** 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 249 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 202 time to evaluate : 0.976 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 232 ARG cc_start: 0.8333 (OUTLIER) cc_final: 0.8079 (ttp-170) REVERT: A 381 ASP cc_start: 0.8271 (t0) cc_final: 0.7890 (t70) REVERT: B 45 MET cc_start: 0.6528 (ttm) cc_final: 0.6225 (ttm) REVERT: B 69 LEU cc_start: 0.7734 (mt) cc_final: 0.7448 (mt) REVERT: B 79 LEU cc_start: 0.8210 (OUTLIER) cc_final: 0.7213 (mp) REVERT: B 111 TYR cc_start: 0.6660 (m-80) cc_final: 0.6078 (m-10) REVERT: B 234 PHE cc_start: 0.8391 (OUTLIER) cc_final: 0.7431 (m-80) REVERT: B 261 LEU cc_start: 0.7585 (OUTLIER) cc_final: 0.7356 (mt) REVERT: E 2851 LEU cc_start: 0.6544 (tt) cc_final: 0.5454 (mm) REVERT: E 2943 MET cc_start: 0.5708 (ttp) cc_final: 0.5478 (mtp) REVERT: S 20 LEU cc_start: 0.7219 (tp) cc_final: 0.6971 (tp) REVERT: S 47 TRP cc_start: 0.6891 (t60) cc_final: 0.6322 (t60) REVERT: S 98 ARG cc_start: 0.7718 (ttp-170) cc_final: 0.7305 (ttp80) REVERT: N 60 TYR cc_start: 0.7918 (m-80) cc_final: 0.7354 (m-80) outliers start: 47 outliers final: 39 residues processed: 228 average time/residue: 0.1914 time to fit residues: 61.9317 Evaluate side-chains 240 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 197 time to evaluate : 1.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASP Chi-restraints excluded: chain A residue 25 MET Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 223 ASP 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 79 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 110 ASN Chi-restraints excluded: chain B residue 146 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 261 LEU 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 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 2944 SER Chi-restraints excluded: chain E residue 2951 LEU Chi-restraints excluded: chain S residue 78 THR 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 231 GLN Chi-restraints excluded: chain S residue 235 TYR Chi-restraints excluded: chain S residue 238 THR Chi-restraints excluded: chain Y residue 16 VAL Chi-restraints excluded: chain Y residue 31 SER Chi-restraints excluded: chain Y residue 52 THR Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 59 SER 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 108 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 63 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 32 optimal weight: 0.8980 chunk 95 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 69 optimal weight: 0.6980 chunk 112 optimal weight: 10.0000 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E2782 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6988 moved from start: 0.3439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8785 Z= 0.234 Angle : 0.582 9.245 11991 Z= 0.309 Chirality : 0.043 0.161 1434 Planarity : 0.004 0.048 1496 Dihedral : 4.946 21.484 1268 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 19.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 5.63 % Allowed : 25.70 % Favored : 68.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.25), residues: 1171 helix: 0.54 (0.28), residues: 358 sheet: -1.89 (0.30), residues: 267 loop : -1.11 (0.27), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 234 HIS 0.008 0.001 HIS B 142 PHE 0.018 0.002 PHE B 241 TYR 0.021 0.002 TYR S 235 ARG 0.006 0.001 ARG B 49 *********************** 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 245 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 201 time to evaluate : 0.938 Fit side-chains revert: symmetry clash REVERT: A 232 ARG cc_start: 0.8407 (OUTLIER) cc_final: 0.8162 (ttp-170) REVERT: A 381 ASP cc_start: 0.8257 (t0) cc_final: 0.7881 (t70) REVERT: B 45 MET cc_start: 0.6576 (ttm) cc_final: 0.6272 (ttm) REVERT: B 79 LEU cc_start: 0.8192 (OUTLIER) cc_final: 0.7339 (mp) REVERT: B 111 TYR cc_start: 0.6667 (m-80) cc_final: 0.6014 (m-80) REVERT: B 234 PHE cc_start: 0.8423 (OUTLIER) cc_final: 0.7562 (m-80) REVERT: B 261 LEU cc_start: 0.7642 (OUTLIER) cc_final: 0.7411 (mt) REVERT: B 280 LYS cc_start: 0.8833 (mtmt) cc_final: 0.8598 (mtpp) REVERT: E 2851 LEU cc_start: 0.6568 (tt) cc_final: 0.5586 (mm) REVERT: S 20 LEU cc_start: 0.7137 (tp) cc_final: 0.6906 (tp) REVERT: S 47 TRP cc_start: 0.6942 (t60) cc_final: 0.6375 (t60) REVERT: N 60 TYR cc_start: 0.7887 (m-80) cc_final: 0.7266 (m-80) outliers start: 44 outliers final: 37 residues processed: 226 average time/residue: 0.1849 time to fit residues: 59.2874 Evaluate side-chains 236 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 195 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 MET Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 223 ASP 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 79 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 110 ASN Chi-restraints excluded: chain B residue 146 LEU 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 261 LEU 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 2827 MET Chi-restraints excluded: chain E residue 2871 VAL Chi-restraints excluded: chain E residue 2890 ASP Chi-restraints excluded: chain E residue 2908 MET Chi-restraints excluded: chain E residue 2917 LEU Chi-restraints excluded: chain S residue 78 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 231 GLN Chi-restraints excluded: chain S residue 235 TYR Chi-restraints excluded: chain S residue 238 THR Chi-restraints excluded: chain Y residue 16 VAL Chi-restraints excluded: chain Y residue 31 SER Chi-restraints excluded: chain Y residue 52 THR Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 59 SER 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 68 optimal weight: 0.0270 chunk 53 optimal weight: 7.9990 chunk 77 optimal weight: 0.3980 chunk 117 optimal weight: 8.9990 chunk 108 optimal weight: 0.4980 chunk 93 optimal weight: 8.9990 chunk 9 optimal weight: 0.9980 chunk 72 optimal weight: 3.9990 chunk 57 optimal weight: 0.0010 chunk 74 optimal weight: 0.9980 chunk 99 optimal weight: 0.5980 overall best weight: 0.3044 ------------------------------------------------------------------------------- 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 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E2782 ASN Y 44 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6810 moved from start: 0.3876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8785 Z= 0.157 Angle : 0.554 8.966 11991 Z= 0.294 Chirality : 0.042 0.138 1434 Planarity : 0.004 0.050 1496 Dihedral : 4.697 19.143 1268 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 17.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 4.73 % Allowed : 26.73 % Favored : 68.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.25), residues: 1171 helix: 0.83 (0.28), residues: 361 sheet: -1.61 (0.31), residues: 263 loop : -1.24 (0.27), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 211 HIS 0.005 0.001 HIS B 142 PHE 0.017 0.001 PHE B 241 TYR 0.026 0.001 TYR S 103 ARG 0.006 0.001 ARG A 38 ********************** 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 253 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 216 time to evaluate : 0.982 Fit side-chains revert: symmetry clash REVERT: A 54 SER cc_start: 0.7393 (m) cc_final: 0.6604 (p) REVERT: A 232 ARG cc_start: 0.8037 (OUTLIER) cc_final: 0.7796 (ttm170) REVERT: A 281 TRP cc_start: 0.8083 (m100) cc_final: 0.7867 (m100) REVERT: A 381 ASP cc_start: 0.8006 (t0) cc_final: 0.7602 (t70) REVERT: B 45 MET cc_start: 0.6368 (ttm) cc_final: 0.6061 (ttm) REVERT: B 99 TRP cc_start: 0.7823 (m100) cc_final: 0.7284 (m100) REVERT: B 111 TYR cc_start: 0.6271 (m-80) cc_final: 0.5567 (m-10) REVERT: B 234 PHE cc_start: 0.8221 (OUTLIER) cc_final: 0.7321 (m-80) REVERT: B 338 ILE cc_start: 0.7890 (mt) cc_final: 0.7670 (mm) REVERT: E 2851 LEU cc_start: 0.6405 (tt) cc_final: 0.5594 (mm) REVERT: E 2917 LEU cc_start: 0.6828 (OUTLIER) cc_final: 0.6284 (tp) REVERT: E 2943 MET cc_start: 0.5469 (ttp) cc_final: 0.5075 (mtp) REVERT: S 20 LEU cc_start: 0.7214 (tp) cc_final: 0.6953 (tp) REVERT: S 34 MET cc_start: 0.7316 (mmp) cc_final: 0.7038 (mmp) REVERT: S 47 TRP cc_start: 0.6739 (t60) cc_final: 0.6154 (t60) REVERT: S 226 VAL cc_start: 0.8117 (OUTLIER) cc_final: 0.7849 (m) REVERT: Y 29 LYS cc_start: 0.7825 (ttmt) cc_final: 0.7572 (tttp) outliers start: 37 outliers final: 27 residues processed: 233 average time/residue: 0.2019 time to fit residues: 65.2948 Evaluate side-chains 231 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 200 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 MET Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 223 ASP 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 93 ILE Chi-restraints excluded: chain B residue 100 VAL 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 E residue 2758 LEU Chi-restraints excluded: chain E residue 2821 LEU Chi-restraints excluded: chain E residue 2827 MET Chi-restraints excluded: chain E residue 2890 ASP Chi-restraints excluded: chain E residue 2908 MET Chi-restraints excluded: chain E residue 2917 LEU Chi-restraints excluded: chain S residue 78 THR 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 Y residue 52 THR Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 59 SER 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 28 optimal weight: 2.9990 chunk 86 optimal weight: 10.0000 chunk 13 optimal weight: 3.9990 chunk 26 optimal weight: 20.0000 chunk 93 optimal weight: 10.0000 chunk 39 optimal weight: 0.0370 chunk 96 optimal weight: 6.9990 chunk 11 optimal weight: 0.3980 chunk 17 optimal weight: 5.9990 chunk 82 optimal weight: 8.9990 chunk 5 optimal weight: 0.0030 overall best weight: 1.4872 ------------------------------------------------------------------------------- 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 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E2782 ASN ** E2978 GLN ** 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 = 0.4202 r_free = 0.4202 target = 0.192763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.165968 restraints weight = 9534.652| |-----------------------------------------------------------------------------| r_work (start): 0.3929 rms_B_bonded: 1.67 r_work: 0.3784 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3655 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7184 moved from start: 0.3719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8785 Z= 0.259 Angle : 0.604 8.850 11991 Z= 0.320 Chirality : 0.044 0.179 1434 Planarity : 0.004 0.050 1496 Dihedral : 4.934 20.801 1268 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 20.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 4.35 % Allowed : 28.26 % Favored : 67.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.25), residues: 1171 helix: 0.68 (0.28), residues: 361 sheet: -1.63 (0.30), residues: 285 loop : -1.10 (0.28), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 82 HIS 0.006 0.001 HIS B 54 PHE 0.023 0.002 PHE A 246 TYR 0.024 0.002 TYR S 103 ARG 0.009 0.001 ARG B 49 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2350.61 seconds wall clock time: 43 minutes 46.23 seconds (2626.23 seconds total)