Starting phenix.real_space_refine on Fri Dec 8 22:31:33 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wuj_32837/12_2023/7wuj_32837.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wuj_32837/12_2023/7wuj_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_32837/12_2023/7wuj_32837.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wuj_32837/12_2023/7wuj_32837.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wuj_32837/12_2023/7wuj_32837.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wuj_32837/12_2023/7wuj_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: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 5.48, per 1000 atoms: 0.64 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: 3.72 Conformation dependent library (CDL) restraints added in 1.9 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: 1.15 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: 3.86 Time building geometry restraints manager: 4.09 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: 0.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 1.400 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 35.040 Find NCS groups from input model: 0.320 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:3.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.260 ------------------------------------------------------------------------------- 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 : 0.973 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 262 average time/residue: 0.2188 time to fit residues: 77.8921 Evaluate side-chains 211 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 210 time to evaluate : 0.937 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 0.0841 time to fit residues: 1.4922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 99 optimal weight: 0.9980 chunk 89 optimal weight: 6.9990 chunk 49 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 60 optimal weight: 7.9990 chunk 47 optimal weight: 0.8980 chunk 92 optimal weight: 0.7980 chunk 35 optimal weight: 0.3980 chunk 56 optimal weight: 6.9990 chunk 68 optimal weight: 0.9980 chunk 107 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 E2975 ASN ** E2978 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E2996 GLN S 179 GLN N 3 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6992 moved from start: 0.2002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8785 Z= 0.194 Angle : 0.595 8.902 11991 Z= 0.325 Chirality : 0.044 0.243 1434 Planarity : 0.005 0.058 1496 Dihedral : 5.759 23.078 1268 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 17.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 2.17 % Allowed : 18.29 % Favored : 79.54 % 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: -3.12 (0.23), residues: 1171 helix: -2.27 (0.22), residues: 358 sheet: -2.55 (0.28), residues: 267 loop : -1.47 (0.27), residues: 546 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 0.027 0.002 TYR S 235 ARG 0.007 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 253 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 236 time to evaluate : 1.112 Fit side-chains outliers start: 17 outliers final: 10 residues processed: 248 average time/residue: 0.2094 time to fit residues: 73.1227 Evaluate side-chains 224 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 214 time to evaluate : 1.131 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0838 time to fit residues: 2.8748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.4980 chunk 89 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 chunk 107 optimal weight: 9.9990 chunk 115 optimal weight: 9.9990 chunk 95 optimal weight: 20.0000 chunk 106 optimal weight: 4.9990 chunk 36 optimal weight: 5.9990 chunk 86 optimal weight: 9.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** E2791 ASN ** E2978 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7079 moved from start: 0.2342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8785 Z= 0.262 Angle : 0.597 7.868 11991 Z= 0.322 Chirality : 0.044 0.279 1434 Planarity : 0.004 0.054 1496 Dihedral : 5.522 24.346 1268 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 19.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 3.84 % Allowed : 20.72 % Favored : 75.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.52 (0.24), residues: 1171 helix: -1.37 (0.24), residues: 363 sheet: -2.58 (0.28), residues: 269 loop : -1.20 (0.28), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 82 HIS 0.007 0.002 HIS S 167 PHE 0.028 0.002 PHE B 241 TYR 0.029 0.002 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 244 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 214 time to evaluate : 0.897 Fit side-chains outliers start: 30 outliers final: 17 residues processed: 232 average time/residue: 0.1888 time to fit residues: 61.0667 Evaluate side-chains 208 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 191 time to evaluate : 0.875 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.0845 time to fit residues: 3.7845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 106 optimal weight: 7.9990 chunk 80 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 11 optimal weight: 6.9990 chunk 51 optimal weight: 0.0970 chunk 72 optimal weight: 10.0000 chunk 107 optimal weight: 5.9990 chunk 114 optimal weight: 30.0000 chunk 56 optimal weight: 1.9990 chunk 102 optimal weight: 9.9990 chunk 30 optimal weight: 0.7980 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2978 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7095 moved from start: 0.2607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8785 Z= 0.274 Angle : 0.603 8.360 11991 Z= 0.323 Chirality : 0.044 0.244 1434 Planarity : 0.004 0.052 1496 Dihedral : 5.407 24.611 1268 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 20.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 2.43 % Allowed : 23.27 % 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 (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: -0.82 (0.26), residues: 362 sheet: -2.45 (0.28), residues: 273 loop : -1.08 (0.28), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 82 HIS 0.005 0.001 HIS A 387 PHE 0.016 0.002 PHE B 199 TYR 0.028 0.002 TYR S 235 ARG 0.004 0.000 ARG B 251 *********************** 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 236 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 217 time to evaluate : 0.899 Fit side-chains outliers start: 19 outliers final: 9 residues processed: 229 average time/residue: 0.2007 time to fit residues: 64.0168 Evaluate side-chains 206 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 197 time to evaluate : 1.017 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0912 time to fit residues: 2.8074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9980 chunk 1 optimal weight: 2.9990 chunk 84 optimal weight: 10.0000 chunk 47 optimal weight: 0.7980 chunk 97 optimal weight: 9.9990 chunk 78 optimal weight: 0.8980 chunk 0 optimal weight: 0.9980 chunk 58 optimal weight: 9.9990 chunk 102 optimal weight: 8.9990 chunk 28 optimal weight: 0.8980 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2978 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7012 moved from start: 0.2828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8785 Z= 0.203 Angle : 0.559 6.428 11991 Z= 0.300 Chirality : 0.043 0.159 1434 Planarity : 0.004 0.053 1496 Dihedral : 5.151 21.898 1268 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 18.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 2.69 % Allowed : 24.17 % Favored : 73.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.80 (0.24), residues: 1171 helix: -0.33 (0.26), residues: 362 sheet: -2.27 (0.29), residues: 271 loop : -1.04 (0.28), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 82 HIS 0.006 0.001 HIS B 142 PHE 0.016 0.002 PHE B 199 TYR 0.024 0.002 TYR S 103 ARG 0.004 0.000 ARG S 38 *********************** 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 237 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 216 time to evaluate : 0.962 Fit side-chains outliers start: 21 outliers final: 12 residues processed: 231 average time/residue: 0.1921 time to fit residues: 62.4468 Evaluate side-chains 211 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 199 time to evaluate : 0.904 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.0889 time to fit residues: 3.2030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 38 optimal weight: 0.9990 chunk 102 optimal weight: 9.9990 chunk 22 optimal weight: 0.8980 chunk 66 optimal weight: 0.8980 chunk 28 optimal weight: 8.9990 chunk 114 optimal weight: 9.9990 chunk 94 optimal weight: 9.9990 chunk 52 optimal weight: 8.9990 chunk 9 optimal weight: 0.2980 chunk 37 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 0.6968 moved from start: 0.3114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8785 Z= 0.196 Angle : 0.560 6.780 11991 Z= 0.299 Chirality : 0.043 0.162 1434 Planarity : 0.004 0.054 1496 Dihedral : 5.001 21.238 1268 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 18.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 2.17 % Allowed : 24.30 % Favored : 73.53 % 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: -1.55 (0.25), residues: 1171 helix: 0.01 (0.27), residues: 361 sheet: -2.02 (0.30), residues: 264 loop : -1.10 (0.28), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.006 0.001 HIS B 142 PHE 0.018 0.001 PHE B 199 TYR 0.024 0.002 TYR S 103 ARG 0.006 0.000 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 227 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 210 time to evaluate : 1.028 Fit side-chains outliers start: 17 outliers final: 9 residues processed: 221 average time/residue: 0.2037 time to fit residues: 62.8350 Evaluate side-chains 204 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 195 time to evaluate : 0.895 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0918 time to fit residues: 2.8429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 5.9990 chunk 65 optimal weight: 3.9990 chunk 83 optimal weight: 0.1980 chunk 64 optimal weight: 3.9990 chunk 96 optimal weight: 0.0060 chunk 63 optimal weight: 0.8980 chunk 113 optimal weight: 0.0070 chunk 71 optimal weight: 6.9990 chunk 69 optimal weight: 0.6980 chunk 52 optimal weight: 5.9990 overall best weight: 0.3614 ------------------------------------------------------------------------------- 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** E2782 ASN E2833 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6870 moved from start: 0.3486 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= 0.168 Angle : 0.538 6.303 11991 Z= 0.290 Chirality : 0.042 0.156 1434 Planarity : 0.004 0.056 1496 Dihedral : 4.818 20.704 1268 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 16.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 1.92 % Allowed : 26.34 % Favored : 71.74 % 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: -1.34 (0.25), residues: 1171 helix: 0.39 (0.28), residues: 360 sheet: -1.88 (0.30), residues: 265 loop : -1.14 (0.27), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 82 HIS 0.006 0.001 HIS B 142 PHE 0.015 0.001 PHE E2902 TYR 0.017 0.001 TYR S 103 ARG 0.006 0.001 ARG B 52 *********************** 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 229 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 214 time to evaluate : 1.031 Fit side-chains outliers start: 15 outliers final: 7 residues processed: 222 average time/residue: 0.1946 time to fit residues: 60.9478 Evaluate side-chains 200 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 193 time to evaluate : 0.906 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1006 time to fit residues: 2.5919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 5.9990 chunk 67 optimal weight: 0.8980 chunk 34 optimal weight: 0.2980 chunk 22 optimal weight: 1.9990 chunk 72 optimal weight: 9.9990 chunk 77 optimal weight: 0.9990 chunk 56 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 103 optimal weight: 8.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- 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 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6993 moved from start: 0.3402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8785 Z= 0.261 Angle : 0.597 7.900 11991 Z= 0.318 Chirality : 0.044 0.160 1434 Planarity : 0.004 0.052 1496 Dihedral : 5.022 21.514 1268 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 20.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 1.79 % Allowed : 26.98 % 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 (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: -1.30 (0.25), residues: 1171 helix: 0.38 (0.27), residues: 362 sheet: -1.84 (0.30), residues: 264 loop : -1.11 (0.28), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 82 HIS 0.006 0.001 HIS B 54 PHE 0.037 0.002 PHE B 241 TYR 0.027 0.002 TYR S 103 ARG 0.007 0.001 ARG B 49 *********************** 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 216 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 202 time to evaluate : 0.990 Fit side-chains outliers start: 14 outliers final: 10 residues processed: 212 average time/residue: 0.1957 time to fit residues: 58.5264 Evaluate side-chains 197 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 187 time to evaluate : 0.962 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0927 time to fit residues: 2.9275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 5.9990 chunk 99 optimal weight: 9.9990 chunk 105 optimal weight: 0.0470 chunk 63 optimal weight: 3.9990 chunk 46 optimal weight: 6.9990 chunk 83 optimal weight: 6.9990 chunk 32 optimal weight: 0.9990 chunk 95 optimal weight: 4.9990 chunk 100 optimal weight: 20.0000 chunk 69 optimal weight: 2.9990 chunk 112 optimal weight: 10.0000 overall best weight: 2.6086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2782 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2978 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7113 moved from start: 0.3303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 8785 Z= 0.378 Angle : 0.668 7.917 11991 Z= 0.354 Chirality : 0.046 0.180 1434 Planarity : 0.004 0.050 1496 Dihedral : 5.472 22.549 1268 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 23.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 1.28 % Allowed : 27.88 % 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 (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: -1.51 (0.25), residues: 1171 helix: 0.08 (0.27), residues: 364 sheet: -1.94 (0.30), residues: 267 loop : -1.13 (0.28), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 234 HIS 0.007 0.002 HIS A 387 PHE 0.041 0.003 PHE B 241 TYR 0.033 0.002 TYR S 103 ARG 0.008 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 195 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 185 time to evaluate : 0.936 Fit side-chains outliers start: 10 outliers final: 3 residues processed: 191 average time/residue: 0.2059 time to fit residues: 54.6898 Evaluate side-chains 180 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 177 time to evaluate : 0.984 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0967 time to fit residues: 1.8404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 68 optimal weight: 0.7980 chunk 53 optimal weight: 6.9990 chunk 77 optimal weight: 0.5980 chunk 117 optimal weight: 5.9990 chunk 108 optimal weight: 0.9990 chunk 93 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 72 optimal weight: 9.9990 chunk 57 optimal weight: 0.6980 chunk 74 optimal weight: 0.9990 chunk 99 optimal weight: 0.0060 overall best weight: 0.6198 ------------------------------------------------------------------------------- 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** ** E2782 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2978 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 44 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6923 moved from start: 0.3582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8785 Z= 0.205 Angle : 0.585 7.547 11991 Z= 0.311 Chirality : 0.044 0.178 1434 Planarity : 0.004 0.050 1496 Dihedral : 5.116 29.436 1268 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 19.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 0.77 % Allowed : 29.54 % 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: -1.24 (0.25), residues: 1171 helix: 0.39 (0.28), residues: 364 sheet: -1.68 (0.31), residues: 258 loop : -1.13 (0.27), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 63 HIS 0.005 0.001 HIS S 35 PHE 0.033 0.002 PHE B 241 TYR 0.025 0.002 TYR S 103 ARG 0.006 0.001 ARG B 49 ********************** 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 198 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 192 time to evaluate : 0.977 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 195 average time/residue: 0.2027 time to fit residues: 56.1118 Evaluate side-chains 190 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 187 time to evaluate : 1.075 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1164 time to fit residues: 1.9745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 28 optimal weight: 5.9990 chunk 86 optimal weight: 7.9990 chunk 13 optimal weight: 0.5980 chunk 26 optimal weight: 20.0000 chunk 93 optimal weight: 3.9990 chunk 39 optimal weight: 0.2980 chunk 96 optimal weight: 10.0000 chunk 11 optimal weight: 0.0070 chunk 17 optimal weight: 3.9990 chunk 82 optimal weight: 0.0980 chunk 5 optimal weight: 6.9990 overall best weight: 1.0000 ------------------------------------------------------------------------------- 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 110 ASN ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2782 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2978 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 44 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.191343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.160544 restraints weight = 9586.101| |-----------------------------------------------------------------------------| r_work (start): 0.3879 rms_B_bonded: 1.87 r_work: 0.3769 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3634 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7125 moved from start: 0.3673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8785 Z= 0.231 Angle : 0.594 8.705 11991 Z= 0.315 Chirality : 0.044 0.173 1434 Planarity : 0.004 0.051 1496 Dihedral : 5.095 27.185 1268 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 21.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 1.02 % Allowed : 29.41 % Favored : 69.57 % 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: -1.19 (0.25), residues: 1171 helix: 0.50 (0.28), residues: 364 sheet: -1.61 (0.30), residues: 278 loop : -1.14 (0.28), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 82 HIS 0.005 0.001 HIS B 142 PHE 0.034 0.002 PHE B 241 TYR 0.029 0.002 TYR E2876 ARG 0.005 0.001 ARG B 251 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2312.33 seconds wall clock time: 42 minutes 52.26 seconds (2572.26 seconds total)