Starting phenix.real_space_refine on Thu Feb 5 17:52:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9q2d_72160/02_2026/9q2d_72160_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9q2d_72160/02_2026/9q2d_72160.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9q2d_72160/02_2026/9q2d_72160_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9q2d_72160/02_2026/9q2d_72160_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9q2d_72160/02_2026/9q2d_72160.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9q2d_72160/02_2026/9q2d_72160.map" } resolution = 2.94 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 S 60 5.16 5 Cl 1 4.86 5 C 5939 2.51 5 N 1583 2.21 5 O 1767 1.98 5 H 9095 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18447 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 398 Classifications: {'peptide': 26} Link IDs: {'TRANS': 25} Chain: "B" Number of atoms: 5780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 5780 Classifications: {'peptide': 368} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 346} Chain breaks: 2 Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'HIS:plan': 1, 'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 12 Chain: "C" Number of atoms: 12236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 806, 12236 Classifications: {'peptide': 806} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 779} Chain breaks: 4 Unresolved non-hydrogen bonds: 151 Unresolved non-hydrogen angles: 179 Unresolved non-hydrogen dihedrals: 126 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 3, 'ARG:plan': 5, 'GLN:plan1': 4, 'TYR:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 84 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' ZN': 1, '85C': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 57 SG CYS A 147 41.751 34.177 105.189 1.00 87.27 S ATOM 98 SG CYS A 150 45.559 34.280 104.500 1.00 83.61 S ATOM 4544 SG CYS B 323 50.299 45.955 97.347 1.00188.60 S ATOM 4593 SG CYS B 326 51.142 49.037 99.467 1.00187.00 S ATOM 5590 SG CYS B 391 52.713 45.714 100.294 1.00188.75 S ATOM 5641 SG CYS B 394 49.059 46.299 100.994 1.00195.42 S Time building chain proxies: 2.40, per 1000 atoms: 0.13 Number of scatterers: 18447 At special positions: 0 Unit cell: (95.095, 95.095, 126.445, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 Cl 1 17.00 S 60 16.00 O 1767 8.00 N 1583 7.00 C 5939 6.00 H 9095 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.49 Conformation dependent library (CDL) restraints added in 485.7 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 201 " pdb="ZN ZN A 201 " - pdb=" NE2 HIS A 163 " pdb="ZN ZN A 201 " - pdb=" NE2 HIS A 167 " pdb="ZN ZN A 201 " - pdb=" SG CYS A 147 " pdb="ZN ZN A 201 " - pdb=" SG CYS A 150 " pdb=" ZN B 501 " pdb="ZN ZN B 501 " - pdb=" SG CYS B 391 " pdb="ZN ZN B 501 " - pdb=" SG CYS B 326 " pdb="ZN ZN B 501 " - pdb=" SG CYS B 394 " pdb="ZN ZN B 501 " - pdb=" SG CYS B 323 " Number of angles added : 8 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2246 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 22 sheets defined 16.8% alpha, 40.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing helix chain 'A' and resid 156 through 167 removed outlier: 3.740A pdb=" N LYS A 165 " --> pdb=" O LEU A 161 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LEU A 166 " --> pdb=" O ARG A 162 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N HIS A 167 " --> pdb=" O HIS A 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 57 removed outlier: 4.003A pdb=" N SER B 56 " --> pdb=" O SER B 52 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N HIS B 57 " --> pdb=" O LEU B 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 52 through 57' Processing helix chain 'B' and resid 58 through 61 Processing helix chain 'B' and resid 103 through 116 removed outlier: 4.049A pdb=" N GLN B 115 " --> pdb=" O ARG B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 206 removed outlier: 3.820A pdb=" N LYS B 204 " --> pdb=" O SER B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 219 through 232 Processing helix chain 'B' and resid 233 through 238 Processing helix chain 'B' and resid 241 through 246 removed outlier: 3.501A pdb=" N TYR B 245 " --> pdb=" O PRO B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 263 removed outlier: 3.974A pdb=" N GLU B 263 " --> pdb=" O LYS B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 273 removed outlier: 3.910A pdb=" N LEU B 273 " --> pdb=" O LYS B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 286 Processing helix chain 'B' and resid 291 through 301 Processing helix chain 'B' and resid 303 through 318 Processing helix chain 'B' and resid 335 through 337 No H-bonds generated for 'chain 'B' and resid 335 through 337' Processing helix chain 'C' and resid 252 through 256 removed outlier: 3.812A pdb=" N GLN C 255 " --> pdb=" O ILE C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 381 through 384 Processing helix chain 'C' and resid 985 through 990 Processing helix chain 'C' and resid 1044 through 1059 Processing helix chain 'C' and resid 1069 through 1075 Processing helix chain 'C' and resid 1091 through 1096 Processing helix chain 'C' and resid 1097 through 1099 No H-bonds generated for 'chain 'C' and resid 1097 through 1099' Processing helix chain 'C' and resid 1101 through 1109 Processing helix chain 'C' and resid 1125 through 1138 Processing sheet with id=AA1, first strand: chain 'A' and resid 145 through 146 Processing sheet with id=AA2, first strand: chain 'B' and resid 96 through 101 removed outlier: 6.150A pdb=" N VAL B 167 " --> pdb=" O GLN B 183 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N GLN B 183 " --> pdb=" O VAL B 167 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N GLN B 178 " --> pdb=" O VAL B 83 " (cutoff:3.500A) removed outlier: 14.682A pdb=" N THR B 119 " --> pdb=" O CYS B 78 " (cutoff:3.500A) removed outlier: 9.770A pdb=" N VAL B 80 " --> pdb=" O THR B 119 " (cutoff:3.500A) removed outlier: 8.412A pdb=" N ALA B 121 " --> pdb=" O VAL B 80 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N LEU B 123 " --> pdb=" O PRO B 82 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N PHE B 135 " --> pdb=" O LYS B 166 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N LYS B 166 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N THR B 137 " --> pdb=" O ARG B 164 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N ARG B 164 " --> pdb=" O THR B 137 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N ALA B 139 " --> pdb=" O ARG B 162 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ARG B 162 " --> pdb=" O ALA B 139 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N ILE B 141 " --> pdb=" O ILE B 160 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ILE B 160 " --> pdb=" O ILE B 141 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 330 through 333 removed outlier: 6.947A pdb=" N GLU B 330 " --> pdb=" O CYS B 323 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N CYS B 323 " --> pdb=" O GLU B 330 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 346 through 350 removed outlier: 7.048A pdb=" N ILE B 398 " --> pdb=" O THR B 418 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N ALA B 389 " --> pdb=" O ILE B 398 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N TRP B 400 " --> pdb=" O THR B 387 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N THR B 387 " --> pdb=" O TRP B 400 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 1004 through 1009 removed outlier: 6.631A pdb=" N GLY C1031 " --> pdb=" O ASN C1005 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N PHE C1007 " --> pdb=" O LEU C1029 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N LEU C1029 " --> pdb=" O PHE C1007 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ILE C1037 " --> pdb=" O ALA C 9 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 17 through 21 removed outlier: 5.851A pdb=" N VAL C 43 " --> pdb=" O PRO C 51 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 61 through 67 removed outlier: 3.507A pdb=" N VAL C 63 " --> pdb=" O LEU C 80 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ASN C 85 " --> pdb=" O THR C 81 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ALA C 86 " --> pdb=" O HIS C 105 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N HIS C 105 " --> pdb=" O ALA C 86 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ILE C 88 " --> pdb=" O ARG C 103 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 121 through 124 Processing sheet with id=AA9, first strand: chain 'C' and resid 163 through 169 removed outlier: 5.780A pdb=" N VAL C 164 " --> pdb=" O GLN C 183 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N GLN C 183 " --> pdb=" O VAL C 164 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 163 through 169 removed outlier: 5.780A pdb=" N VAL C 164 " --> pdb=" O GLN C 183 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N GLN C 183 " --> pdb=" O VAL C 164 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 218 through 221 Processing sheet with id=AB3, first strand: chain 'C' and resid 258 through 263 removed outlier: 6.794A pdb=" N GLY C 274 " --> pdb=" O VAL C 259 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N HIS C 261 " --> pdb=" O LEU C 272 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N LEU C 272 " --> pdb=" O HIS C 261 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N ARG C 263 " --> pdb=" O ARG C 270 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N ARG C 270 " --> pdb=" O ARG C 263 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N ARG C 279 " --> pdb=" O ASP C 275 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N LEU C 280 " --> pdb=" O LEU C 305 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ASP C 299 " --> pdb=" O GLU C 286 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N GLU C 288 " --> pdb=" O LEU C 297 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N LEU C 297 " --> pdb=" O GLU C 288 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 313 through 318 removed outlier: 3.538A pdb=" N GLY C 325 " --> pdb=" O CYS C 313 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N VAL C 321 " --> pdb=" O LEU C 317 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N LEU C 333 " --> pdb=" O MET C 350 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 361 through 365 removed outlier: 4.255A pdb=" N ASP C 361 " --> pdb=" O CYS C 378 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 720 through 727 removed outlier: 6.667A pdb=" N LEU C 736 " --> pdb=" O ARG C 722 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N ILE C 724 " --> pdb=" O GLY C 734 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N GLY C 734 " --> pdb=" O ILE C 724 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N TYR C 726 " --> pdb=" O CYS C 732 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N CYS C 732 " --> pdb=" O TYR C 726 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 720 through 727 removed outlier: 6.667A pdb=" N LEU C 736 " --> pdb=" O ARG C 722 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N ILE C 724 " --> pdb=" O GLY C 734 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N GLY C 734 " --> pdb=" O ILE C 724 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N TYR C 726 " --> pdb=" O CYS C 732 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N CYS C 732 " --> pdb=" O TYR C 726 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ASP C 795 " --> pdb=" O VAL C 801 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N VAL C 801 " --> pdb=" O ASP C 795 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N SER C 762 " --> pdb=" O ALA C 804 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N GLN C 806 " --> pdb=" O SER C 762 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N SER C 764 " --> pdb=" O GLN C 806 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 811 through 821 removed outlier: 5.453A pdb=" N ALA C 813 " --> pdb=" O ALA C 834 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ALA C 834 " --> pdb=" O ALA C 813 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N SER C 815 " --> pdb=" O GLY C 832 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N TYR C 828 " --> pdb=" O CYS C 819 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N LEU C 821 " --> pdb=" O ASN C 826 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ASN C 826 " --> pdb=" O LEU C 821 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N THR C 827 " --> pdb=" O TYR C 853 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N TYR C 853 " --> pdb=" O THR C 827 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N GLN C 852 " --> pdb=" O THR C 860 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N THR C 860 " --> pdb=" O GLN C 852 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N SER C 854 " --> pdb=" O LEU C 858 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N LEU C 858 " --> pdb=" O SER C 854 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 874 through 876 removed outlier: 5.559A pdb=" N GLU C 892 " --> pdb=" O THR C 901 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N THR C 901 " --> pdb=" O GLU C 892 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 913 through 917 removed outlier: 3.668A pdb=" N ALA C 946 " --> pdb=" O LEU C 932 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N ALA C 934 " --> pdb=" O GLU C 944 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N GLU C 944 " --> pdb=" O ALA C 934 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N LYS C 936 " --> pdb=" O PHE C 942 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N PHE C 942 " --> pdb=" O LYS C 936 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 954 through 959 removed outlier: 3.724A pdb=" N ALA C 956 " --> pdb=" O ALA C 968 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N LEU C 974 " --> pdb=" O LEU C 997 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N LEU C 997 " --> pdb=" O LEU C 974 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N VAL C 976 " --> pdb=" O VAL C 995 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 1076 through 1077 Processing sheet with id=AC4, first strand: chain 'C' and resid 1113 through 1114 375 hydrogen bonds defined for protein. 990 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: 4.55 Time building geometry restraints manager: 2.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 9069 1.03 - 1.23: 29 1.23 - 1.42: 3960 1.42 - 1.62: 5486 1.62 - 1.81: 89 Bond restraints: 18633 Sorted by residual: bond pdb=" C16 85C B 502 " pdb=" N4 85C B 502 " ideal model delta sigma weight residual 1.393 1.416 -0.023 2.00e-02 2.50e+03 1.31e+00 bond pdb=" C13 85C B 502 " pdb=" O2 85C B 502 " ideal model delta sigma weight residual 1.208 1.228 -0.020 2.00e-02 2.50e+03 1.03e+00 bond pdb=" C12 85C B 502 " pdb=" O3 85C B 502 " ideal model delta sigma weight residual 1.209 1.228 -0.019 2.00e-02 2.50e+03 8.99e-01 bond pdb=" CB LYS B 406 " pdb=" CG LYS B 406 " ideal model delta sigma weight residual 1.520 1.546 -0.026 3.00e-02 1.11e+03 7.43e-01 bond pdb=" CA ILE B 81 " pdb=" CB ILE B 81 " ideal model delta sigma weight residual 1.537 1.548 -0.010 1.29e-02 6.01e+03 6.51e-01 ... (remaining 18628 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.11: 32177 1.11 - 2.22: 1381 2.22 - 3.34: 52 3.34 - 4.45: 19 4.45 - 5.56: 3 Bond angle restraints: 33632 Sorted by residual: angle pdb=" C ASN C 885 " pdb=" CA ASN C 885 " pdb=" CB ASN C 885 " ideal model delta sigma weight residual 110.42 115.98 -5.56 1.99e+00 2.53e-01 7.80e+00 angle pdb=" CA ASN C 885 " pdb=" C ASN C 885 " pdb=" N SER C 886 " ideal model delta sigma weight residual 116.84 120.09 -3.25 1.71e+00 3.42e-01 3.62e+00 angle pdb=" C21 85C B 502 " pdb=" C16 85C B 502 " pdb=" N4 85C B 502 " ideal model delta sigma weight residual 124.33 118.86 5.47 3.00e+00 1.11e-01 3.33e+00 angle pdb=" CA PRO B 289 " pdb=" C PRO B 289 " pdb=" O PRO B 289 " ideal model delta sigma weight residual 123.16 120.54 2.62 1.49e+00 4.50e-01 3.08e+00 angle pdb=" CB LYS B 324 " pdb=" CG LYS B 324 " pdb=" CD LYS B 324 " ideal model delta sigma weight residual 111.30 114.93 -3.63 2.30e+00 1.89e-01 2.49e+00 ... (remaining 33627 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.95: 8471 20.95 - 41.91: 247 41.91 - 62.86: 73 62.86 - 83.81: 5 83.81 - 104.77: 3 Dihedral angle restraints: 8799 sinusoidal: 4744 harmonic: 4055 Sorted by residual: dihedral pdb=" C12 85C B 502 " pdb=" C10 85C B 502 " pdb=" C11 85C B 502 " pdb=" C9 85C B 502 " ideal model delta sinusoidal sigma weight residual -50.28 54.49 -104.77 1 3.00e+01 1.11e-03 1.34e+01 dihedral pdb=" C11 85C B 502 " pdb=" C10 85C B 502 " pdb=" C9 85C B 502 " pdb=" N1 85C B 502 " ideal model delta sinusoidal sigma weight residual 74.52 176.31 -101.79 1 3.00e+01 1.11e-03 1.28e+01 dihedral pdb=" C11 85C B 502 " pdb=" C10 85C B 502 " pdb=" C9 85C B 502 " pdb=" C13 85C B 502 " ideal model delta sinusoidal sigma weight residual -50.00 50.68 -100.68 1 3.00e+01 1.11e-03 1.26e+01 ... (remaining 8796 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 879 0.029 - 0.058: 400 0.058 - 0.088: 64 0.088 - 0.117: 90 0.117 - 0.146: 35 Chirality restraints: 1468 Sorted by residual: chirality pdb=" CA ILE B 81 " pdb=" N ILE B 81 " pdb=" C ILE B 81 " pdb=" CB ILE B 81 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.34e-01 chirality pdb=" CA ILE B 426 " pdb=" N ILE B 426 " pdb=" C ILE B 426 " pdb=" CB ILE B 426 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.20e-01 chirality pdb=" CA ILE C 88 " pdb=" N ILE C 88 " pdb=" C ILE C 88 " pdb=" CB ILE C 88 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.54e-01 ... (remaining 1465 not shown) Planarity restraints: 2809 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C11 85C B 502 " 0.014 2.00e-02 2.50e+03 5.68e-02 4.03e+01 pdb=" C12 85C B 502 " 0.013 2.00e-02 2.50e+03 pdb=" C13 85C B 502 " -0.068 2.00e-02 2.50e+03 pdb=" N2 85C B 502 " 0.092 2.00e-02 2.50e+03 pdb=" O3 85C B 502 " -0.052 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE B 81 " -0.023 5.00e-02 4.00e+02 3.47e-02 1.93e+00 pdb=" N PRO B 82 " 0.060 5.00e-02 4.00e+02 pdb=" CA PRO B 82 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 82 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 208 " -0.019 5.00e-02 4.00e+02 2.82e-02 1.28e+00 pdb=" N PRO B 209 " 0.049 5.00e-02 4.00e+02 pdb=" CA PRO B 209 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO B 209 " -0.016 5.00e-02 4.00e+02 ... (remaining 2806 not shown) Histogram of nonbonded interaction distances: 1.62 - 2.21: 1059 2.21 - 2.81: 38273 2.81 - 3.41: 46078 3.41 - 4.00: 63672 4.00 - 4.60: 97001 Nonbonded interactions: 246083 Sorted by model distance: nonbonded pdb=" HG SER C 256 " pdb=" OD2 ASP C 275 " model vdw 1.616 2.450 nonbonded pdb=" OD1 ASP B 265 " pdb=" H GLU B 266 " model vdw 1.654 2.450 nonbonded pdb=" OD2 ASP C 824 " pdb=" HH TYR C 828 " model vdw 1.657 2.450 nonbonded pdb=" OE1 GLU C 785 " pdb=" H GLU C 785 " model vdw 1.658 2.450 nonbonded pdb=" O GLY C 329 " pdb="HD21 ASN C 355 " model vdw 1.676 2.450 ... (remaining 246078 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.070 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 20.520 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 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 : 0.002 0.033 9546 Z= 0.089 Angle : 0.456 5.559 12941 Z= 0.236 Chirality : 0.043 0.146 1468 Planarity : 0.003 0.057 1665 Dihedral : 9.971 104.768 3475 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.39 % Allowed : 4.77 % Favored : 93.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.25), residues: 1182 helix: 1.73 (0.45), residues: 178 sheet: 0.04 (0.25), residues: 452 loop : -1.21 (0.25), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 118 TYR 0.013 0.001 TYR C 891 PHE 0.014 0.001 PHE C1030 TRP 0.008 0.001 TRP B 415 HIS 0.002 0.000 HIS A 167 Details of bonding type rmsd covalent geometry : bond 0.00192 ( 9538) covalent geometry : angle 0.45269 (12933) hydrogen bonds : bond 0.13177 ( 360) hydrogen bonds : angle 5.64235 ( 990) metal coordination : bond 0.00493 ( 8) metal coordination : angle 2.09959 ( 8) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 84 is missing expected H atoms. Skipping. Residue LEU 99 is missing expected H atoms. Skipping. Residue LEU 101 is missing expected H atoms. Skipping. Residue VAL 110 is missing expected H atoms. Skipping. Residue LEU 113 is missing expected H atoms. Skipping. Residue ILE 141 is missing expected H atoms. Skipping. Residue VAL 157 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue LYS 204 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LYS 204 is missing expected H atoms. Skipping. Residue LYS 208 is missing expected H atoms. Skipping. Residue ILE 220 is missing expected H atoms. Skipping. Residue ILE 230 is missing expected H atoms. Skipping. Residue ILE 232 is missing expected H atoms. Skipping. Residue ILE 237 is missing expected H atoms. Skipping. Residue TYR 271 is missing expected H atoms. Skipping. Residue LEU 273 is missing expected H atoms. Skipping. Residue LEU 283 is missing expected H atoms. Skipping. Residue MET 291 is missing expected H atoms. Skipping. Residue LYS 709 is missing expected H atoms. Skipping. Residue LYS 823 is missing expected H atoms. Skipping. Residue LYS 844 is missing expected H atoms. Skipping. Residue LYS 867 is missing expected H atoms. Skipping. Residue SER 981 is missing expected H atoms. Skipping. Residue MET 1120 is missing expected H atoms. Skipping. Residue LYS 1121 is missing expected H atoms. Skipping. Residue LYS 1131 is missing expected H atoms. Skipping. Evaluate side-chains 154 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 140 time to evaluate : 0.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 75 ASP cc_start: 0.8673 (m-30) cc_final: 0.8358 (p0) REVERT: B 353 HIS cc_start: 0.8904 (m90) cc_final: 0.8641 (m-70) REVERT: B 369 ASN cc_start: 0.7948 (m-40) cc_final: 0.7746 (m-40) REVERT: B 402 PHE cc_start: 0.8692 (m-80) cc_final: 0.8333 (m-80) REVERT: B 412 GLN cc_start: 0.6824 (OUTLIER) cc_final: 0.6611 (tm-30) REVERT: C 1 MET cc_start: 0.5969 (ttt) cc_final: 0.5341 (tmt) REVERT: C 38 ARG cc_start: 0.8048 (mmt180) cc_final: 0.7671 (mmp80) REVERT: C 111 ARG cc_start: 0.8954 (mmm160) cc_final: 0.8728 (mmm160) REVERT: C 117 GLU cc_start: 0.8905 (mt-10) cc_final: 0.8558 (mt-10) REVERT: C 141 LYS cc_start: 0.7378 (OUTLIER) cc_final: 0.7127 (ttmt) REVERT: C 166 ASP cc_start: 0.7535 (t0) cc_final: 0.7144 (t0) REVERT: C 198 ARG cc_start: 0.8893 (tpt-90) cc_final: 0.8255 (mmm160) REVERT: C 299 ASP cc_start: 0.8495 (t0) cc_final: 0.8140 (t0) REVERT: C 898 GLU cc_start: 0.7481 (mt-10) cc_final: 0.7155 (mt-10) REVERT: C 900 ARG cc_start: 0.7516 (tpp-160) cc_final: 0.7077 (ttp80) REVERT: C 943 GLU cc_start: 0.7964 (tt0) cc_final: 0.7661 (tt0) REVERT: C 1063 LYS cc_start: 0.9236 (mttm) cc_final: 0.8770 (ptpp) outliers start: 14 outliers final: 7 residues processed: 151 average time/residue: 1.0352 time to fit residues: 168.8397 Evaluate side-chains 125 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 116 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain B residue 102 PHE Chi-restraints excluded: chain B residue 106 GLU Chi-restraints excluded: chain B residue 406 LYS Chi-restraints excluded: chain B residue 412 GLN Chi-restraints excluded: chain C residue 75 ASP Chi-restraints excluded: chain C residue 141 LYS Chi-restraints excluded: chain C residue 178 ILE Chi-restraints excluded: chain C residue 961 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 0.7980 chunk 113 optimal weight: 0.9980 chunk 53 optimal weight: 0.4980 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 117 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 332 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.122451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.086701 restraints weight = 43327.108| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 3.80 r_work: 0.2953 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 moved from start: 0.0915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9546 Z= 0.116 Angle : 0.493 5.208 12941 Z= 0.256 Chirality : 0.044 0.299 1468 Planarity : 0.003 0.035 1665 Dihedral : 6.204 59.531 1320 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 1.19 % Allowed : 9.14 % Favored : 89.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.25), residues: 1182 helix: 1.30 (0.43), residues: 182 sheet: -0.09 (0.25), residues: 463 loop : -1.25 (0.25), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 188 TYR 0.013 0.001 TYR C 891 PHE 0.011 0.001 PHE C1030 TRP 0.010 0.001 TRP B 386 HIS 0.003 0.001 HIS C 240 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 9538) covalent geometry : angle 0.49013 (12933) hydrogen bonds : bond 0.03948 ( 360) hydrogen bonds : angle 4.88863 ( 990) metal coordination : bond 0.00837 ( 8) metal coordination : angle 2.14601 ( 8) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 84 is missing expected H atoms. Skipping. Residue LEU 99 is missing expected H atoms. Skipping. Residue LEU 101 is missing expected H atoms. Skipping. Residue VAL 110 is missing expected H atoms. Skipping. Residue LEU 113 is missing expected H atoms. Skipping. Residue ILE 141 is missing expected H atoms. Skipping. Residue VAL 157 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue LYS 204 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LYS 204 is missing expected H atoms. Skipping. Residue LYS 208 is missing expected H atoms. Skipping. Residue ILE 220 is missing expected H atoms. Skipping. Residue ILE 230 is missing expected H atoms. Skipping. Residue ILE 232 is missing expected H atoms. Skipping. Residue ILE 237 is missing expected H atoms. Skipping. Residue TYR 271 is missing expected H atoms. Skipping. Residue LEU 273 is missing expected H atoms. Skipping. Residue LEU 283 is missing expected H atoms. Skipping. Residue MET 291 is missing expected H atoms. Skipping. Residue LYS 709 is missing expected H atoms. Skipping. Residue LYS 823 is missing expected H atoms. Skipping. Residue LYS 844 is missing expected H atoms. Skipping. Residue LYS 867 is missing expected H atoms. Skipping. Residue SER 981 is missing expected H atoms. Skipping. Residue MET 1120 is missing expected H atoms. Skipping. Residue LYS 1121 is missing expected H atoms. Skipping. Residue LYS 1131 is missing expected H atoms. Skipping. Evaluate side-chains 144 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 132 time to evaluate : 0.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 74 ASP cc_start: 0.7954 (t0) cc_final: 0.7649 (t0) REVERT: B 75 ASP cc_start: 0.8699 (m-30) cc_final: 0.8303 (p0) REVERT: B 88 MET cc_start: 0.8393 (tpp) cc_final: 0.8088 (mpp) REVERT: B 89 MET cc_start: 0.8789 (ptm) cc_final: 0.8417 (ptm) REVERT: B 402 PHE cc_start: 0.8715 (m-80) cc_final: 0.8278 (m-80) REVERT: C 1 MET cc_start: 0.5975 (ttt) cc_final: 0.5397 (tmt) REVERT: C 117 GLU cc_start: 0.8856 (mt-10) cc_final: 0.8492 (mt-10) REVERT: C 141 LYS cc_start: 0.7492 (OUTLIER) cc_final: 0.7258 (ttmt) REVERT: C 166 ASP cc_start: 0.7603 (t0) cc_final: 0.7179 (t0) REVERT: C 198 ARG cc_start: 0.8952 (tpt-90) cc_final: 0.8287 (mmm160) REVERT: C 201 GLU cc_start: 0.7532 (mt-10) cc_final: 0.7129 (mp0) REVERT: C 299 ASP cc_start: 0.8694 (t0) cc_final: 0.8367 (t0) REVERT: C 812 TYR cc_start: 0.8318 (OUTLIER) cc_final: 0.7626 (m-80) REVERT: C 898 GLU cc_start: 0.7489 (mt-10) cc_final: 0.7167 (mt-10) REVERT: C 900 ARG cc_start: 0.7611 (tpp-160) cc_final: 0.7149 (ttp80) REVERT: C 943 GLU cc_start: 0.8049 (tt0) cc_final: 0.7760 (tt0) REVERT: C 1063 LYS cc_start: 0.9249 (mttm) cc_final: 0.8780 (ptpp) outliers start: 12 outliers final: 7 residues processed: 142 average time/residue: 1.0039 time to fit residues: 154.5386 Evaluate side-chains 122 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 113 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 406 LYS Chi-restraints excluded: chain C residue 141 LYS Chi-restraints excluded: chain C residue 178 ILE Chi-restraints excluded: chain C residue 207 TRP Chi-restraints excluded: chain C residue 812 TYR Chi-restraints excluded: chain C residue 855 ASP Chi-restraints excluded: chain C residue 1054 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 75 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 chunk 37 optimal weight: 4.9990 chunk 84 optimal weight: 1.9990 chunk 99 optimal weight: 0.3980 chunk 26 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 overall best weight: 1.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 GLN B 198 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.120296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.084294 restraints weight = 43366.464| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 3.78 r_work: 0.2918 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.1218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 9546 Z= 0.182 Angle : 0.520 13.025 12941 Z= 0.268 Chirality : 0.044 0.185 1468 Planarity : 0.004 0.036 1665 Dihedral : 5.536 54.751 1308 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 1.59 % Allowed : 9.73 % Favored : 88.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.24), residues: 1182 helix: 1.49 (0.43), residues: 170 sheet: -0.08 (0.24), residues: 465 loop : -1.34 (0.25), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 188 TYR 0.014 0.001 TYR C 891 PHE 0.012 0.001 PHE C1030 TRP 0.014 0.001 TRP B 386 HIS 0.004 0.001 HIS C 240 Details of bonding type rmsd covalent geometry : bond 0.00428 ( 9538) covalent geometry : angle 0.50522 (12933) hydrogen bonds : bond 0.03997 ( 360) hydrogen bonds : angle 4.79552 ( 990) metal coordination : bond 0.00929 ( 8) metal coordination : angle 5.05743 ( 8) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 84 is missing expected H atoms. Skipping. Residue LEU 99 is missing expected H atoms. Skipping. Residue LEU 101 is missing expected H atoms. Skipping. Residue VAL 110 is missing expected H atoms. Skipping. Residue LEU 113 is missing expected H atoms. Skipping. Residue ILE 141 is missing expected H atoms. Skipping. Residue VAL 157 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue LYS 204 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LYS 204 is missing expected H atoms. Skipping. Residue LYS 208 is missing expected H atoms. Skipping. Residue ILE 220 is missing expected H atoms. Skipping. Residue ILE 230 is missing expected H atoms. Skipping. Residue ILE 232 is missing expected H atoms. Skipping. Residue ILE 237 is missing expected H atoms. Skipping. Residue TYR 271 is missing expected H atoms. Skipping. Residue LEU 273 is missing expected H atoms. Skipping. Residue LEU 283 is missing expected H atoms. Skipping. Residue MET 291 is missing expected H atoms. Skipping. Residue LYS 709 is missing expected H atoms. Skipping. Residue LYS 823 is missing expected H atoms. Skipping. Residue LYS 844 is missing expected H atoms. Skipping. Residue LYS 867 is missing expected H atoms. Skipping. Residue SER 981 is missing expected H atoms. Skipping. Residue MET 1120 is missing expected H atoms. Skipping. Residue LYS 1121 is missing expected H atoms. Skipping. Residue LYS 1131 is missing expected H atoms. Skipping. Evaluate side-chains 135 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 119 time to evaluate : 0.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 74 ASP cc_start: 0.7981 (t0) cc_final: 0.7654 (t0) REVERT: B 75 ASP cc_start: 0.8706 (m-30) cc_final: 0.8294 (p0) REVERT: B 89 MET cc_start: 0.8828 (ptm) cc_final: 0.8470 (ptm) REVERT: B 412 GLN cc_start: 0.6798 (OUTLIER) cc_final: 0.6587 (tm-30) REVERT: C 1 MET cc_start: 0.6082 (ttt) cc_final: 0.5425 (tmt) REVERT: C 117 GLU cc_start: 0.8830 (mt-10) cc_final: 0.8480 (mt-10) REVERT: C 166 ASP cc_start: 0.7744 (t0) cc_final: 0.7253 (t0) REVERT: C 198 ARG cc_start: 0.8913 (tpt-90) cc_final: 0.8270 (mmm160) REVERT: C 299 ASP cc_start: 0.8709 (t0) cc_final: 0.8319 (t0) REVERT: C 898 GLU cc_start: 0.7517 (mt-10) cc_final: 0.7168 (mt-10) REVERT: C 900 ARG cc_start: 0.7690 (tpp-160) cc_final: 0.7185 (tmm-80) REVERT: C 1063 LYS cc_start: 0.9249 (mttm) cc_final: 0.8786 (ptpp) outliers start: 16 outliers final: 10 residues processed: 131 average time/residue: 0.9904 time to fit residues: 141.4907 Evaluate side-chains 122 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 111 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 406 LYS Chi-restraints excluded: chain B residue 412 GLN Chi-restraints excluded: chain C residue 178 ILE Chi-restraints excluded: chain C residue 207 TRP Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 855 ASP Chi-restraints excluded: chain C residue 938 MET Chi-restraints excluded: chain C residue 961 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 116 optimal weight: 7.9990 chunk 57 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 78 optimal weight: 0.5980 chunk 24 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 4 optimal weight: 9.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.119727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.083676 restraints weight = 43162.119| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 3.78 r_work: 0.2912 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.1431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 9546 Z= 0.183 Angle : 0.511 7.487 12941 Z= 0.267 Chirality : 0.044 0.171 1468 Planarity : 0.003 0.038 1665 Dihedral : 5.262 54.694 1302 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 1.49 % Allowed : 11.02 % Favored : 87.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.24), residues: 1182 helix: 1.37 (0.42), residues: 176 sheet: -0.10 (0.24), residues: 465 loop : -1.37 (0.25), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 188 TYR 0.013 0.001 TYR C 891 PHE 0.015 0.001 PHE A 145 TRP 0.014 0.001 TRP B 386 HIS 0.005 0.001 HIS A 167 Details of bonding type rmsd covalent geometry : bond 0.00430 ( 9538) covalent geometry : angle 0.50312 (12933) hydrogen bonds : bond 0.03900 ( 360) hydrogen bonds : angle 4.78757 ( 990) metal coordination : bond 0.00586 ( 8) metal coordination : angle 3.55997 ( 8) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 84 is missing expected H atoms. Skipping. Residue LEU 99 is missing expected H atoms. Skipping. Residue LEU 101 is missing expected H atoms. Skipping. Residue VAL 110 is missing expected H atoms. Skipping. Residue LEU 113 is missing expected H atoms. Skipping. Residue ILE 141 is missing expected H atoms. Skipping. Residue VAL 157 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue LYS 204 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LYS 204 is missing expected H atoms. Skipping. Residue LYS 208 is missing expected H atoms. Skipping. Residue ILE 220 is missing expected H atoms. Skipping. Residue ILE 230 is missing expected H atoms. Skipping. Residue ILE 232 is missing expected H atoms. Skipping. Residue ILE 237 is missing expected H atoms. Skipping. Residue TYR 271 is missing expected H atoms. Skipping. Residue LEU 273 is missing expected H atoms. Skipping. Residue LEU 283 is missing expected H atoms. Skipping. Residue MET 291 is missing expected H atoms. Skipping. Residue LYS 709 is missing expected H atoms. Skipping. Residue LYS 823 is missing expected H atoms. Skipping. Residue LYS 844 is missing expected H atoms. Skipping. Residue LYS 867 is missing expected H atoms. Skipping. Residue SER 981 is missing expected H atoms. Skipping. Residue MET 1120 is missing expected H atoms. Skipping. Residue LYS 1121 is missing expected H atoms. Skipping. Residue LYS 1131 is missing expected H atoms. Skipping. Evaluate side-chains 132 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 117 time to evaluate : 0.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 GLN cc_start: 0.7733 (pp30) cc_final: 0.7452 (pp30) REVERT: B 74 ASP cc_start: 0.8007 (t0) cc_final: 0.7677 (t0) REVERT: B 75 ASP cc_start: 0.8706 (m-30) cc_final: 0.8306 (p0) REVERT: B 89 MET cc_start: 0.8826 (ptm) cc_final: 0.8468 (ptm) REVERT: B 412 GLN cc_start: 0.7036 (OUTLIER) cc_final: 0.6667 (tm-30) REVERT: C 1 MET cc_start: 0.6085 (ttt) cc_final: 0.5451 (tmt) REVERT: C 11 LYS cc_start: 0.8899 (mtmm) cc_final: 0.8675 (mtpt) REVERT: C 117 GLU cc_start: 0.8856 (mt-10) cc_final: 0.8508 (mt-10) REVERT: C 166 ASP cc_start: 0.7718 (t0) cc_final: 0.7208 (t0) REVERT: C 198 ARG cc_start: 0.8907 (tpt-90) cc_final: 0.8265 (mmm160) REVERT: C 299 ASP cc_start: 0.8719 (t0) cc_final: 0.8356 (t0) REVERT: C 898 GLU cc_start: 0.7565 (mt-10) cc_final: 0.7203 (mt-10) REVERT: C 900 ARG cc_start: 0.7709 (tpp-160) cc_final: 0.7191 (tmm-80) REVERT: C 1063 LYS cc_start: 0.9250 (mttm) cc_final: 0.8788 (ptpp) outliers start: 15 outliers final: 12 residues processed: 128 average time/residue: 0.9589 time to fit residues: 133.3991 Evaluate side-chains 128 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 115 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 406 LYS Chi-restraints excluded: chain B residue 412 GLN Chi-restraints excluded: chain C residue 178 ILE Chi-restraints excluded: chain C residue 207 TRP Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 855 ASP Chi-restraints excluded: chain C residue 961 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 28 optimal weight: 0.9980 chunk 97 optimal weight: 2.9990 chunk 49 optimal weight: 0.0370 chunk 32 optimal weight: 0.5980 chunk 102 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 1 optimal weight: 8.9990 chunk 53 optimal weight: 0.7980 chunk 47 optimal weight: 0.9990 chunk 4 optimal weight: 5.9990 overall best weight: 0.6860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.121639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.085881 restraints weight = 42873.000| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 3.77 r_work: 0.2943 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 moved from start: 0.1431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9546 Z= 0.100 Angle : 0.480 6.695 12941 Z= 0.248 Chirality : 0.043 0.143 1468 Planarity : 0.003 0.036 1665 Dihedral : 5.015 56.190 1302 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 1.29 % Allowed : 11.72 % Favored : 86.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.71 (0.24), residues: 1182 helix: 1.23 (0.42), residues: 182 sheet: -0.12 (0.24), residues: 469 loop : -1.37 (0.25), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C1080 TYR 0.012 0.001 TYR C 891 PHE 0.012 0.001 PHE A 145 TRP 0.015 0.001 TRP B 386 HIS 0.004 0.001 HIS C1140 Details of bonding type rmsd covalent geometry : bond 0.00232 ( 9538) covalent geometry : angle 0.47425 (12933) hydrogen bonds : bond 0.03284 ( 360) hydrogen bonds : angle 4.62262 ( 990) metal coordination : bond 0.00631 ( 8) metal coordination : angle 3.09119 ( 8) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 84 is missing expected H atoms. Skipping. Residue LEU 99 is missing expected H atoms. Skipping. Residue LEU 101 is missing expected H atoms. Skipping. Residue VAL 110 is missing expected H atoms. Skipping. Residue LEU 113 is missing expected H atoms. Skipping. Residue ILE 141 is missing expected H atoms. Skipping. Residue VAL 157 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue LYS 204 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LYS 204 is missing expected H atoms. Skipping. Residue LYS 208 is missing expected H atoms. Skipping. Residue ILE 220 is missing expected H atoms. Skipping. Residue ILE 230 is missing expected H atoms. Skipping. Residue ILE 232 is missing expected H atoms. Skipping. Residue ILE 237 is missing expected H atoms. Skipping. Residue TYR 271 is missing expected H atoms. Skipping. Residue LEU 273 is missing expected H atoms. Skipping. Residue LEU 283 is missing expected H atoms. Skipping. Residue MET 291 is missing expected H atoms. Skipping. Residue LYS 709 is missing expected H atoms. Skipping. Residue LYS 823 is missing expected H atoms. Skipping. Residue LYS 844 is missing expected H atoms. Skipping. Residue LYS 867 is missing expected H atoms. Skipping. Residue SER 981 is missing expected H atoms. Skipping. Residue MET 1120 is missing expected H atoms. Skipping. Residue LYS 1121 is missing expected H atoms. Skipping. Residue LYS 1131 is missing expected H atoms. Skipping. Evaluate side-chains 133 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 120 time to evaluate : 0.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 GLN cc_start: 0.7754 (pp30) cc_final: 0.7515 (pp30) REVERT: B 74 ASP cc_start: 0.7991 (t0) cc_final: 0.7626 (t0) REVERT: B 75 ASP cc_start: 0.8700 (m-30) cc_final: 0.8293 (p0) REVERT: B 89 MET cc_start: 0.8863 (ptm) cc_final: 0.8493 (ptm) REVERT: B 412 GLN cc_start: 0.6974 (OUTLIER) cc_final: 0.6586 (tm-30) REVERT: C 1 MET cc_start: 0.6056 (ttt) cc_final: 0.5457 (tmt) REVERT: C 11 LYS cc_start: 0.8900 (mtmm) cc_final: 0.8676 (mtpt) REVERT: C 117 GLU cc_start: 0.8851 (mt-10) cc_final: 0.8498 (mt-10) REVERT: C 166 ASP cc_start: 0.7646 (t0) cc_final: 0.7144 (t0) REVERT: C 198 ARG cc_start: 0.8910 (tpt-90) cc_final: 0.8264 (mmm160) REVERT: C 299 ASP cc_start: 0.8723 (t0) cc_final: 0.8364 (t0) REVERT: C 313 CYS cc_start: 0.8735 (p) cc_final: 0.8238 (p) REVERT: C 812 TYR cc_start: 0.8485 (OUTLIER) cc_final: 0.7792 (m-80) REVERT: C 898 GLU cc_start: 0.7518 (mt-10) cc_final: 0.7169 (mt-10) REVERT: C 1063 LYS cc_start: 0.9247 (mttm) cc_final: 0.8783 (ptpp) outliers start: 13 outliers final: 12 residues processed: 129 average time/residue: 0.9980 time to fit residues: 139.6160 Evaluate side-chains 125 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 111 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 PHE Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 406 LYS Chi-restraints excluded: chain B residue 412 GLN Chi-restraints excluded: chain C residue 178 ILE Chi-restraints excluded: chain C residue 207 TRP Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 812 TYR Chi-restraints excluded: chain C residue 855 ASP Chi-restraints excluded: chain C residue 961 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 110 optimal weight: 1.9990 chunk 6 optimal weight: 0.3980 chunk 26 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 66 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 95 optimal weight: 4.9990 chunk 105 optimal weight: 2.9990 chunk 115 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 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 149 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.121217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.084969 restraints weight = 43090.115| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 3.80 r_work: 0.2931 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.1550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9546 Z= 0.142 Angle : 0.495 6.787 12941 Z= 0.256 Chirality : 0.043 0.146 1468 Planarity : 0.003 0.039 1665 Dihedral : 5.057 57.565 1302 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 1.49 % Allowed : 12.02 % Favored : 86.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.24), residues: 1182 helix: 1.16 (0.42), residues: 182 sheet: -0.15 (0.24), residues: 476 loop : -1.36 (0.25), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 111 TYR 0.015 0.001 TYR B 144 PHE 0.010 0.001 PHE C1030 TRP 0.016 0.001 TRP B 386 HIS 0.005 0.001 HIS C1140 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 9538) covalent geometry : angle 0.48842 (12933) hydrogen bonds : bond 0.03482 ( 360) hydrogen bonds : angle 4.65851 ( 990) metal coordination : bond 0.00579 ( 8) metal coordination : angle 3.29971 ( 8) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 84 is missing expected H atoms. Skipping. Residue LEU 99 is missing expected H atoms. Skipping. Residue LEU 101 is missing expected H atoms. Skipping. Residue VAL 110 is missing expected H atoms. Skipping. Residue LEU 113 is missing expected H atoms. Skipping. Residue ILE 141 is missing expected H atoms. Skipping. Residue VAL 157 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue LYS 204 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LYS 204 is missing expected H atoms. Skipping. Residue LYS 208 is missing expected H atoms. Skipping. Residue ILE 220 is missing expected H atoms. Skipping. Residue ILE 230 is missing expected H atoms. Skipping. Residue ILE 232 is missing expected H atoms. Skipping. Residue ILE 237 is missing expected H atoms. Skipping. Residue TYR 271 is missing expected H atoms. Skipping. Residue LEU 273 is missing expected H atoms. Skipping. Residue LEU 283 is missing expected H atoms. Skipping. Residue MET 291 is missing expected H atoms. Skipping. Residue LYS 709 is missing expected H atoms. Skipping. Residue LYS 823 is missing expected H atoms. Skipping. Residue LYS 844 is missing expected H atoms. Skipping. Residue LYS 867 is missing expected H atoms. Skipping. Residue SER 981 is missing expected H atoms. Skipping. Residue MET 1120 is missing expected H atoms. Skipping. Residue LYS 1121 is missing expected H atoms. Skipping. Residue LYS 1131 is missing expected H atoms. Skipping. Evaluate side-chains 130 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 115 time to evaluate : 0.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 GLN cc_start: 0.7770 (pp30) cc_final: 0.7525 (pp30) REVERT: B 74 ASP cc_start: 0.8007 (t0) cc_final: 0.7630 (t0) REVERT: B 75 ASP cc_start: 0.8707 (m-30) cc_final: 0.8303 (p0) REVERT: B 412 GLN cc_start: 0.7069 (OUTLIER) cc_final: 0.6665 (tm-30) REVERT: C 1 MET cc_start: 0.6063 (ttt) cc_final: 0.5451 (tmt) REVERT: C 11 LYS cc_start: 0.8913 (mtmm) cc_final: 0.8692 (mtpt) REVERT: C 117 GLU cc_start: 0.8858 (mt-10) cc_final: 0.8506 (mt-10) REVERT: C 166 ASP cc_start: 0.7683 (t0) cc_final: 0.7177 (t0) REVERT: C 198 ARG cc_start: 0.8889 (tpt-90) cc_final: 0.8242 (mmm160) REVERT: C 299 ASP cc_start: 0.8709 (t0) cc_final: 0.8344 (t0) REVERT: C 313 CYS cc_start: 0.8744 (p) cc_final: 0.8220 (p) REVERT: C 812 TYR cc_start: 0.8535 (OUTLIER) cc_final: 0.7835 (m-80) REVERT: C 898 GLU cc_start: 0.7564 (mt-10) cc_final: 0.7245 (mt-10) REVERT: C 1063 LYS cc_start: 0.9247 (mttm) cc_final: 0.8785 (ptpp) outliers start: 15 outliers final: 12 residues processed: 124 average time/residue: 1.0085 time to fit residues: 135.7840 Evaluate side-chains 123 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 109 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 PHE Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 406 LYS Chi-restraints excluded: chain B residue 412 GLN Chi-restraints excluded: chain C residue 178 ILE Chi-restraints excluded: chain C residue 207 TRP Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 812 TYR Chi-restraints excluded: chain C residue 855 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 54 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 78 optimal weight: 0.9980 chunk 6 optimal weight: 0.5980 chunk 96 optimal weight: 2.9990 chunk 3 optimal weight: 5.9990 chunk 28 optimal weight: 4.9990 chunk 95 optimal weight: 3.9990 chunk 116 optimal weight: 3.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.119092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.082718 restraints weight = 43615.952| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 3.82 r_work: 0.2902 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.1680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 9546 Z= 0.224 Angle : 0.538 6.995 12941 Z= 0.282 Chirality : 0.044 0.145 1468 Planarity : 0.004 0.041 1665 Dihedral : 5.304 59.410 1302 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 1.89 % Allowed : 11.72 % Favored : 86.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.24), residues: 1182 helix: 1.18 (0.43), residues: 177 sheet: -0.15 (0.24), residues: 466 loop : -1.46 (0.25), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 162 TYR 0.014 0.001 TYR C 891 PHE 0.012 0.001 PHE C1030 TRP 0.019 0.001 TRP B 386 HIS 0.007 0.001 HIS A 167 Details of bonding type rmsd covalent geometry : bond 0.00532 ( 9538) covalent geometry : angle 0.53066 (12933) hydrogen bonds : bond 0.04010 ( 360) hydrogen bonds : angle 4.82827 ( 990) metal coordination : bond 0.00590 ( 8) metal coordination : angle 3.57570 ( 8) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 84 is missing expected H atoms. Skipping. Residue LEU 99 is missing expected H atoms. Skipping. Residue LEU 101 is missing expected H atoms. Skipping. Residue VAL 110 is missing expected H atoms. Skipping. Residue LEU 113 is missing expected H atoms. Skipping. Residue ILE 141 is missing expected H atoms. Skipping. Residue VAL 157 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue LYS 204 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LYS 204 is missing expected H atoms. Skipping. Residue LYS 208 is missing expected H atoms. Skipping. Residue ILE 220 is missing expected H atoms. Skipping. Residue ILE 230 is missing expected H atoms. Skipping. Residue ILE 232 is missing expected H atoms. Skipping. Residue ILE 237 is missing expected H atoms. Skipping. Residue TYR 271 is missing expected H atoms. Skipping. Residue LEU 273 is missing expected H atoms. Skipping. Residue LEU 283 is missing expected H atoms. Skipping. Residue MET 291 is missing expected H atoms. Skipping. Residue LYS 709 is missing expected H atoms. Skipping. Residue LYS 823 is missing expected H atoms. Skipping. Residue LYS 844 is missing expected H atoms. Skipping. Residue LYS 867 is missing expected H atoms. Skipping. Residue SER 981 is missing expected H atoms. Skipping. Residue MET 1120 is missing expected H atoms. Skipping. Residue LYS 1121 is missing expected H atoms. Skipping. Residue LYS 1131 is missing expected H atoms. Skipping. Evaluate side-chains 127 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 108 time to evaluate : 0.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 GLN cc_start: 0.7793 (pp30) cc_final: 0.7508 (pp30) REVERT: B 74 ASP cc_start: 0.7986 (t0) cc_final: 0.7634 (t0) REVERT: B 75 ASP cc_start: 0.8721 (m-30) cc_final: 0.8319 (p0) REVERT: B 89 MET cc_start: 0.8881 (ptm) cc_final: 0.8533 (ptm) REVERT: B 117 ASP cc_start: 0.8553 (p0) cc_final: 0.8267 (p0) REVERT: B 225 GLN cc_start: 0.8459 (tp40) cc_final: 0.8243 (mm110) REVERT: B 412 GLN cc_start: 0.7272 (OUTLIER) cc_final: 0.6802 (tm-30) REVERT: C 1 MET cc_start: 0.6145 (ttt) cc_final: 0.5427 (tmt) REVERT: C 11 LYS cc_start: 0.8916 (mtmm) cc_final: 0.8697 (mtpt) REVERT: C 117 GLU cc_start: 0.8860 (mt-10) cc_final: 0.8500 (mt-10) REVERT: C 166 ASP cc_start: 0.7754 (t0) cc_final: 0.7231 (t0) REVERT: C 198 ARG cc_start: 0.8883 (tpt-90) cc_final: 0.8244 (mmm160) REVERT: C 299 ASP cc_start: 0.8717 (t0) cc_final: 0.8349 (t0) REVERT: C 313 CYS cc_start: 0.8714 (p) cc_final: 0.8196 (p) REVERT: C 361 ASP cc_start: 0.9014 (t0) cc_final: 0.8769 (t0) REVERT: C 812 TYR cc_start: 0.8572 (OUTLIER) cc_final: 0.7872 (m-80) REVERT: C 898 GLU cc_start: 0.7577 (mt-10) cc_final: 0.7263 (mt-10) REVERT: C 1063 LYS cc_start: 0.9249 (mttm) cc_final: 0.8797 (ptpp) outliers start: 19 outliers final: 13 residues processed: 121 average time/residue: 0.8860 time to fit residues: 117.0792 Evaluate side-chains 119 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 104 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 PHE Chi-restraints excluded: chain B residue 64 MET Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 406 LYS Chi-restraints excluded: chain B residue 412 GLN Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 178 ILE Chi-restraints excluded: chain C residue 207 TRP Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 812 TYR Chi-restraints excluded: chain C residue 855 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 52.7001 > 50: distance: 155 - 164: 4.755 distance: 164 - 169: 6.280 distance: 165 - 166: 3.283 distance: 165 - 168: 4.919 distance: 165 - 170: 5.382 distance: 166 - 167: 3.494 distance: 166 - 174: 7.605 distance: 167 - 338: 5.498 distance: 168 - 171: 3.717 distance: 174 - 175: 4.920 distance: 175 - 176: 4.518 distance: 175 - 182: 7.438 distance: 176 - 177: 3.533 distance: 176 - 190: 3.954 distance: 178 - 179: 4.750 distance: 178 - 180: 4.881 distance: 178 - 183: 7.775 distance: 179 - 184: 3.819 distance: 179 - 185: 9.825 distance: 179 - 186: 8.143 distance: 180 - 187: 8.993 distance: 180 - 188: 9.986 distance: 180 - 189: 12.126 distance: 190 - 191: 8.533 distance: 190 - 199: 6.636 distance: 190 - 316: 4.263 distance: 191 - 192: 7.558 distance: 191 - 194: 5.605 distance: 191 - 200: 4.823 distance: 192 - 205: 11.944 distance: 193 - 313: 12.791 distance: 194 - 195: 7.639 distance: 194 - 201: 3.881 distance: 194 - 202: 9.602 distance: 195 - 203: 3.923 distance: 195 - 204: 10.895 distance: 196 - 197: 7.316 distance: 196 - 198: 6.275 distance: 205 - 206: 8.394 distance: 205 - 213: 12.354 distance: 206 - 207: 8.543 distance: 206 - 214: 5.044 distance: 207 - 208: 24.675 distance: 207 - 224: 12.016 distance: 209 - 210: 9.309 distance: 209 - 211: 3.486 distance: 210 - 212: 13.491 distance: 210 - 216: 6.556 distance: 210 - 217: 4.219 distance: 211 - 218: 6.335 distance: 211 - 219: 5.609 distance: 212 - 221: 10.615 distance: 212 - 222: 3.536 distance: 224 - 225: 8.124 distance: 224 - 232: 21.923 distance: 225 - 226: 5.214 distance: 225 - 228: 6.034 distance: 225 - 233: 3.565 distance: 226 - 227: 11.378 distance: 226 - 243: 5.091 distance: 228 - 229: 3.235 distance: 228 - 234: 7.897 distance: 228 - 235: 3.645 distance: 229 - 230: 5.732 distance: 229 - 231: 9.294 distance: 229 - 236: 10.919 distance: 230 - 237: 5.707 distance: 230 - 238: 6.768 distance: 230 - 239: 4.068 distance: 231 - 240: 3.173 distance: 231 - 241: 3.699 distance: 243 - 244: 8.542 distance: 243 - 251: 6.996 distance: 244 - 245: 5.644 distance: 244 - 247: 4.419 distance: 244 - 252: 3.338 distance: 245 - 246: 3.546 distance: 245 - 255: 8.775 distance: 247 - 248: 4.904 distance: 247 - 254: 7.009 distance: 248 - 250: 6.915 distance: 255 - 263: 6.540 distance: 256 - 259: 3.571 distance: 256 - 264: 3.510 distance: 257 - 258: 3.099 distance: 259 - 260: 9.594 distance: 259 - 265: 7.615 distance: 259 - 266: 5.368 distance: 260 - 261: 11.100 distance: 260 - 262: 4.712 distance: 267 - 268: 12.910 distance: 267 - 275: 11.528 distance: 268 - 269: 11.280 distance: 268 - 271: 7.172 distance: 268 - 276: 7.324 distance: 269 - 270: 11.664 distance: 269 - 279: 12.023 distance: 271 - 272: 14.589 distance: 271 - 277: 7.772 distance: 271 - 278: 8.021 distance: 272 - 273: 4.987 distance: 272 - 274: 10.403 distance: 279 - 280: 4.585 distance: 279 - 287: 8.696 distance: 280 - 283: 9.182 distance: 280 - 288: 5.158 distance: 281 - 282: 4.848 distance: 281 - 293: 4.176 distance: 283 - 284: 11.638 distance: 283 - 289: 10.483 distance: 283 - 290: 11.131 distance: 284 - 285: 11.888 distance: 284 - 286: 4.562 distance: 293 - 304: 8.771 distance: 294 - 295: 4.696 distance: 294 - 297: 5.386 distance: 295 - 296: 5.285 distance: 295 - 313: 4.833 distance: 296 - 370: 4.139 distance: 297 - 298: 4.889 distance: 297 - 307: 4.027 distance: 298 - 299: 8.141 distance: 299 - 308: 5.226 distance: 300 - 302: 4.468 distance: 301 - 310: 4.344 distance: 303 - 312: 4.031