Starting phenix.real_space_refine on Fri Aug 22 21:43:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gvf_34292/08_2025/8gvf_34292.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gvf_34292/08_2025/8gvf_34292.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.09 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8gvf_34292/08_2025/8gvf_34292.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gvf_34292/08_2025/8gvf_34292.map" model { file = "/net/cci-nas-00/data/ceres_data/8gvf_34292/08_2025/8gvf_34292.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gvf_34292/08_2025/8gvf_34292.cif" } resolution = 3.09 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= 0.002 sd= 0.145 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 46 5.16 5 C 5370 2.51 5 N 1326 2.21 5 O 1330 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8072 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4036 Number of conformers: 1 Conformer: "" Number of residues, atoms: 511, 4036 Classifications: {'peptide': 511} Link IDs: {'PTRANS': 27, 'TRANS': 483} Chain breaks: 1 Chain: "B" Number of atoms: 4036 Number of conformers: 1 Conformer: "" Number of residues, atoms: 511, 4036 Classifications: {'peptide': 511} Link IDs: {'PTRANS': 27, 'TRANS': 483} Chain breaks: 1 Time building chain proxies: 1.95, per 1000 atoms: 0.24 Number of scatterers: 8072 At special positions: 0 Unit cell: (84.7, 135.3, 81.4, 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 46 16.00 O 1330 8.00 N 1326 7.00 C 5370 6.00 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: 0.49 Conformation dependent library (CDL) restraints added in 360.3 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1904 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 4 sheets defined 73.6% alpha, 1.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'A' and resid 682 through 693 Processing helix chain 'A' and resid 696 through 702 removed outlier: 3.536A pdb=" N PHE A 700 " --> pdb=" O TYR A 696 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 734 removed outlier: 3.606A pdb=" N LEU A 709 " --> pdb=" O ASP A 705 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N PHE A 717 " --> pdb=" O ILE A 713 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ALA A 718 " --> pdb=" O PHE A 714 " (cutoff:3.500A) Proline residue: A 722 - end of helix Processing helix chain 'A' and resid 740 through 758 Processing helix chain 'A' and resid 768 through 784 removed outlier: 3.569A pdb=" N LEU A 772 " --> pdb=" O SER A 768 " (cutoff:3.500A) Processing helix chain 'A' and resid 791 through 810 removed outlier: 4.175A pdb=" N TRP A 795 " --> pdb=" O VAL A 791 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ILE A 796 " --> pdb=" O GLY A 792 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLY A 797 " --> pdb=" O ARG A 793 " (cutoff:3.500A) Processing helix chain 'A' and resid 811 through 818 removed outlier: 3.758A pdb=" N PHE A 814 " --> pdb=" O GLU A 811 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU A 815 " --> pdb=" O GLY A 812 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N VAL A 816 " --> pdb=" O SER A 813 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE A 818 " --> pdb=" O LEU A 815 " (cutoff:3.500A) Processing helix chain 'A' and resid 820 through 850 removed outlier: 3.529A pdb=" N GLN A 824 " --> pdb=" O SER A 820 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ILE A 826 " --> pdb=" O PHE A 822 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LEU A 843 " --> pdb=" O THR A 839 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL A 844 " --> pdb=" O PHE A 840 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS A 845 " --> pdb=" O TYR A 841 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ILE A 846 " --> pdb=" O LYS A 842 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N PHE A 847 " --> pdb=" O LEU A 843 " (cutoff:3.500A) Processing helix chain 'A' and resid 900 through 921 removed outlier: 3.507A pdb=" N SER A 904 " --> pdb=" O THR A 900 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU A 905 " --> pdb=" O ALA A 901 " (cutoff:3.500A) Processing helix chain 'A' and resid 922 through 924 No H-bonds generated for 'chain 'A' and resid 922 through 924' Processing helix chain 'A' and resid 928 through 938 Processing helix chain 'A' and resid 938 through 954 removed outlier: 3.781A pdb=" N ILE A 954 " --> pdb=" O VAL A 950 " (cutoff:3.500A) Processing helix chain 'A' and resid 972 through 976 removed outlier: 3.928A pdb=" N ARG A 976 " --> pdb=" O PRO A 973 " (cutoff:3.500A) Processing helix chain 'A' and resid 990 through 997 removed outlier: 3.694A pdb=" N MET A 994 " --> pdb=" O PRO A 990 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 997 through 1020 removed outlier: 3.579A pdb=" N ALA A1001 " --> pdb=" O SER A 997 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU A1003 " --> pdb=" O LEU A 999 " (cutoff:3.500A) Processing helix chain 'A' and resid 1033 through 1047 Processing helix chain 'A' and resid 1048 through 1050 No H-bonds generated for 'chain 'A' and resid 1048 through 1050' Processing helix chain 'A' and resid 1057 through 1066 Processing helix chain 'A' and resid 1091 through 1102 Processing helix chain 'A' and resid 1109 through 1113 removed outlier: 3.691A pdb=" N ILE A1113 " --> pdb=" O LEU A1110 " (cutoff:3.500A) Processing helix chain 'A' and resid 1114 through 1129 removed outlier: 4.034A pdb=" N LEU A1118 " --> pdb=" O PRO A1114 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLY A1120 " --> pdb=" O ALA A1116 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE A1121 " --> pdb=" O VAL A1117 " (cutoff:3.500A) Processing helix chain 'A' and resid 1133 through 1141 removed outlier: 3.687A pdb=" N LEU A1141 " --> pdb=" O GLU A1137 " (cutoff:3.500A) Processing helix chain 'A' and resid 1145 through 1149 removed outlier: 3.945A pdb=" N HIS A1149 " --> pdb=" O PRO A1146 " (cutoff:3.500A) Processing helix chain 'A' and resid 1152 through 1157 removed outlier: 3.729A pdb=" N LYS A1156 " --> pdb=" O VAL A1152 " (cutoff:3.500A) Processing helix chain 'A' and resid 1159 through 1183 removed outlier: 3.522A pdb=" N MET A1181 " --> pdb=" O LEU A1177 " (cutoff:3.500A) Processing helix chain 'A' and resid 1185 through 1187 No H-bonds generated for 'chain 'A' and resid 1185 through 1187' Processing helix chain 'A' and resid 1188 through 1195 Processing helix chain 'A' and resid 1195 through 1208 removed outlier: 3.562A pdb=" N LEU A1199 " --> pdb=" O LEU A1195 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N MET A1201 " --> pdb=" O VAL A1197 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LEU A1204 " --> pdb=" O ARG A1200 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N THR A1205 " --> pdb=" O MET A1201 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ARG A1206 " --> pdb=" O VAL A1202 " (cutoff:3.500A) Processing helix chain 'A' and resid 1209 through 1217 removed outlier: 3.640A pdb=" N CYS A1215 " --> pdb=" O ARG A1211 " (cutoff:3.500A) Processing helix chain 'B' and resid 682 through 693 Processing helix chain 'B' and resid 696 through 702 removed outlier: 3.561A pdb=" N PHE B 700 " --> pdb=" O TYR B 696 " (cutoff:3.500A) Processing helix chain 'B' and resid 705 through 734 removed outlier: 3.618A pdb=" N LEU B 709 " --> pdb=" O ASP B 705 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N PHE B 717 " --> pdb=" O ILE B 713 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ALA B 718 " --> pdb=" O PHE B 714 " (cutoff:3.500A) Proline residue: B 722 - end of helix Processing helix chain 'B' and resid 740 through 758 Processing helix chain 'B' and resid 768 through 786 removed outlier: 3.518A pdb=" N LEU B 772 " --> pdb=" O SER B 768 " (cutoff:3.500A) Processing helix chain 'B' and resid 788 through 810 removed outlier: 4.139A pdb=" N GLY B 792 " --> pdb=" O GLU B 788 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ARG B 793 " --> pdb=" O TYR B 789 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N VAL B 794 " --> pdb=" O LEU B 790 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N TRP B 795 " --> pdb=" O VAL B 791 " (cutoff:3.500A) Processing helix chain 'B' and resid 811 through 818 removed outlier: 3.897A pdb=" N PHE B 814 " --> pdb=" O GLU B 811 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU B 815 " --> pdb=" O GLY B 812 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N VAL B 816 " --> pdb=" O SER B 813 " (cutoff:3.500A) Processing helix chain 'B' and resid 820 through 850 removed outlier: 3.531A pdb=" N GLN B 824 " --> pdb=" O SER B 820 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ILE B 826 " --> pdb=" O PHE B 822 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LEU B 843 " --> pdb=" O THR B 839 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL B 844 " --> pdb=" O PHE B 840 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LYS B 845 " --> pdb=" O TYR B 841 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ILE B 846 " --> pdb=" O LYS B 842 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE B 847 " --> pdb=" O LEU B 843 " (cutoff:3.500A) Processing helix chain 'B' and resid 900 through 921 removed outlier: 3.647A pdb=" N LEU B 905 " --> pdb=" O ALA B 901 " (cutoff:3.500A) Processing helix chain 'B' and resid 922 through 924 No H-bonds generated for 'chain 'B' and resid 922 through 924' Processing helix chain 'B' and resid 928 through 938 Processing helix chain 'B' and resid 938 through 954 removed outlier: 3.787A pdb=" N ILE B 954 " --> pdb=" O VAL B 950 " (cutoff:3.500A) Processing helix chain 'B' and resid 972 through 976 removed outlier: 3.890A pdb=" N ARG B 976 " --> pdb=" O PRO B 973 " (cutoff:3.500A) Processing helix chain 'B' and resid 990 through 997 removed outlier: 3.789A pdb=" N MET B 994 " --> pdb=" O PRO B 990 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N VAL B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) Processing helix chain 'B' and resid 997 through 1020 removed outlier: 3.550A pdb=" N ALA B1001 " --> pdb=" O SER B 997 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU B1003 " --> pdb=" O LEU B 999 " (cutoff:3.500A) Processing helix chain 'B' and resid 1033 through 1047 Processing helix chain 'B' and resid 1048 through 1050 No H-bonds generated for 'chain 'B' and resid 1048 through 1050' Processing helix chain 'B' and resid 1058 through 1066 Processing helix chain 'B' and resid 1091 through 1102 Processing helix chain 'B' and resid 1109 through 1113 removed outlier: 3.650A pdb=" N ILE B1113 " --> pdb=" O LEU B1110 " (cutoff:3.500A) Processing helix chain 'B' and resid 1114 through 1129 removed outlier: 4.058A pdb=" N LEU B1118 " --> pdb=" O PRO B1114 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLY B1120 " --> pdb=" O ALA B1116 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE B1121 " --> pdb=" O VAL B1117 " (cutoff:3.500A) Processing helix chain 'B' and resid 1133 through 1141 removed outlier: 3.692A pdb=" N LEU B1141 " --> pdb=" O GLU B1137 " (cutoff:3.500A) Processing helix chain 'B' and resid 1145 through 1149 removed outlier: 3.758A pdb=" N HIS B1149 " --> pdb=" O PRO B1146 " (cutoff:3.500A) Processing helix chain 'B' and resid 1152 through 1157 removed outlier: 3.814A pdb=" N LYS B1156 " --> pdb=" O VAL B1152 " (cutoff:3.500A) Processing helix chain 'B' and resid 1159 through 1183 Processing helix chain 'B' and resid 1185 through 1187 No H-bonds generated for 'chain 'B' and resid 1185 through 1187' Processing helix chain 'B' and resid 1188 through 1195 Processing helix chain 'B' and resid 1195 through 1208 removed outlier: 4.018A pdb=" N LEU B1204 " --> pdb=" O ARG B1200 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N THR B1205 " --> pdb=" O MET B1201 " (cutoff:3.500A) Processing helix chain 'B' and resid 1209 through 1217 Processing sheet with id=AA1, first strand: chain 'A' and resid 765 through 766 removed outlier: 3.622A pdb=" N ALA A1055 " --> pdb=" O GLY A 766 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1070 through 1071 removed outlier: 6.810A pdb=" N VAL A1070 " --> pdb=" O GLN A1084 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 765 through 766 removed outlier: 3.593A pdb=" N ALA B1055 " --> pdb=" O GLY B 766 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 1070 through 1071 removed outlier: 6.773A pdb=" N VAL B1070 " --> pdb=" O GLN B1084 " (cutoff:3.500A) 456 hydrogen bonds defined for protein. 1341 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.04 Time building geometry restraints manager: 0.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2457 1.34 - 1.46: 1194 1.46 - 1.57: 4543 1.57 - 1.69: 0 1.69 - 1.81: 78 Bond restraints: 8272 Sorted by residual: bond pdb=" CG1 ILE A 834 " pdb=" CD1 ILE A 834 " ideal model delta sigma weight residual 1.513 1.467 0.046 3.90e-02 6.57e+02 1.38e+00 bond pdb=" CA SER B1103 " pdb=" C SER B1103 " ideal model delta sigma weight residual 1.523 1.502 0.021 1.80e-02 3.09e+03 1.35e+00 bond pdb=" CA VAL B 819 " pdb=" CB VAL B 819 " ideal model delta sigma weight residual 1.540 1.525 0.015 1.36e-02 5.41e+03 1.24e+00 bond pdb=" CG LYS B1022 " pdb=" CD LYS B1022 " ideal model delta sigma weight residual 1.520 1.552 -0.032 3.00e-02 1.11e+03 1.13e+00 bond pdb=" N THR B1058 " pdb=" CA THR B1058 " ideal model delta sigma weight residual 1.457 1.471 -0.013 1.29e-02 6.01e+03 1.08e+00 ... (remaining 8267 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.67: 10943 1.67 - 3.33: 228 3.33 - 5.00: 43 5.00 - 6.67: 9 6.67 - 8.33: 3 Bond angle restraints: 11226 Sorted by residual: angle pdb=" C ALA B1057 " pdb=" N THR B1058 " pdb=" CA THR B1058 " ideal model delta sigma weight residual 121.54 129.87 -8.33 1.91e+00 2.74e-01 1.90e+01 angle pdb=" C ALA B1074 " pdb=" N VAL B1075 " pdb=" CA VAL B1075 " ideal model delta sigma weight residual 121.97 127.85 -5.88 1.80e+00 3.09e-01 1.07e+01 angle pdb=" CB LYS A1022 " pdb=" CG LYS A1022 " pdb=" CD LYS A1022 " ideal model delta sigma weight residual 111.30 118.53 -7.23 2.30e+00 1.89e-01 9.88e+00 angle pdb=" CB LYS B1022 " pdb=" CG LYS B1022 " pdb=" CD LYS B1022 " ideal model delta sigma weight residual 111.30 118.44 -7.14 2.30e+00 1.89e-01 9.64e+00 angle pdb=" N LYS A1073 " pdb=" CA LYS A1073 " pdb=" C LYS A1073 " ideal model delta sigma weight residual 108.19 112.16 -3.97 1.29e+00 6.01e-01 9.47e+00 ... (remaining 11221 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 4411 17.95 - 35.89: 410 35.89 - 53.84: 56 53.84 - 71.78: 11 71.78 - 89.73: 6 Dihedral angle restraints: 4894 sinusoidal: 1950 harmonic: 2944 Sorted by residual: dihedral pdb=" CA SER B1072 " pdb=" C SER B1072 " pdb=" N LYS B1073 " pdb=" CA LYS B1073 " ideal model delta harmonic sigma weight residual 180.00 -160.38 -19.62 0 5.00e+00 4.00e-02 1.54e+01 dihedral pdb=" CA SER A 784 " pdb=" C SER A 784 " pdb=" N ASN A 785 " pdb=" CA ASN A 785 " ideal model delta harmonic sigma weight residual 180.00 161.28 18.72 0 5.00e+00 4.00e-02 1.40e+01 dihedral pdb=" CA GLY A1107 " pdb=" C GLY A1107 " pdb=" N ASP A1108 " pdb=" CA ASP A1108 " ideal model delta harmonic sigma weight residual 180.00 162.01 17.99 0 5.00e+00 4.00e-02 1.30e+01 ... (remaining 4891 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 726 0.030 - 0.060: 450 0.060 - 0.090: 84 0.090 - 0.120: 54 0.120 - 0.150: 16 Chirality restraints: 1330 Sorted by residual: chirality pdb=" CA ASN A1066 " pdb=" N ASN A1066 " pdb=" C ASN A1066 " pdb=" CB ASN A1066 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.61e-01 chirality pdb=" CA ASN B1066 " pdb=" N ASN B1066 " pdb=" C ASN B1066 " pdb=" CB ASN B1066 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.58e-01 chirality pdb=" CA MET B 947 " pdb=" N MET B 947 " pdb=" C MET B 947 " pdb=" CB MET B 947 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.15e-01 ... (remaining 1327 not shown) Planarity restraints: 1378 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR A 693 " -0.042 5.00e-02 4.00e+02 6.31e-02 6.37e+00 pdb=" N PRO A 694 " 0.109 5.00e-02 4.00e+02 pdb=" CA PRO A 694 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 694 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR B 693 " 0.041 5.00e-02 4.00e+02 6.29e-02 6.33e+00 pdb=" N PRO B 694 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO B 694 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 694 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 705 " 0.026 5.00e-02 4.00e+02 3.98e-02 2.53e+00 pdb=" N PRO B 706 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO B 706 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 706 " 0.022 5.00e-02 4.00e+02 ... (remaining 1375 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.82: 2304 2.82 - 3.34: 7636 3.34 - 3.86: 12166 3.86 - 4.38: 13877 4.38 - 4.90: 25290 Nonbonded interactions: 61273 Sorted by model distance: nonbonded pdb=" N GLY A 684 " pdb=" OE2 GLU A 811 " model vdw 2.306 3.120 nonbonded pdb=" NE2 GLN B1089 " pdb=" OG1 THR B1092 " model vdw 2.314 3.120 nonbonded pdb=" N GLY B 684 " pdb=" OE2 GLU B 811 " model vdw 2.328 3.120 nonbonded pdb=" O ALA B1074 " pdb=" N ALA B1076 " model vdw 2.377 3.120 nonbonded pdb=" O GLY A 758 " pdb=" NH2 ARG A1090 " model vdw 2.432 3.120 ... (remaining 61268 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 1.220 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: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 7.920 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.010 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:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 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 : 0.005 0.046 8272 Z= 0.206 Angle : 0.637 8.332 11226 Z= 0.340 Chirality : 0.042 0.150 1330 Planarity : 0.005 0.063 1378 Dihedral : 14.001 89.730 2990 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.30 % Allowed : 3.94 % Favored : 95.76 % Rotamer: Outliers : 0.11 % Allowed : 0.11 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.79 (0.26), residues: 1014 helix: 1.41 (0.21), residues: 634 sheet: None (None), residues: 0 loop : -1.00 (0.31), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 933 TYR 0.011 0.002 TYR B1124 PHE 0.009 0.002 PHE A1166 TRP 0.010 0.001 TRP B 795 HIS 0.007 0.001 HIS A1149 Details of bonding type rmsd covalent geometry : bond 0.00509 ( 8272) covalent geometry : angle 0.63665 (11226) hydrogen bonds : bond 0.15890 ( 456) hydrogen bonds : angle 4.52948 ( 1341) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 144 time to evaluate : 0.295 Fit side-chains REVERT: A 688 ASP cc_start: 0.7135 (m-30) cc_final: 0.6919 (m-30) outliers start: 1 outliers final: 1 residues processed: 145 average time/residue: 0.1032 time to fit residues: 19.3518 Evaluate side-chains 132 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 131 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1089 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 0.5980 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 8.9990 chunk 100 optimal weight: 0.3980 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 785 ASN A1027 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.141571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.102028 restraints weight = 8698.898| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 1.82 r_work: 0.2888 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2737 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.0843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8272 Z= 0.131 Angle : 0.535 8.764 11226 Z= 0.273 Chirality : 0.039 0.141 1330 Planarity : 0.005 0.068 1378 Dihedral : 4.324 50.109 1099 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.30 % Allowed : 3.94 % Favored : 95.76 % Rotamer: Outliers : 1.71 % Allowed : 5.81 % Favored : 92.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.26 (0.27), residues: 1014 helix: 1.80 (0.21), residues: 660 sheet: None (None), residues: 0 loop : -1.04 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 933 TYR 0.010 0.001 TYR B1124 PHE 0.010 0.001 PHE A 774 TRP 0.009 0.001 TRP B 795 HIS 0.004 0.001 HIS A1149 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 8272) covalent geometry : angle 0.53463 (11226) hydrogen bonds : bond 0.05678 ( 456) hydrogen bonds : angle 3.66209 ( 1341) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 137 time to evaluate : 0.329 Fit side-chains REVERT: A 688 ASP cc_start: 0.6609 (m-30) cc_final: 0.6391 (m-30) REVERT: A 805 LEU cc_start: 0.7649 (OUTLIER) cc_final: 0.7258 (mp) REVERT: A 1163 MET cc_start: 0.8045 (ttp) cc_final: 0.7831 (ttm) REVERT: B 805 LEU cc_start: 0.7752 (OUTLIER) cc_final: 0.7346 (mp) outliers start: 15 outliers final: 9 residues processed: 143 average time/residue: 0.1005 time to fit residues: 19.0280 Evaluate side-chains 141 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 130 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 698 SER Chi-restraints excluded: chain A residue 735 GLN Chi-restraints excluded: chain A residue 785 ASN Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 916 PHE Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 698 SER Chi-restraints excluded: chain B residue 735 GLN Chi-restraints excluded: chain B residue 805 LEU Chi-restraints excluded: chain B residue 1205 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 61 optimal weight: 0.6980 chunk 39 optimal weight: 4.9990 chunk 75 optimal weight: 1.9990 chunk 96 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 chunk 2 optimal weight: 0.7980 chunk 4 optimal weight: 0.5980 chunk 9 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.142219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.101911 restraints weight = 8590.123| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 1.95 r_work: 0.2881 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2730 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.1000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 8272 Z= 0.127 Angle : 0.510 8.726 11226 Z= 0.261 Chirality : 0.039 0.135 1330 Planarity : 0.005 0.069 1378 Dihedral : 3.692 18.189 1096 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.30 % Allowed : 3.85 % Favored : 95.86 % Rotamer: Outliers : 1.14 % Allowed : 8.43 % Favored : 90.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.41 (0.27), residues: 1014 helix: 1.95 (0.21), residues: 660 sheet: None (None), residues: 0 loop : -1.05 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 690 TYR 0.009 0.001 TYR B1124 PHE 0.010 0.001 PHE A 774 TRP 0.010 0.001 TRP B 795 HIS 0.005 0.001 HIS A 786 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 8272) covalent geometry : angle 0.51019 (11226) hydrogen bonds : bond 0.05350 ( 456) hydrogen bonds : angle 3.56414 ( 1341) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 133 time to evaluate : 0.228 Fit side-chains REVERT: A 688 ASP cc_start: 0.6591 (m-30) cc_final: 0.6362 (m-30) REVERT: A 805 LEU cc_start: 0.7621 (OUTLIER) cc_final: 0.7261 (mp) REVERT: B 805 LEU cc_start: 0.7717 (OUTLIER) cc_final: 0.7313 (mp) outliers start: 10 outliers final: 6 residues processed: 137 average time/residue: 0.0999 time to fit residues: 17.8344 Evaluate side-chains 138 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 130 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 698 SER Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 916 PHE Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 698 SER Chi-restraints excluded: chain B residue 735 GLN Chi-restraints excluded: chain B residue 805 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 26 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 45 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 chunk 41 optimal weight: 0.6980 chunk 15 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 86 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.143478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.106240 restraints weight = 8754.840| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 1.69 r_work: 0.2921 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2778 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.1152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 8272 Z= 0.123 Angle : 0.496 8.632 11226 Z= 0.252 Chirality : 0.038 0.138 1330 Planarity : 0.005 0.068 1378 Dihedral : 3.615 17.667 1096 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.30 % Allowed : 3.55 % Favored : 96.15 % Rotamer: Outliers : 1.59 % Allowed : 9.68 % Favored : 88.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.50 (0.27), residues: 1014 helix: 2.01 (0.21), residues: 660 sheet: None (None), residues: 0 loop : -1.01 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 690 TYR 0.009 0.001 TYR B1124 PHE 0.010 0.001 PHE A 774 TRP 0.009 0.001 TRP B 795 HIS 0.004 0.001 HIS A1149 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 8272) covalent geometry : angle 0.49571 (11226) hydrogen bonds : bond 0.05098 ( 456) hydrogen bonds : angle 3.50578 ( 1341) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 129 time to evaluate : 0.313 Fit side-chains REVERT: A 805 LEU cc_start: 0.7676 (OUTLIER) cc_final: 0.7285 (mp) REVERT: B 805 LEU cc_start: 0.7705 (OUTLIER) cc_final: 0.7300 (mp) outliers start: 14 outliers final: 7 residues processed: 135 average time/residue: 0.0934 time to fit residues: 16.5543 Evaluate side-chains 137 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 128 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 698 SER Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 970 VAL Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 698 SER Chi-restraints excluded: chain B residue 805 LEU Chi-restraints excluded: chain B residue 970 VAL Chi-restraints excluded: chain B residue 1023 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 46 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 34 optimal weight: 3.9990 chunk 2 optimal weight: 0.0870 chunk 3 optimal weight: 2.9990 chunk 71 optimal weight: 0.9990 chunk 78 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 overall best weight: 0.8162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.142978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.105281 restraints weight = 8715.484| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 1.65 r_work: 0.2923 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2780 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.1228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 8272 Z= 0.124 Angle : 0.493 8.585 11226 Z= 0.251 Chirality : 0.038 0.142 1330 Planarity : 0.005 0.068 1378 Dihedral : 3.575 16.665 1096 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.35 % Favored : 96.45 % Rotamer: Outliers : 1.59 % Allowed : 10.71 % Favored : 87.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.54 (0.27), residues: 1014 helix: 2.04 (0.21), residues: 660 sheet: None (None), residues: 0 loop : -0.98 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 690 TYR 0.009 0.001 TYR A1124 PHE 0.010 0.001 PHE A 774 TRP 0.009 0.001 TRP B 795 HIS 0.004 0.001 HIS A1149 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 8272) covalent geometry : angle 0.49337 (11226) hydrogen bonds : bond 0.05068 ( 456) hydrogen bonds : angle 3.48377 ( 1341) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 130 time to evaluate : 0.192 Fit side-chains REVERT: A 805 LEU cc_start: 0.7642 (OUTLIER) cc_final: 0.7277 (mp) REVERT: B 805 LEU cc_start: 0.7662 (OUTLIER) cc_final: 0.7268 (mp) outliers start: 14 outliers final: 10 residues processed: 135 average time/residue: 0.0824 time to fit residues: 14.7061 Evaluate side-chains 142 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 130 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 698 SER Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 947 MET Chi-restraints excluded: chain A residue 970 VAL Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 698 SER Chi-restraints excluded: chain B residue 805 LEU Chi-restraints excluded: chain B residue 916 PHE Chi-restraints excluded: chain B residue 947 MET Chi-restraints excluded: chain B residue 970 VAL Chi-restraints excluded: chain B residue 1088 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 31 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 51 optimal weight: 8.9990 chunk 89 optimal weight: 3.9990 chunk 5 optimal weight: 0.8980 chunk 39 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 28 optimal weight: 4.9990 chunk 30 optimal weight: 0.9980 chunk 69 optimal weight: 4.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.139464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.100786 restraints weight = 8711.070| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 1.77 r_work: 0.2869 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2719 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.1157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 8272 Z= 0.174 Angle : 0.548 8.493 11226 Z= 0.279 Chirality : 0.040 0.153 1330 Planarity : 0.005 0.069 1378 Dihedral : 3.717 17.258 1096 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.85 % Favored : 95.96 % Rotamer: Outliers : 1.71 % Allowed : 11.16 % Favored : 87.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.43 (0.27), residues: 1014 helix: 2.05 (0.21), residues: 646 sheet: None (None), residues: 0 loop : -1.11 (0.31), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1090 TYR 0.012 0.001 TYR A1124 PHE 0.010 0.001 PHE A 774 TRP 0.009 0.001 TRP B 795 HIS 0.005 0.001 HIS A1149 Details of bonding type rmsd covalent geometry : bond 0.00438 ( 8272) covalent geometry : angle 0.54825 (11226) hydrogen bonds : bond 0.06200 ( 456) hydrogen bonds : angle 3.57163 ( 1341) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 134 time to evaluate : 0.313 Fit side-chains REVERT: A 805 LEU cc_start: 0.7618 (OUTLIER) cc_final: 0.7260 (mp) REVERT: B 805 LEU cc_start: 0.7651 (OUTLIER) cc_final: 0.7271 (mp) outliers start: 15 outliers final: 7 residues processed: 139 average time/residue: 0.0890 time to fit residues: 16.3917 Evaluate side-chains 140 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 131 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 698 SER Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 970 VAL Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 698 SER Chi-restraints excluded: chain B residue 805 LEU Chi-restraints excluded: chain B residue 970 VAL Chi-restraints excluded: chain B residue 1088 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 88 optimal weight: 8.9990 chunk 17 optimal weight: 0.8980 chunk 63 optimal weight: 0.4980 chunk 32 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 chunk 68 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 chunk 43 optimal weight: 0.0770 overall best weight: 0.6940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.142242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.102431 restraints weight = 8755.000| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 1.98 r_work: 0.2886 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2736 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.1313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 8272 Z= 0.116 Angle : 0.488 8.487 11226 Z= 0.249 Chirality : 0.038 0.145 1330 Planarity : 0.005 0.068 1378 Dihedral : 3.566 15.766 1096 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.45 % Favored : 96.35 % Rotamer: Outliers : 1.14 % Allowed : 11.96 % Favored : 86.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.54 (0.27), residues: 1014 helix: 2.03 (0.21), residues: 660 sheet: None (None), residues: 0 loop : -0.95 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B1090 TYR 0.009 0.001 TYR A1124 PHE 0.010 0.001 PHE A 774 TRP 0.010 0.001 TRP B 795 HIS 0.003 0.001 HIS B 850 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 8272) covalent geometry : angle 0.48840 (11226) hydrogen bonds : bond 0.04823 ( 456) hydrogen bonds : angle 3.50982 ( 1341) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 137 time to evaluate : 0.326 Fit side-chains REVERT: A 805 LEU cc_start: 0.7648 (OUTLIER) cc_final: 0.7311 (mp) REVERT: B 805 LEU cc_start: 0.7650 (OUTLIER) cc_final: 0.7292 (mp) outliers start: 10 outliers final: 8 residues processed: 141 average time/residue: 0.1211 time to fit residues: 22.3304 Evaluate side-chains 142 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 132 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 698 SER Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 970 VAL Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 698 SER Chi-restraints excluded: chain B residue 785 ASN Chi-restraints excluded: chain B residue 805 LEU Chi-restraints excluded: chain B residue 970 VAL Chi-restraints excluded: chain B residue 1088 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 52 optimal weight: 2.9990 chunk 91 optimal weight: 0.0010 chunk 30 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 chunk 4 optimal weight: 0.5980 chunk 83 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 31 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 overall best weight: 0.8790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.141458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.101862 restraints weight = 8615.206| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 1.92 r_work: 0.2879 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2728 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.1331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8272 Z= 0.130 Angle : 0.501 8.455 11226 Z= 0.255 Chirality : 0.039 0.150 1330 Planarity : 0.005 0.069 1378 Dihedral : 3.552 15.474 1096 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.65 % Favored : 96.15 % Rotamer: Outliers : 1.25 % Allowed : 12.41 % Favored : 86.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.58 (0.27), residues: 1014 helix: 2.16 (0.21), residues: 646 sheet: None (None), residues: 0 loop : -1.04 (0.32), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1090 TYR 0.010 0.001 TYR A1124 PHE 0.010 0.001 PHE A 774 TRP 0.010 0.001 TRP B 795 HIS 0.003 0.001 HIS A 850 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 8272) covalent geometry : angle 0.50121 (11226) hydrogen bonds : bond 0.05176 ( 456) hydrogen bonds : angle 3.49982 ( 1341) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 135 time to evaluate : 0.318 Fit side-chains REVERT: A 805 LEU cc_start: 0.7632 (OUTLIER) cc_final: 0.7298 (mp) REVERT: B 805 LEU cc_start: 0.7599 (OUTLIER) cc_final: 0.7238 (mp) outliers start: 11 outliers final: 7 residues processed: 141 average time/residue: 0.1137 time to fit residues: 21.0856 Evaluate side-chains 143 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 134 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 698 SER Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 970 VAL Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 698 SER Chi-restraints excluded: chain B residue 805 LEU Chi-restraints excluded: chain B residue 970 VAL Chi-restraints excluded: chain B residue 1088 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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: 51.0142 > 50: distance: 25 - 26: 4.274 distance: 26 - 29: 3.630 distance: 27 - 28: 4.364 distance: 27 - 33: 5.673 distance: 29 - 30: 10.978 distance: 30 - 31: 10.436 distance: 30 - 32: 9.682 distance: 33 - 34: 6.587 distance: 34 - 35: 5.255 distance: 34 - 37: 5.786 distance: 35 - 36: 26.310 distance: 35 - 43: 15.173 distance: 37 - 38: 7.585 distance: 38 - 39: 12.441 distance: 38 - 40: 3.304 distance: 39 - 41: 6.026 distance: 40 - 42: 3.208 distance: 41 - 42: 7.622 distance: 43 - 44: 11.046 distance: 44 - 45: 25.804 distance: 45 - 46: 8.804 distance: 45 - 47: 9.744 distance: 47 - 48: 11.372 distance: 48 - 49: 6.036 distance: 48 - 51: 10.503 distance: 49 - 50: 16.135 distance: 51 - 52: 15.406 distance: 53 - 54: 25.155 distance: 54 - 55: 9.684 distance: 54 - 57: 19.285 distance: 55 - 56: 4.088 distance: 55 - 62: 9.285 distance: 57 - 58: 20.782 distance: 58 - 59: 10.222 distance: 59 - 60: 26.079 distance: 60 - 61: 15.975 distance: 62 - 63: 14.452 distance: 62 - 68: 11.349 distance: 63 - 66: 8.423 distance: 64 - 65: 4.048 distance: 64 - 69: 5.821 distance: 66 - 67: 16.338 distance: 67 - 68: 7.247 distance: 69 - 70: 15.036 distance: 70 - 71: 16.833 distance: 70 - 73: 12.497 distance: 71 - 72: 9.255 distance: 71 - 80: 17.324 distance: 73 - 74: 17.135 distance: 74 - 75: 15.528 distance: 75 - 76: 14.515 distance: 76 - 77: 8.428 distance: 77 - 78: 13.930 distance: 77 - 79: 5.719 distance: 80 - 81: 48.648 distance: 81 - 82: 40.139 distance: 82 - 83: 31.052 distance: 82 - 84: 17.113 distance: 84 - 85: 19.057 distance: 85 - 86: 8.041 distance: 85 - 88: 10.409 distance: 86 - 87: 17.403 distance: 86 - 93: 3.850 distance: 88 - 89: 11.920 distance: 89 - 90: 14.448 distance: 90 - 91: 16.868 distance: 90 - 92: 11.009 distance: 93 - 94: 3.217 distance: 93 - 99: 7.899 distance: 94 - 95: 11.522 distance: 94 - 97: 17.453 distance: 95 - 96: 7.130 distance: 95 - 100: 13.185 distance: 97 - 98: 4.056 distance: 98 - 99: 13.786