Starting phenix.real_space_refine on Sat Aug 3 12:15:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gve_34291/08_2024/8gve_34291.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gve_34291/08_2024/8gve_34291.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gve_34291/08_2024/8gve_34291.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gve_34291/08_2024/8gve_34291.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gve_34291/08_2024/8gve_34291.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gve_34291/08_2024/8gve_34291.cif" } resolution = 3.17 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.142 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 5359 2.51 5 N 1323 2.21 5 O 1326 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 682": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 742": "OE1" <-> "OE2" Residue "B GLU 849": "OE1" <-> "OE2" Residue "B PHE 926": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 937": "OD1" <-> "OD2" Residue "B PHE 1005": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1085": "OE1" <-> "OE2" Residue "B GLU 1220": "OE1" <-> "OE2" Residue "A ASP 673": "OD1" <-> "OD2" Residue "A ASP 688": "OD1" <-> "OD2" Residue "A ASP 699": "OD1" <-> "OD2" Residue "A TYR 716": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 776": "OE1" <-> "OE2" Residue "A PHE 818": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 847": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 937": "OD1" <-> "OD2" Residue "A ASP 951": "OD1" <-> "OD2" Residue "A ASP 956": "OD1" <-> "OD2" Residue "A PHE 1049": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1217": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 8054 Number of models: 1 Model: "" Number of chains: 2 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 Chain: "A" Number of atoms: 4018 Number of conformers: 1 Conformer: "" Number of residues, atoms: 509, 4018 Classifications: {'peptide': 509} Link IDs: {'PTRANS': 27, 'TRANS': 481} Chain breaks: 1 Time building chain proxies: 5.20, per 1000 atoms: 0.65 Number of scatterers: 8054 At special positions: 0 Unit cell: (80.3, 73.7, 132, 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 1326 8.00 N 1323 7.00 C 5359 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.08 Conformation dependent library (CDL) restraints added in 1.4 seconds 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1900 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 3 sheets defined 72.1% alpha, 0.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.87 Creating SS restraints... Processing helix chain 'B' and resid 682 through 693 removed outlier: 3.509A pdb=" N TYR B 693 " --> pdb=" O VAL B 689 " (cutoff:3.500A) Processing helix chain 'B' and resid 696 through 702 removed outlier: 3.615A pdb=" N PHE B 700 " --> pdb=" O TYR B 696 " (cutoff:3.500A) Processing helix chain 'B' and resid 705 through 734 removed outlier: 3.973A pdb=" N LEU B 709 " --> pdb=" O ASP B 705 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA B 710 " --> pdb=" O PRO B 706 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N PHE B 717 " --> pdb=" O ILE B 713 " (cutoff:3.500A) removed outlier: 3.731A 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 739 through 758 removed outlier: 3.839A pdb=" N LEU B 743 " --> pdb=" O GLY B 739 " (cutoff:3.500A) Processing helix chain 'B' and resid 768 through 785 Processing helix chain 'B' and resid 789 through 810 removed outlier: 3.767A pdb=" N VAL B 794 " --> pdb=" O LEU B 790 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N TRP B 795 " --> pdb=" O VAL B 791 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ILE B 796 " --> pdb=" O GLY B 792 " (cutoff:3.500A) Processing helix chain 'B' and resid 811 through 819 removed outlier: 3.868A pdb=" N PHE B 814 " --> pdb=" O GLU B 811 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU B 815 " --> pdb=" O GLY B 812 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL B 816 " --> pdb=" O SER B 813 " (cutoff:3.500A) Processing helix chain 'B' and resid 820 through 848 removed outlier: 4.121A pdb=" N ILE B 826 " --> pdb=" O PHE B 822 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA B 828 " --> pdb=" O GLN B 824 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N THR B 839 " --> pdb=" O PHE B 835 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LYS B 842 " --> pdb=" O GLU B 838 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N LEU B 843 " --> pdb=" O THR B 839 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL B 844 " --> pdb=" O PHE B 840 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LYS B 845 " --> pdb=" O TYR B 841 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ILE B 846 " --> pdb=" O LYS B 842 " (cutoff:3.500A) Processing helix chain 'B' and resid 900 through 923 removed outlier: 3.773A pdb=" N ASN B 923 " --> pdb=" O ARG B 919 " (cutoff:3.500A) Processing helix chain 'B' and resid 928 through 938 Processing helix chain 'B' and resid 938 through 954 removed outlier: 3.778A pdb=" N ILE B 942 " --> pdb=" O PHE B 938 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ILE B 954 " --> pdb=" O VAL B 950 " (cutoff:3.500A) Processing helix chain 'B' and resid 990 through 997 removed outlier: 3.871A pdb=" N MET B 994 " --> pdb=" O PRO B 990 " (cutoff:3.500A) removed outlier: 3.693A 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) Processing helix chain 'B' and resid 1035 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 1057 through 1067 Processing helix chain 'B' and resid 1090 through 1102 removed outlier: 4.104A pdb=" N LEU B1094 " --> pdb=" O ARG B1090 " (cutoff:3.500A) Processing helix chain 'B' and resid 1109 through 1113 removed outlier: 3.549A pdb=" N GLN B1112 " --> pdb=" O LEU B1109 " (cutoff:3.500A) Processing helix chain 'B' and resid 1114 through 1129 removed outlier: 4.004A pdb=" N LEU B1118 " --> pdb=" O PRO B1114 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N GLY B1120 " --> pdb=" O ALA B1116 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ILE B1121 " --> pdb=" O VAL B1117 " (cutoff:3.500A) Processing helix chain 'B' and resid 1133 through 1144 removed outlier: 3.591A pdb=" N GLU B1137 " --> pdb=" O ILE B1133 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU B1142 " --> pdb=" O ARG B1138 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N LEU B1143 " --> pdb=" O LEU B1139 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N MET B1144 " --> pdb=" O HIS B1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 1145 through 1149 removed outlier: 3.620A pdb=" N HIS B1149 " --> pdb=" O PRO B1146 " (cutoff:3.500A) Processing helix chain 'B' and resid 1152 through 1157 removed outlier: 3.656A pdb=" N LYS B1156 " --> pdb=" O VAL B1152 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LYS B1157 " --> pdb=" O THR B1153 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1152 through 1157' Processing helix chain 'B' and resid 1160 through 1183 removed outlier: 3.610A pdb=" N HIS B1164 " --> pdb=" O THR B1160 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU B1165 " --> pdb=" O LEU B1161 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N PHE B1166 " --> pdb=" O ARG B1162 " (cutoff:3.500A) Processing helix chain 'B' and resid 1188 through 1195 Processing helix chain 'B' and resid 1195 through 1208 removed outlier: 3.582A pdb=" N LEU B1199 " --> pdb=" O LEU B1195 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N LEU B1204 " --> pdb=" O ARG B1200 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N THR B1205 " --> pdb=" O MET B1201 " (cutoff:3.500A) Processing helix chain 'B' and resid 1209 through 1217 removed outlier: 3.639A pdb=" N ASP B1217 " --> pdb=" O MET B1213 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 690 Processing helix chain 'A' and resid 692 through 694 No H-bonds generated for 'chain 'A' and resid 692 through 694' Processing helix chain 'A' and resid 695 through 702 removed outlier: 3.963A pdb=" N ASP A 702 " --> pdb=" O SER A 698 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 735 removed outlier: 3.999A pdb=" N ALA A 710 " --> pdb=" O PRO A 706 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA A 711 " --> pdb=" O GLN A 707 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N SER A 721 " --> pdb=" O PHE A 717 " (cutoff:3.500A) Proline residue: A 722 - end of helix removed outlier: 3.862A pdb=" N GLN A 735 " --> pdb=" O GLY A 731 " (cutoff:3.500A) Processing helix chain 'A' and resid 740 through 757 removed outlier: 3.558A pdb=" N VAL A 753 " --> pdb=" O LEU A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 768 through 785 Processing helix chain 'A' and resid 788 through 811 removed outlier: 3.767A pdb=" N TRP A 799 " --> pdb=" O TRP A 795 " (cutoff:3.500A) Processing helix chain 'A' and resid 812 through 819 removed outlier: 3.548A pdb=" N LEU A 815 " --> pdb=" O GLY A 812 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL A 816 " --> pdb=" O SER A 813 " (cutoff:3.500A) Processing helix chain 'A' and resid 820 through 845 removed outlier: 3.589A pdb=" N GLN A 824 " --> pdb=" O SER A 820 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ILE A 826 " --> pdb=" O PHE A 822 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N THR A 839 " --> pdb=" O PHE A 835 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N PHE A 840 " --> pdb=" O ILE A 836 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LYS A 842 " --> pdb=" O GLU A 838 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU A 843 " --> pdb=" O THR A 839 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL A 844 " --> pdb=" O PHE A 840 " (cutoff:3.500A) Processing helix chain 'A' and resid 845 through 850 removed outlier: 3.916A pdb=" N GLU A 849 " --> pdb=" O LYS A 845 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N HIS A 850 " --> pdb=" O ILE A 846 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 845 through 850' Processing helix chain 'A' and resid 899 through 923 removed outlier: 3.624A pdb=" N LEU A 903 " --> pdb=" O ASN A 899 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N SER A 904 " --> pdb=" O THR A 900 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LEU A 905 " --> pdb=" O ALA A 901 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ASN A 923 " --> pdb=" O ARG A 919 " (cutoff:3.500A) Processing helix chain 'A' and resid 929 through 938 Processing helix chain 'A' and resid 939 through 954 removed outlier: 3.533A pdb=" N ILE A 954 " --> pdb=" O VAL A 950 " (cutoff:3.500A) Processing helix chain 'A' and resid 990 through 994 Processing helix chain 'A' and resid 998 through 1020 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 1058 through 1068 Processing helix chain 'A' and resid 1093 through 1102 removed outlier: 3.620A pdb=" N LEU A1099 " --> pdb=" O LEU A1095 " (cutoff:3.500A) Processing helix chain 'A' and resid 1106 through 1111 Processing helix chain 'A' and resid 1114 through 1129 removed outlier: 4.358A pdb=" N LEU A1118 " --> pdb=" O PRO A1114 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N PHE A1119 " --> pdb=" O LEU A1115 " (cutoff:3.500A) Processing helix chain 'A' and resid 1133 through 1142 removed outlier: 3.677A pdb=" N GLU A1137 " --> pdb=" O ILE A1133 " (cutoff:3.500A) Processing helix chain 'A' and resid 1143 through 1144 No H-bonds generated for 'chain 'A' and resid 1143 through 1144' Processing helix chain 'A' and resid 1145 through 1149 removed outlier: 3.693A pdb=" N HIS A1149 " --> pdb=" O PRO A1146 " (cutoff:3.500A) Processing helix chain 'A' and resid 1152 through 1157 removed outlier: 3.970A pdb=" N LYS A1156 " --> pdb=" O VAL A1152 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LYS A1157 " --> pdb=" O THR A1153 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1152 through 1157' Processing helix chain 'A' and resid 1159 through 1183 removed outlier: 3.899A pdb=" N CYS A1173 " --> pdb=" O LEU A1169 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU A1174 " --> pdb=" O GLN A1170 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER A1182 " --> pdb=" O TRP A1178 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N THR A1183 " --> pdb=" O ALA A1179 " (cutoff:3.500A) Processing helix chain 'A' and resid 1188 through 1208 removed outlier: 3.795A pdb=" N ILE A1192 " --> pdb=" O ALA A1188 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU A1193 " --> pdb=" O PHE A1189 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE A1194 " --> pdb=" O PRO A1190 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N VAL A1197 " --> pdb=" O LEU A1193 " (cutoff:3.500A) Proline residue: A1198 - end of helix removed outlier: 4.322A pdb=" N LEU A1204 " --> pdb=" O ARG A1200 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N THR A1205 " --> pdb=" O MET A1201 " (cutoff:3.500A) Processing helix chain 'A' and resid 1211 through 1216 removed outlier: 3.641A pdb=" N CYS A1215 " --> pdb=" O ARG A1211 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 765 through 766 removed outlier: 3.641A pdb=" N ALA B1055 " --> pdb=" O GLY B 766 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 1070 through 1071 Processing sheet with id=AA3, first strand: chain 'A' and resid 764 through 766 removed outlier: 4.462A pdb=" N VAL A 764 " --> pdb=" O ALA A1057 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALA A1055 " --> pdb=" O GLY A 766 " (cutoff:3.500A) 439 hydrogen bonds defined for protein. 1281 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: 2.24 Time building geometry restraints manager: 3.40 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: 2460 1.34 - 1.46: 1796 1.46 - 1.58: 3920 1.58 - 1.70: 0 1.70 - 1.82: 78 Bond restraints: 8254 Sorted by residual: bond pdb=" C LYS B 893 " pdb=" N PRO B 894 " ideal model delta sigma weight residual 1.332 1.355 -0.023 1.34e-02 5.57e+03 3.06e+00 bond pdb=" CB MET A1042 " pdb=" CG MET A1042 " ideal model delta sigma weight residual 1.520 1.493 0.027 3.00e-02 1.11e+03 8.28e-01 bond pdb=" CB PHE A1122 " pdb=" CG PHE A1122 " ideal model delta sigma weight residual 1.502 1.482 0.020 2.30e-02 1.89e+03 7.87e-01 bond pdb=" N PHE B 916 " pdb=" CA PHE B 916 " ideal model delta sigma weight residual 1.459 1.470 -0.010 1.21e-02 6.83e+03 7.41e-01 bond pdb=" C SER A 721 " pdb=" N PRO A 722 " ideal model delta sigma weight residual 1.335 1.347 -0.012 1.36e-02 5.41e+03 7.22e-01 ... (remaining 8249 not shown) Histogram of bond angle deviations from ideal: 99.47 - 106.39: 263 106.39 - 113.31: 4544 113.31 - 120.24: 3105 120.24 - 127.16: 3198 127.16 - 134.09: 92 Bond angle restraints: 11202 Sorted by residual: angle pdb=" CB MET B1213 " pdb=" CG MET B1213 " pdb=" SD MET B1213 " ideal model delta sigma weight residual 112.70 121.03 -8.33 3.00e+00 1.11e-01 7.71e+00 angle pdb=" N PHE B 916 " pdb=" CA PHE B 916 " pdb=" CB PHE B 916 " ideal model delta sigma weight residual 110.12 114.17 -4.05 1.47e+00 4.63e-01 7.58e+00 angle pdb=" C ARG A 692 " pdb=" N TYR A 693 " pdb=" CA TYR A 693 " ideal model delta sigma weight residual 120.09 123.20 -3.11 1.25e+00 6.40e-01 6.20e+00 angle pdb=" N TYR A 789 " pdb=" CA TYR A 789 " pdb=" C TYR A 789 " ideal model delta sigma weight residual 110.80 115.81 -5.01 2.13e+00 2.20e-01 5.53e+00 angle pdb=" N TYR B 693 " pdb=" CA TYR B 693 " pdb=" C TYR B 693 " ideal model delta sigma weight residual 109.81 114.94 -5.13 2.21e+00 2.05e-01 5.39e+00 ... (remaining 11197 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 4389 17.90 - 35.79: 413 35.79 - 53.69: 58 53.69 - 71.58: 10 71.58 - 89.48: 11 Dihedral angle restraints: 4881 sinusoidal: 1943 harmonic: 2938 Sorted by residual: dihedral pdb=" CA SER A1182 " pdb=" C SER A1182 " pdb=" N THR A1183 " pdb=" CA THR A1183 " ideal model delta harmonic sigma weight residual -180.00 -162.52 -17.48 0 5.00e+00 4.00e-02 1.22e+01 dihedral pdb=" CA GLY B1107 " pdb=" C GLY B1107 " pdb=" N ASP B1108 " pdb=" CA ASP B1108 " ideal model delta harmonic sigma weight residual 180.00 162.54 17.46 0 5.00e+00 4.00e-02 1.22e+01 dihedral pdb=" CA MET A1213 " pdb=" C MET A1213 " pdb=" N LYS A1214 " pdb=" CA LYS A1214 " ideal model delta harmonic sigma weight residual 180.00 163.04 16.96 0 5.00e+00 4.00e-02 1.15e+01 ... (remaining 4878 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 883 0.038 - 0.077: 347 0.077 - 0.115: 87 0.115 - 0.154: 8 0.154 - 0.192: 3 Chirality restraints: 1328 Sorted by residual: chirality pdb=" CA PHE B 916 " pdb=" N PHE B 916 " pdb=" C PHE B 916 " pdb=" CB PHE B 916 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.24e-01 chirality pdb=" CA ILE A 738 " pdb=" N ILE A 738 " pdb=" C ILE A 738 " pdb=" CB ILE A 738 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.20e-01 chirality pdb=" CB THR A1183 " pdb=" CA THR A1183 " pdb=" OG1 THR A1183 " pdb=" CG2 THR A1183 " both_signs ideal model delta sigma weight residual False 2.55 2.40 0.15 2.00e-01 2.50e+01 5.97e-01 ... (remaining 1325 not shown) Planarity restraints: 1374 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 916 " -0.031 2.00e-02 2.50e+03 2.53e-02 1.12e+01 pdb=" CG PHE B 916 " 0.058 2.00e-02 2.50e+03 pdb=" CD1 PHE B 916 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE B 916 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE B 916 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE B 916 " -0.011 2.00e-02 2.50e+03 pdb=" CZ PHE B 916 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR B 693 " 0.039 5.00e-02 4.00e+02 5.97e-02 5.70e+00 pdb=" N PRO B 694 " -0.103 5.00e-02 4.00e+02 pdb=" CA PRO B 694 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO B 694 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 893 " 0.037 5.00e-02 4.00e+02 5.67e-02 5.15e+00 pdb=" N PRO B 894 " -0.098 5.00e-02 4.00e+02 pdb=" CA PRO B 894 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 894 " 0.032 5.00e-02 4.00e+02 ... (remaining 1371 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 45 2.67 - 3.23: 7622 3.23 - 3.79: 11657 3.79 - 4.34: 15078 4.34 - 4.90: 26275 Nonbonded interactions: 60677 Sorted by model distance: nonbonded pdb=" OG SER A 820 " pdb=" NH1 ARG A1200 " model vdw 2.113 3.120 nonbonded pdb=" O LYS B 922 " pdb=" NH1 ARG B 933 " model vdw 2.327 3.120 nonbonded pdb=" NE2 GLN B1089 " pdb=" OG1 THR B1092 " model vdw 2.342 3.120 nonbonded pdb=" OE1 GLU B 775 " pdb=" OH TYR B 789 " model vdw 2.350 3.040 nonbonded pdb=" OD1 ASP A 699 " pdb=" NZ LYS A1028 " model vdw 2.358 3.120 ... (remaining 60672 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 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 673 through 855 or resid 894 through 1219)) } 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: 0.010 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: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 25.310 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 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 : 0.003 0.029 8254 Z= 0.224 Angle : 0.623 8.330 11202 Z= 0.316 Chirality : 0.042 0.192 1328 Planarity : 0.005 0.060 1374 Dihedral : 14.331 89.477 2981 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.28), residues: 1012 helix: 1.03 (0.21), residues: 646 sheet: None (None), residues: 0 loop : -1.27 (0.33), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 992 HIS 0.007 0.001 HIS A1064 PHE 0.058 0.002 PHE B 916 TYR 0.008 0.001 TYR B1154 ARG 0.008 0.000 ARG B 701 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 139 time to evaluate : 0.909 Fit side-chains REVERT: B 1157 LYS cc_start: 0.8708 (mppt) cc_final: 0.8354 (mptt) REVERT: A 1157 LYS cc_start: 0.8577 (mmmt) cc_final: 0.8318 (mmmt) outliers start: 0 outliers final: 0 residues processed: 139 average time/residue: 0.1937 time to fit residues: 37.0103 Evaluate side-chains 121 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 121 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 85 optimal weight: 3.9990 chunk 76 optimal weight: 5.9990 chunk 42 optimal weight: 2.9990 chunk 26 optimal weight: 6.9990 chunk 51 optimal weight: 9.9990 chunk 40 optimal weight: 2.9990 chunk 79 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 chunk 58 optimal weight: 0.6980 chunk 91 optimal weight: 0.6980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 735 GLN ** A1170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.0751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 8254 Z= 0.266 Angle : 0.607 7.360 11202 Z= 0.304 Chirality : 0.042 0.156 1328 Planarity : 0.005 0.059 1374 Dihedral : 4.184 19.018 1094 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 1.37 % Allowed : 7.31 % Favored : 91.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.28), residues: 1012 helix: 1.12 (0.22), residues: 648 sheet: None (None), residues: 0 loop : -1.35 (0.33), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 992 HIS 0.006 0.001 HIS A1064 PHE 0.021 0.002 PHE A1122 TYR 0.010 0.002 TYR B1124 ARG 0.003 0.000 ARG A 976 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 120 time to evaluate : 1.003 Fit side-chains REVERT: B 1071 MET cc_start: 0.7872 (mmm) cc_final: 0.7561 (mtt) REVERT: B 1157 LYS cc_start: 0.8757 (mppt) cc_final: 0.8421 (mptt) REVERT: A 1157 LYS cc_start: 0.8580 (mmmt) cc_final: 0.8337 (mmmt) outliers start: 12 outliers final: 9 residues processed: 124 average time/residue: 0.2210 time to fit residues: 36.5900 Evaluate side-chains 124 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 115 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 686 ILE Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 808 VAL Chi-restraints excluded: chain B residue 970 VAL Chi-restraints excluded: chain B residue 1180 VAL Chi-restraints excluded: chain A residue 756 LEU Chi-restraints excluded: chain A residue 979 VAL Chi-restraints excluded: chain A residue 1095 LEU Chi-restraints excluded: chain A residue 1176 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 50 optimal weight: 0.8980 chunk 28 optimal weight: 3.9990 chunk 76 optimal weight: 0.6980 chunk 62 optimal weight: 6.9990 chunk 25 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 81 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 73 optimal weight: 4.9990 chunk 90 optimal weight: 4.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 735 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.0996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8254 Z= 0.242 Angle : 0.573 7.599 11202 Z= 0.289 Chirality : 0.041 0.153 1328 Planarity : 0.005 0.059 1374 Dihedral : 4.167 18.734 1094 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 1.48 % Allowed : 10.16 % Favored : 88.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.28), residues: 1012 helix: 1.28 (0.22), residues: 643 sheet: None (None), residues: 0 loop : -1.43 (0.33), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 992 HIS 0.007 0.001 HIS A1064 PHE 0.016 0.001 PHE A1189 TYR 0.012 0.001 TYR B1124 ARG 0.006 0.000 ARG A 817 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 120 time to evaluate : 0.991 Fit side-chains revert: symmetry clash REVERT: B 916 PHE cc_start: 0.7887 (OUTLIER) cc_final: 0.7554 (t80) REVERT: A 1157 LYS cc_start: 0.8548 (mmmt) cc_final: 0.8334 (mmmt) outliers start: 13 outliers final: 7 residues processed: 126 average time/residue: 0.1915 time to fit residues: 33.4927 Evaluate side-chains 125 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 117 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 808 VAL Chi-restraints excluded: chain B residue 916 PHE Chi-restraints excluded: chain B residue 1180 VAL Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 756 LEU Chi-restraints excluded: chain A residue 757 LEU Chi-restraints excluded: chain A residue 979 VAL Chi-restraints excluded: chain A residue 1122 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 69 optimal weight: 0.9990 chunk 47 optimal weight: 0.3980 chunk 10 optimal weight: 0.8980 chunk 43 optimal weight: 0.0870 chunk 61 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 97 optimal weight: 0.7980 chunk 48 optimal weight: 0.8980 chunk 87 optimal weight: 0.0770 chunk 26 optimal weight: 3.9990 chunk 81 optimal weight: 5.9990 overall best weight: 0.4516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 735 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.1158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8254 Z= 0.153 Angle : 0.518 7.122 11202 Z= 0.259 Chirality : 0.039 0.159 1328 Planarity : 0.004 0.057 1374 Dihedral : 3.951 18.142 1094 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 1.48 % Allowed : 12.44 % Favored : 86.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.28), residues: 1012 helix: 1.49 (0.22), residues: 645 sheet: None (None), residues: 0 loop : -1.39 (0.33), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 992 HIS 0.003 0.000 HIS A1064 PHE 0.015 0.001 PHE A1189 TYR 0.007 0.001 TYR B 789 ARG 0.004 0.000 ARG B 701 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 123 time to evaluate : 0.926 Fit side-chains revert: symmetry clash REVERT: B 916 PHE cc_start: 0.7840 (OUTLIER) cc_final: 0.7510 (t80) REVERT: A 733 LYS cc_start: 0.7107 (ttmt) cc_final: 0.6572 (tptm) REVERT: A 1157 LYS cc_start: 0.8538 (mmmt) cc_final: 0.8332 (mmmt) REVERT: A 1206 ARG cc_start: 0.7720 (mpt180) cc_final: 0.7315 (tpp-160) outliers start: 13 outliers final: 8 residues processed: 129 average time/residue: 0.2123 time to fit residues: 36.8824 Evaluate side-chains 125 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 116 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 916 PHE Chi-restraints excluded: chain B residue 1183 THR Chi-restraints excluded: chain A residue 756 LEU Chi-restraints excluded: chain A residue 757 LEU Chi-restraints excluded: chain A residue 979 VAL Chi-restraints excluded: chain A residue 1095 LEU Chi-restraints excluded: chain A residue 1122 PHE Chi-restraints excluded: chain A residue 1195 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 55 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 83 optimal weight: 0.9990 chunk 67 optimal weight: 0.6980 chunk 0 optimal weight: 7.9990 chunk 49 optimal weight: 2.9990 chunk 87 optimal weight: 0.0010 chunk 24 optimal weight: 0.7980 chunk 32 optimal weight: 3.9990 overall best weight: 1.0990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 735 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.1216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 8254 Z= 0.240 Angle : 0.565 7.253 11202 Z= 0.283 Chirality : 0.041 0.152 1328 Planarity : 0.005 0.058 1374 Dihedral : 4.031 18.153 1094 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 2.05 % Allowed : 13.13 % Favored : 84.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.28), residues: 1012 helix: 1.43 (0.22), residues: 645 sheet: None (None), residues: 0 loop : -1.39 (0.33), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 992 HIS 0.007 0.001 HIS A1064 PHE 0.016 0.001 PHE A1189 TYR 0.012 0.001 TYR B1124 ARG 0.006 0.000 ARG B 701 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 120 time to evaluate : 0.841 Fit side-chains revert: symmetry clash REVERT: B 916 PHE cc_start: 0.7897 (OUTLIER) cc_final: 0.7584 (t80) REVERT: B 952 TYR cc_start: 0.8199 (t80) cc_final: 0.7921 (t80) REVERT: A 1157 LYS cc_start: 0.8513 (mmmt) cc_final: 0.8301 (mmmt) REVERT: A 1195 LEU cc_start: 0.8082 (OUTLIER) cc_final: 0.7731 (mp) REVERT: A 1206 ARG cc_start: 0.7762 (mpt180) cc_final: 0.7374 (tpp-160) outliers start: 18 outliers final: 15 residues processed: 128 average time/residue: 0.1994 time to fit residues: 34.6704 Evaluate side-chains 133 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 116 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 808 VAL Chi-restraints excluded: chain B residue 916 PHE Chi-restraints excluded: chain B residue 1022 LYS Chi-restraints excluded: chain B residue 1180 VAL Chi-restraints excluded: chain B residue 1183 THR Chi-restraints excluded: chain B residue 1199 LEU Chi-restraints excluded: chain B residue 1201 MET Chi-restraints excluded: chain A residue 756 LEU Chi-restraints excluded: chain A residue 757 LEU Chi-restraints excluded: chain A residue 908 MET Chi-restraints excluded: chain A residue 918 LEU Chi-restraints excluded: chain A residue 979 VAL Chi-restraints excluded: chain A residue 1083 ILE Chi-restraints excluded: chain A residue 1095 LEU Chi-restraints excluded: chain A residue 1122 PHE Chi-restraints excluded: chain A residue 1176 LEU Chi-restraints excluded: chain A residue 1195 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 87 optimal weight: 10.0000 chunk 19 optimal weight: 0.0870 chunk 57 optimal weight: 4.9990 chunk 24 optimal weight: 0.9990 chunk 97 optimal weight: 0.0970 chunk 81 optimal weight: 0.9980 chunk 45 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 32 optimal weight: 0.3980 chunk 51 optimal weight: 10.0000 chunk 94 optimal weight: 0.0370 overall best weight: 0.3234 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 735 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.1361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8254 Z= 0.145 Angle : 0.513 7.470 11202 Z= 0.254 Chirality : 0.038 0.161 1328 Planarity : 0.004 0.057 1374 Dihedral : 3.856 17.815 1094 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 1.37 % Allowed : 14.50 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.28), residues: 1012 helix: 1.63 (0.22), residues: 644 sheet: None (None), residues: 0 loop : -1.26 (0.33), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 795 HIS 0.002 0.000 HIS A1148 PHE 0.014 0.001 PHE A1189 TYR 0.007 0.001 TYR A 958 ARG 0.006 0.000 ARG B 701 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 121 time to evaluate : 0.916 Fit side-chains revert: symmetry clash REVERT: B 916 PHE cc_start: 0.7857 (OUTLIER) cc_final: 0.7559 (t80) REVERT: B 952 TYR cc_start: 0.8092 (t80) cc_final: 0.7842 (t80) REVERT: A 817 ARG cc_start: 0.7799 (mtm110) cc_final: 0.7434 (ttm110) REVERT: A 1157 LYS cc_start: 0.8516 (mmmt) cc_final: 0.8294 (mmmt) outliers start: 12 outliers final: 11 residues processed: 127 average time/residue: 0.2030 time to fit residues: 35.4439 Evaluate side-chains 129 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 117 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 916 PHE Chi-restraints excluded: chain B residue 1022 LYS Chi-restraints excluded: chain B residue 1183 THR Chi-restraints excluded: chain B residue 1199 LEU Chi-restraints excluded: chain A residue 756 LEU Chi-restraints excluded: chain A residue 908 MET Chi-restraints excluded: chain A residue 979 VAL Chi-restraints excluded: chain A residue 1083 ILE Chi-restraints excluded: chain A residue 1095 LEU Chi-restraints excluded: chain A residue 1122 PHE Chi-restraints excluded: chain A residue 1176 LEU Chi-restraints excluded: chain A residue 1195 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 11 optimal weight: 6.9990 chunk 55 optimal weight: 3.9990 chunk 71 optimal weight: 0.0770 chunk 82 optimal weight: 4.9990 chunk 54 optimal weight: 4.9990 chunk 97 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 chunk 59 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 overall best weight: 0.9542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 735 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.1332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8254 Z= 0.216 Angle : 0.551 7.351 11202 Z= 0.274 Chirality : 0.040 0.154 1328 Planarity : 0.005 0.057 1374 Dihedral : 3.921 18.066 1094 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 1.94 % Allowed : 15.18 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.28), residues: 1012 helix: 1.56 (0.22), residues: 644 sheet: None (None), residues: 0 loop : -1.31 (0.33), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 795 HIS 0.006 0.001 HIS A1064 PHE 0.015 0.001 PHE A1189 TYR 0.012 0.001 TYR B1124 ARG 0.006 0.000 ARG B 701 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 121 time to evaluate : 0.996 Fit side-chains revert: symmetry clash REVERT: B 916 PHE cc_start: 0.7882 (OUTLIER) cc_final: 0.7570 (t80) REVERT: B 952 TYR cc_start: 0.8109 (t80) cc_final: 0.7863 (t80) REVERT: A 994 MET cc_start: 0.7088 (ptt) cc_final: 0.6611 (ptm) REVERT: A 1157 LYS cc_start: 0.8529 (mmmt) cc_final: 0.8306 (mmmt) REVERT: A 1195 LEU cc_start: 0.8153 (OUTLIER) cc_final: 0.7748 (mp) outliers start: 17 outliers final: 13 residues processed: 130 average time/residue: 0.1937 time to fit residues: 34.9769 Evaluate side-chains 134 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 119 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 916 PHE Chi-restraints excluded: chain B residue 1022 LYS Chi-restraints excluded: chain B residue 1183 THR Chi-restraints excluded: chain B residue 1199 LEU Chi-restraints excluded: chain B residue 1201 MET Chi-restraints excluded: chain A residue 756 LEU Chi-restraints excluded: chain A residue 757 LEU Chi-restraints excluded: chain A residue 908 MET Chi-restraints excluded: chain A residue 918 LEU Chi-restraints excluded: chain A residue 979 VAL Chi-restraints excluded: chain A residue 1083 ILE Chi-restraints excluded: chain A residue 1095 LEU Chi-restraints excluded: chain A residue 1122 PHE Chi-restraints excluded: chain A residue 1176 LEU Chi-restraints excluded: chain A residue 1195 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 29 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 18 optimal weight: 0.8980 chunk 61 optimal weight: 4.9990 chunk 66 optimal weight: 0.9990 chunk 48 optimal weight: 0.2980 chunk 9 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 chunk 88 optimal weight: 0.0980 chunk 93 optimal weight: 0.6980 chunk 85 optimal weight: 0.5980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 735 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.1415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8254 Z= 0.159 Angle : 0.530 7.340 11202 Z= 0.261 Chirality : 0.039 0.161 1328 Planarity : 0.004 0.057 1374 Dihedral : 3.869 18.205 1094 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 1.71 % Allowed : 15.30 % Favored : 82.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.28), residues: 1012 helix: 1.63 (0.21), residues: 645 sheet: None (None), residues: 0 loop : -1.22 (0.33), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 992 HIS 0.003 0.001 HIS A1064 PHE 0.015 0.001 PHE A1189 TYR 0.008 0.001 TYR B1124 ARG 0.007 0.000 ARG B 701 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 120 time to evaluate : 0.928 Fit side-chains revert: symmetry clash REVERT: B 916 PHE cc_start: 0.7865 (OUTLIER) cc_final: 0.7560 (t80) REVERT: B 952 TYR cc_start: 0.8096 (t80) cc_final: 0.7861 (t80) REVERT: A 817 ARG cc_start: 0.7755 (mtm110) cc_final: 0.7427 (ttm110) REVERT: A 918 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.8312 (mt) REVERT: A 994 MET cc_start: 0.7169 (ptt) cc_final: 0.6723 (ptm) REVERT: A 1157 LYS cc_start: 0.8511 (mmmt) cc_final: 0.8296 (mmmt) REVERT: A 1195 LEU cc_start: 0.8062 (OUTLIER) cc_final: 0.7658 (mp) outliers start: 15 outliers final: 10 residues processed: 127 average time/residue: 0.1795 time to fit residues: 31.8779 Evaluate side-chains 132 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 119 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 916 PHE Chi-restraints excluded: chain B residue 1022 LYS Chi-restraints excluded: chain B residue 1183 THR Chi-restraints excluded: chain B residue 1201 MET Chi-restraints excluded: chain A residue 756 LEU Chi-restraints excluded: chain A residue 757 LEU Chi-restraints excluded: chain A residue 908 MET Chi-restraints excluded: chain A residue 918 LEU Chi-restraints excluded: chain A residue 979 VAL Chi-restraints excluded: chain A residue 1083 ILE Chi-restraints excluded: chain A residue 1122 PHE Chi-restraints excluded: chain A residue 1176 LEU Chi-restraints excluded: chain A residue 1195 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 90 optimal weight: 4.9990 chunk 93 optimal weight: 2.9990 chunk 54 optimal weight: 0.2980 chunk 39 optimal weight: 4.9990 chunk 71 optimal weight: 0.0670 chunk 27 optimal weight: 4.9990 chunk 81 optimal weight: 3.9990 chunk 85 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 58 optimal weight: 0.7980 overall best weight: 0.8120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 735 GLN A 750 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.1416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8254 Z= 0.198 Angle : 0.557 8.345 11202 Z= 0.274 Chirality : 0.040 0.158 1328 Planarity : 0.005 0.057 1374 Dihedral : 3.908 19.008 1094 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 1.48 % Allowed : 15.53 % Favored : 82.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.28), residues: 1012 helix: 1.60 (0.21), residues: 644 sheet: None (None), residues: 0 loop : -1.26 (0.33), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 992 HIS 0.005 0.001 HIS A1064 PHE 0.014 0.001 PHE A1189 TYR 0.011 0.001 TYR B1124 ARG 0.007 0.000 ARG B 701 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 118 time to evaluate : 0.953 Fit side-chains revert: symmetry clash REVERT: B 916 PHE cc_start: 0.7864 (OUTLIER) cc_final: 0.7570 (t80) REVERT: B 952 TYR cc_start: 0.8112 (t80) cc_final: 0.7871 (t80) REVERT: A 993 MET cc_start: 0.6146 (mmp) cc_final: 0.5780 (mpp) REVERT: A 994 MET cc_start: 0.7051 (ptt) cc_final: 0.6595 (ptm) REVERT: A 1195 LEU cc_start: 0.8073 (OUTLIER) cc_final: 0.7665 (mp) outliers start: 13 outliers final: 11 residues processed: 124 average time/residue: 0.1842 time to fit residues: 32.2160 Evaluate side-chains 130 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 117 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 916 PHE Chi-restraints excluded: chain B residue 1022 LYS Chi-restraints excluded: chain B residue 1183 THR Chi-restraints excluded: chain B residue 1201 MET Chi-restraints excluded: chain A residue 756 LEU Chi-restraints excluded: chain A residue 757 LEU Chi-restraints excluded: chain A residue 908 MET Chi-restraints excluded: chain A residue 918 LEU Chi-restraints excluded: chain A residue 979 VAL Chi-restraints excluded: chain A residue 1083 ILE Chi-restraints excluded: chain A residue 1122 PHE Chi-restraints excluded: chain A residue 1176 LEU Chi-restraints excluded: chain A residue 1195 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 72.0786 > 50: distance: 38 - 197: 32.671 distance: 48 - 190: 31.902 distance: 93 - 106: 3.513 distance: 142 - 146: 35.483 distance: 146 - 147: 39.614 distance: 147 - 148: 41.198 distance: 148 - 149: 40.191 distance: 148 - 150: 39.027 distance: 150 - 151: 40.955 distance: 151 - 154: 57.838 distance: 152 - 153: 40.222 distance: 152 - 158: 19.994 distance: 154 - 155: 40.642 distance: 155 - 156: 40.141 distance: 155 - 157: 38.875 distance: 158 - 159: 44.441 distance: 158 - 164: 23.390 distance: 159 - 160: 68.299 distance: 159 - 162: 68.707 distance: 160 - 161: 40.814 distance: 162 - 163: 56.518 distance: 163 - 164: 58.098 distance: 165 - 166: 56.591 distance: 166 - 167: 55.380 distance: 166 - 169: 41.092 distance: 167 - 168: 41.191 distance: 167 - 179: 55.629 distance: 169 - 170: 43.121 distance: 170 - 171: 43.987 distance: 170 - 172: 57.909 distance: 172 - 174: 56.058 distance: 172 - 175: 70.163 distance: 173 - 174: 40.678 distance: 174 - 176: 55.820 distance: 175 - 177: 28.549 distance: 176 - 178: 40.786 distance: 177 - 178: 33.622 distance: 179 - 180: 39.701 distance: 180 - 181: 57.155 distance: 180 - 183: 39.496 distance: 181 - 182: 55.374 distance: 181 - 187: 39.652 distance: 183 - 184: 41.087 distance: 184 - 186: 38.645 distance: 187 - 188: 57.137 distance: 188 - 189: 38.963 distance: 188 - 191: 41.209 distance: 189 - 190: 40.246 distance: 189 - 192: 40.569 distance: 192 - 193: 57.064 distance: 193 - 196: 70.773 distance: 194 - 195: 40.005 distance: 194 - 197: 38.927 distance: 197 - 198: 40.986 distance: 199 - 200: 40.061 distance: 199 - 202: 39.283 distance: 203 - 204: 39.434 distance: 203 - 206: 39.871 distance: 204 - 205: 70.448 distance: 204 - 209: 38.824 distance: 205 - 233: 31.979 distance: 206 - 207: 39.656 distance: 206 - 208: 39.378 distance: 209 - 210: 57.581 distance: 210 - 211: 70.309 distance: 210 - 213: 42.792 distance: 211 - 212: 38.923 distance: 211 - 216: 35.062 distance: 212 - 239: 35.516 distance: 213 - 214: 44.789 distance: 213 - 215: 44.429