Starting phenix.real_space_refine on Mon Jun 23 04:40:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fh3_29078/06_2025/8fh3_29078_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fh3_29078/06_2025/8fh3_29078.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8fh3_29078/06_2025/8fh3_29078.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fh3_29078/06_2025/8fh3_29078.map" model { file = "/net/cci-nas-00/data/ceres_data/8fh3_29078/06_2025/8fh3_29078_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fh3_29078/06_2025/8fh3_29078_neut.cif" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.020 sd= 0.063 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: 5 Type Number sf(0) Gaussians Zn 4 6.06 5 S 171 5.16 5 C 17026 2.51 5 N 4657 2.21 5 O 4915 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 26773 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 6761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 868, 6761 Classifications: {'peptide': 868} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 25, 'TRANS': 842} Chain breaks: 6 Unresolved non-hydrogen bonds: 159 Unresolved non-hydrogen angles: 184 Unresolved non-hydrogen dihedrals: 143 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 3, 'GLU:plan': 6, 'ARG:plan': 5, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 79 Chain: "B" Number of atoms: 8709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1152, 8709 Classifications: {'peptide': 1152} Incomplete info: {'truncation_to_alanine': 145} Link IDs: {'PTRANS': 40, 'TRANS': 1111} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 582 Unresolved non-hydrogen angles: 711 Unresolved non-hydrogen dihedrals: 492 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLN:plan1': 9, 'HIS:plan': 3, 'TYR:plan': 4, 'ASN:plan1': 1, 'TRP:plan': 2, 'ASP:plan': 18, 'PHE:plan': 3, 'GLU:plan': 30, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 352 Chain: "C" Number of atoms: 6697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 996, 6697 Classifications: {'peptide': 996} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 327} Link IDs: {'PCIS': 1, 'PTRANS': 37, 'TRANS': 957} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 1273 Unresolved non-hydrogen angles: 1585 Unresolved non-hydrogen dihedrals: 1065 Unresolved non-hydrogen chiralities: 72 Planarities with less than four sites: {'GLN:plan1': 21, 'HIS:plan': 7, 'TYR:plan': 16, 'ASN:plan1': 19, 'TRP:plan': 2, 'ASP:plan': 33, 'PHE:plan': 13, 'GLU:plan': 46, 'ARG:plan': 21} Unresolved non-hydrogen planarities: 772 Chain: "E" Number of atoms: 4298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 590, 4298 Classifications: {'peptide': 590} Incomplete info: {'truncation_to_alanine': 122} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 574} Chain breaks: 11 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 463 Unresolved non-hydrogen angles: 573 Unresolved non-hydrogen dihedrals: 383 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLN:plan1': 11, 'ASP:plan': 11, 'TYR:plan': 3, 'ASN:plan1': 4, 'HIS:plan': 3, 'PHE:plan': 7, 'GLU:plan': 22, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 295 Chain: "I" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 304 Classifications: {'peptide': 36} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 32} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 14444 SG CYS B1057 65.053 108.031 45.738 1.00 68.70 S ATOM 14473 SG CYS B1060 67.981 108.333 43.265 1.00 76.34 S ATOM 14574 SG CYS B1074 66.386 104.976 45.279 1.00 60.26 S ATOM 14596 SG CYS B1077 68.900 107.700 46.309 1.00 69.58 S ATOM 15247 SG CYS B1207 52.642 102.783 68.360 1.00 27.25 S ATOM 15266 SG CYS B1210 55.459 100.595 67.441 1.00 24.74 S ATOM 15418 SG CYS B1229 51.673 99.807 66.650 1.00 34.58 S ATOM 15443 SG CYS B1232 53.147 99.537 70.212 1.00 31.07 S ATOM 21850 SG CYS C1292 101.618 93.839 147.073 1.00 57.51 S ATOM 21873 SG CYS C1295 99.770 91.200 148.974 1.00 59.07 S ATOM 21996 SG CYS C1314 101.544 94.169 150.889 1.00 60.26 S ATOM 22017 SG CYS C1317 103.636 91.832 149.650 1.00 65.81 S ATOM 21558 SG CYS C1253 78.546 92.983 152.466 1.00 90.61 S ATOM 21582 SG CYS C1256 74.802 92.890 151.958 1.00 90.88 S ATOM 21663 SG CYS C1267 75.921 92.055 155.304 1.00 85.68 S ATOM 21680 SG CYS C1270 76.552 89.684 152.446 1.00 78.08 S Time building chain proxies: 15.80, per 1000 atoms: 0.59 Number of scatterers: 26773 At special positions: 0 Unit cell: (151.98, 149, 256.28, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 4 29.99 S 171 16.00 O 4915 8.00 N 4657 7.00 C 17026 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 285 " - pdb=" SG CYS B 327 " distance=2.04 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: 6.70 Conformation dependent library (CDL) restraints added in 3.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B1301 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1077 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1057 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1074 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1060 " pdb=" ZN B1302 " pdb="ZN ZN B1302 " - pdb=" SG CYS B1210 " pdb="ZN ZN B1302 " - pdb=" SG CYS B1207 " pdb="ZN ZN B1302 " - pdb=" SG CYS B1232 " pdb="ZN ZN B1302 " - pdb=" SG CYS B1229 " pdb=" ZN C1401 " pdb="ZN ZN C1401 " - pdb=" SG CYS C1314 " pdb="ZN ZN C1401 " - pdb=" SG CYS C1292 " pdb="ZN ZN C1401 " - pdb=" SG CYS C1317 " pdb="ZN ZN C1401 " - pdb=" SG CYS C1295 " pdb=" ZN C1402 " pdb="ZN ZN C1402 " - pdb=" SG CYS C1256 " pdb="ZN ZN C1402 " - pdb=" SG CYS C1270 " pdb="ZN ZN C1402 " - pdb=" SG CYS C1267 " pdb="ZN ZN C1402 " - pdb=" SG CYS C1253 " Number of angles added : 24 7184 Ramachandran restraints generated. 3592 Oldfield, 0 Emsley, 3592 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6890 Finding SS restraints... Secondary structure from input PDB file: 125 helices and 48 sheets defined 39.6% alpha, 16.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.75 Creating SS restraints... Processing helix chain 'A' and resid 12 through 15 removed outlier: 3.743A pdb=" N VAL A 15 " --> pdb=" O PRO A 12 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 12 through 15' Processing helix chain 'A' and resid 81 through 85 removed outlier: 3.720A pdb=" N GLN A 84 " --> pdb=" O GLU A 81 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N LYS A 85 " --> pdb=" O GLN A 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 81 through 85' Processing helix chain 'A' and resid 483 through 485 No H-bonds generated for 'chain 'A' and resid 483 through 485' Processing helix chain 'A' and resid 647 through 652 Processing helix chain 'A' and resid 659 through 661 No H-bonds generated for 'chain 'A' and resid 659 through 661' Processing helix chain 'A' and resid 668 through 681 Processing helix chain 'A' and resid 682 through 693 removed outlier: 3.896A pdb=" N GLN A 688 " --> pdb=" O LYS A 684 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASN A 693 " --> pdb=" O PHE A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 695 through 710 Processing helix chain 'A' and resid 713 through 722 removed outlier: 3.585A pdb=" N GLN A 717 " --> pdb=" O TYR A 713 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 737 Processing helix chain 'A' and resid 742 through 751 Processing helix chain 'A' and resid 753 through 764 Processing helix chain 'A' and resid 766 through 777 removed outlier: 3.500A pdb=" N ALA A 770 " --> pdb=" O ARG A 766 " (cutoff:3.500A) Processing helix chain 'A' and resid 779 through 789 removed outlier: 3.921A pdb=" N THR A 789 " --> pdb=" O GLN A 785 " (cutoff:3.500A) Processing helix chain 'A' and resid 794 through 812 removed outlier: 3.628A pdb=" N LEU A 798 " --> pdb=" O ALA A 794 " (cutoff:3.500A) Processing helix chain 'A' and resid 829 through 840 removed outlier: 3.971A pdb=" N GLU A 834 " --> pdb=" O GLU A 830 " (cutoff:3.500A) Processing helix chain 'A' and resid 841 through 850 Processing helix chain 'A' and resid 858 through 870 Processing helix chain 'A' and resid 872 through 882 Processing helix chain 'A' and resid 885 through 895 removed outlier: 4.113A pdb=" N THR A 891 " --> pdb=" O ALA A 887 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N CYS A 892 " --> pdb=" O ALA A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 914 through 922 removed outlier: 3.798A pdb=" N ALA A 918 " --> pdb=" O GLY A 914 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 177 Processing helix chain 'B' and resid 189 through 193 removed outlier: 4.085A pdb=" N SER B 192 " --> pdb=" O ARG B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 617 through 627 removed outlier: 3.656A pdb=" N ARG B 627 " --> pdb=" O GLN B 623 " (cutoff:3.500A) Processing helix chain 'B' and resid 629 through 638 Processing helix chain 'B' and resid 642 through 657 Processing helix chain 'B' and resid 658 through 670 Processing helix chain 'B' and resid 671 through 687 removed outlier: 3.554A pdb=" N ARG B 687 " --> pdb=" O GLU B 683 " (cutoff:3.500A) Processing helix chain 'B' and resid 691 through 704 removed outlier: 4.001A pdb=" N PHE B 695 " --> pdb=" O ASN B 691 " (cutoff:3.500A) Processing helix chain 'B' and resid 707 through 716 Processing helix chain 'B' and resid 719 through 729 Processing helix chain 'B' and resid 731 through 736 removed outlier: 3.519A pdb=" N ALA B 735 " --> pdb=" O MET B 731 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 739 No H-bonds generated for 'chain 'B' and resid 737 through 739' Processing helix chain 'B' and resid 746 through 761 Processing helix chain 'B' and resid 763 through 774 removed outlier: 3.907A pdb=" N GLU B 769 " --> pdb=" O LYS B 765 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ALA B 774 " --> pdb=" O MET B 770 " (cutoff:3.500A) Processing helix chain 'B' and resid 776 through 788 Processing helix chain 'B' and resid 792 through 800 Processing helix chain 'B' and resid 809 through 816 removed outlier: 3.674A pdb=" N LYS B 816 " --> pdb=" O ALA B 812 " (cutoff:3.500A) Processing helix chain 'B' and resid 820 through 830 removed outlier: 4.330A pdb=" N ALA B 825 " --> pdb=" O PRO B 821 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N GLU B 826 " --> pdb=" O GLY B 822 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N TYR B 828 " --> pdb=" O ALA B 824 " (cutoff:3.500A) Processing helix chain 'B' and resid 835 through 843 removed outlier: 3.659A pdb=" N VAL B 842 " --> pdb=" O VAL B 838 " (cutoff:3.500A) Processing helix chain 'B' and resid 846 through 857 removed outlier: 3.874A pdb=" N LYS B 856 " --> pdb=" O ALA B 852 " (cutoff:3.500A) Processing helix chain 'B' and resid 857 through 864 Processing helix chain 'B' and resid 865 through 875 Processing helix chain 'B' and resid 877 through 888 Processing helix chain 'B' and resid 892 through 908 Processing helix chain 'B' and resid 910 through 929 Processing helix chain 'B' and resid 930 through 934 removed outlier: 6.105A pdb=" N ALA B 933 " --> pdb=" O GLN B 930 " (cutoff:3.500A) Processing helix chain 'B' and resid 935 through 962 removed outlier: 4.007A pdb=" N GLY B 940 " --> pdb=" O ASP B 936 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N LYS B 941 " --> pdb=" O THR B 937 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ALA B 957 " --> pdb=" O HIS B 953 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ILE B 958 " --> pdb=" O GLY B 954 " (cutoff:3.500A) Processing helix chain 'B' and resid 970 through 983 Processing helix chain 'B' and resid 994 through 1010 removed outlier: 3.830A pdb=" N ILE B 998 " --> pdb=" O SER B 994 " (cutoff:3.500A) Processing helix chain 'B' and resid 1013 through 1023 Processing helix chain 'B' and resid 1028 through 1042 removed outlier: 4.725A pdb=" N LYS B1033 " --> pdb=" O ALA B1029 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N SER B1034 " --> pdb=" O ARG B1030 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N LEU B1040 " --> pdb=" O GLU B1036 " (cutoff:3.500A) Processing helix chain 'B' and resid 1043 through 1045 No H-bonds generated for 'chain 'B' and resid 1043 through 1045' Processing helix chain 'B' and resid 1050 through 1054 Processing helix chain 'B' and resid 1103 through 1113 Processing helix chain 'B' and resid 1169 through 1174 Processing helix chain 'B' and resid 1216 through 1227 removed outlier: 3.502A pdb=" N LEU B1221 " --> pdb=" O GLU B1217 " (cutoff:3.500A) Processing helix chain 'C' and resid 374 through 378 Processing helix chain 'C' and resid 461 through 465 removed outlier: 3.525A pdb=" N GLU C 465 " --> pdb=" O GLN C 461 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 461 through 465' Processing helix chain 'C' and resid 645 through 659 Proline residue: C 651 - end of helix Processing helix chain 'C' and resid 661 through 673 Processing helix chain 'C' and resid 674 through 688 Processing helix chain 'C' and resid 690 through 702 Processing helix chain 'C' and resid 703 through 714 removed outlier: 3.743A pdb=" N VAL C 707 " --> pdb=" O ASN C 703 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N SER C 709 " --> pdb=" O GLY C 705 " (cutoff:3.500A) Processing helix chain 'C' and resid 718 through 730 Processing helix chain 'C' and resid 732 through 741 Processing helix chain 'C' and resid 746 through 756 removed outlier: 3.806A pdb=" N LEU C 750 " --> pdb=" O PRO C 746 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 770 Processing helix chain 'C' and resid 772 through 789 removed outlier: 4.283A pdb=" N PHE C 776 " --> pdb=" O ASP C 772 " (cutoff:3.500A) Processing helix chain 'C' and resid 792 through 801 Processing helix chain 'C' and resid 806 through 824 Processing helix chain 'C' and resid 831 through 837 removed outlier: 3.830A pdb=" N LEU C 835 " --> pdb=" O VAL C 831 " (cutoff:3.500A) Processing helix chain 'C' and resid 839 through 850 Processing helix chain 'C' and resid 856 through 866 Processing helix chain 'C' and resid 871 through 878 Processing helix chain 'C' and resid 882 through 889 Processing helix chain 'C' and resid 894 through 909 removed outlier: 3.974A pdb=" N HIS C 898 " --> pdb=" O SER C 894 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 921 removed outlier: 3.575A pdb=" N ALA C 921 " --> pdb=" O ALA C 917 " (cutoff:3.500A) Processing helix chain 'C' and resid 923 through 934 Processing helix chain 'C' and resid 937 through 948 removed outlier: 4.045A pdb=" N ILE C 944 " --> pdb=" O LYS C 940 " (cutoff:3.500A) Processing helix chain 'C' and resid 953 through 962 removed outlier: 3.673A pdb=" N VAL C 957 " --> pdb=" O GLY C 953 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 974 removed outlier: 4.103A pdb=" N ALA C 970 " --> pdb=" O ASP C 966 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLN C 972 " --> pdb=" O GLY C 968 " (cutoff:3.500A) Processing helix chain 'C' and resid 981 through 990 removed outlier: 3.788A pdb=" N HIS C 990 " --> pdb=" O LEU C 986 " (cutoff:3.500A) Processing helix chain 'C' and resid 993 through 1001 Processing helix chain 'C' and resid 1010 through 1015 Processing helix chain 'C' and resid 1025 through 1031 Processing helix chain 'C' and resid 1051 through 1062 removed outlier: 3.665A pdb=" N ILE C1055 " --> pdb=" O ASP C1051 " (cutoff:3.500A) Processing helix chain 'C' and resid 1068 through 1080 removed outlier: 3.670A pdb=" N ASN C1072 " --> pdb=" O GLU C1068 " (cutoff:3.500A) Processing helix chain 'C' and resid 1089 through 1099 removed outlier: 3.578A pdb=" N LEU C1099 " --> pdb=" O LEU C1095 " (cutoff:3.500A) Processing helix chain 'C' and resid 1101 through 1120 removed outlier: 3.940A pdb=" N GLN C1107 " --> pdb=" O ARG C1103 " (cutoff:3.500A) Processing helix chain 'C' and resid 1123 through 1139 removed outlier: 3.959A pdb=" N GLU C1135 " --> pdb=" O SER C1131 " (cutoff:3.500A) Processing helix chain 'C' and resid 1144 through 1166 removed outlier: 4.095A pdb=" N TYR C1157 " --> pdb=" O ILE C1153 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ILE C1158 " --> pdb=" O LEU C1154 " (cutoff:3.500A) Processing helix chain 'C' and resid 1168 through 1182 removed outlier: 3.630A pdb=" N ALA C1173 " --> pdb=" O HIS C1169 " (cutoff:3.500A) Processing helix chain 'C' and resid 1189 through 1205 removed outlier: 3.518A pdb=" N LEU C1194 " --> pdb=" O ILE C1190 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N SER C1196 " --> pdb=" O PRO C1192 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N ILE C1199 " --> pdb=" O THR C1195 " (cutoff:3.500A) Processing helix chain 'C' and resid 1206 through 1218 removed outlier: 3.625A pdb=" N SER C1212 " --> pdb=" O ASN C1208 " (cutoff:3.500A) Processing helix chain 'C' and resid 1230 through 1240 Processing helix chain 'C' and resid 1285 through 1289 removed outlier: 3.834A pdb=" N TRP C1289 " --> pdb=" O LYS C1286 " (cutoff:3.500A) Processing helix chain 'C' and resid 1300 through 1308 Processing helix chain 'C' and resid 1332 through 1337 Processing helix chain 'E' and resid 562 through 566 Processing helix chain 'E' and resid 769 through 785 Processing helix chain 'E' and resid 787 through 795 Processing helix chain 'E' and resid 800 through 814 removed outlier: 3.755A pdb=" N TRP E 804 " --> pdb=" O SER E 800 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N VAL E 812 " --> pdb=" O ALA E 808 " (cutoff:3.500A) Processing helix chain 'E' and resid 817 through 827 removed outlier: 4.510A pdb=" N VAL E 822 " --> pdb=" O ASP E 818 " (cutoff:3.500A) Processing helix chain 'E' and resid 829 through 840 Processing helix chain 'E' and resid 844 through 856 removed outlier: 4.001A pdb=" N ARG E 848 " --> pdb=" O GLU E 844 " (cutoff:3.500A) Processing helix chain 'E' and resid 858 through 870 removed outlier: 3.568A pdb=" N ALA E 862 " --> pdb=" O MET E 858 " (cutoff:3.500A) Processing helix chain 'E' and resid 871 through 882 Processing helix chain 'E' and resid 884 through 895 removed outlier: 3.848A pdb=" N LEU E 889 " --> pdb=" O TRP E 885 " (cutoff:3.500A) Processing helix chain 'E' and resid 899 through 914 Processing helix chain 'E' and resid 918 through 927 Processing helix chain 'E' and resid 929 through 939 Proline residue: E 935 - end of helix Processing helix chain 'E' and resid 941 through 953 removed outlier: 3.722A pdb=" N LYS E 953 " --> pdb=" O VAL E 949 " (cutoff:3.500A) Processing helix chain 'E' and resid 956 through 965 Processing helix chain 'E' and resid 970 through 981 removed outlier: 3.624A pdb=" N ALA E 974 " --> pdb=" O GLU E 970 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU E 975 " --> pdb=" O MET E 971 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N HIS E 976 " --> pdb=" O ASP E 972 " (cutoff:3.500A) Processing helix chain 'E' and resid 983 through 994 Processing helix chain 'E' and resid 996 through 1006 removed outlier: 4.072A pdb=" N ALA E1000 " --> pdb=" O ASN E 996 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLU E1006 " --> pdb=" O GLN E1002 " (cutoff:3.500A) Processing helix chain 'E' and resid 1009 through 1023 Processing helix chain 'E' and resid 1025 through 1036 removed outlier: 3.669A pdb=" N ALA E1029 " --> pdb=" O GLU E1025 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N TYR E1033 " --> pdb=" O ALA E1029 " (cutoff:3.500A) Processing helix chain 'E' and resid 1038 through 1050 removed outlier: 3.662A pdb=" N ALA E1042 " --> pdb=" O ALA E1038 " (cutoff:3.500A) Processing helix chain 'E' and resid 1051 through 1058 removed outlier: 3.596A pdb=" N MET E1056 " --> pdb=" O ASP E1052 " (cutoff:3.500A) Processing helix chain 'E' and resid 1063 through 1078 removed outlier: 3.558A pdb=" N ILE E1068 " --> pdb=" O PRO E1064 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLU E1069 " --> pdb=" O GLU E1065 " (cutoff:3.500A) Processing helix chain 'E' and resid 1080 through 1091 Processing helix chain 'I' and resid 20 through 45 Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 10 removed outlier: 6.886A pdb=" N PHE A 328 " --> pdb=" O SER A 6 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N LYS A 8 " --> pdb=" O ILE A 326 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N ILE A 326 " --> pdb=" O LYS A 8 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 20 through 22 removed outlier: 3.575A pdb=" N VAL A 40 " --> pdb=" O ASN A 64 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 74 through 77 removed outlier: 6.794A pdb=" N SER A 89 " --> pdb=" O GLN A 75 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N VAL A 77 " --> pdb=" O THR A 87 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N THR A 87 " --> pdb=" O VAL A 77 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASP A 90 " --> pdb=" O LEU A 94 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N LEU A 94 " --> pdb=" O ASP A 90 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N ILE A 95 " --> pdb=" O ILE A 110 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N ILE A 110 " --> pdb=" O ILE A 95 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N MET A 99 " --> pdb=" O ILE A 106 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 118 through 123 removed outlier: 3.631A pdb=" N SER A 120 " --> pdb=" O VAL A 133 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 159 through 161 removed outlier: 6.302A pdb=" N GLY A 174 " --> pdb=" O SER A 160 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 229 through 230 Processing sheet with id=AA7, first strand: chain 'A' and resid 258 through 260 removed outlier: 3.529A pdb=" N ALA A 271 " --> pdb=" O GLY A 258 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N VAL A 286 " --> pdb=" O THR A 298 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N THR A 298 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N PHE A 288 " --> pdb=" O LEU A 296 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU A 296 " --> pdb=" O PHE A 288 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 336 through 340 removed outlier: 4.804A pdb=" N LYS A 336 " --> pdb=" O ALA A 347 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 378 through 381 removed outlier: 3.537A pdb=" N LYS A 425 " --> pdb=" O LEU A 412 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU A 414 " --> pdb=" O ASP A 423 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 433 through 436 Processing sheet with id=AB2, first strand: chain 'A' and resid 507 through 512 removed outlier: 6.560A pdb=" N SER A 530 " --> pdb=" O LEU A 536 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N LEU A 536 " --> pdb=" O SER A 530 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 546 through 551 removed outlier: 6.525A pdb=" N ILE A 561 " --> pdb=" O TYR A 547 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N LEU A 549 " --> pdb=" O ALA A 559 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ALA A 559 " --> pdb=" O LEU A 549 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N LEU A 551 " --> pdb=" O ARG A 557 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N ARG A 557 " --> pdb=" O LEU A 551 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 596 through 601 removed outlier: 3.996A pdb=" N ASP A 598 " --> pdb=" O MET A 612 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 634 through 639 removed outlier: 6.517A pdb=" N LYS A 644 " --> pdb=" O CYS A 636 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N PHE A 638 " --> pdb=" O GLU A 642 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N GLU A 642 " --> pdb=" O PHE A 638 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 2 through 7 removed outlier: 6.569A pdb=" N PHE B 347 " --> pdb=" O THR B 6 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLN B 328 " --> pdb=" O VAL B 337 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N THR B 326 " --> pdb=" O GLY B 339 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 35 through 38 removed outlier: 4.490A pdb=" N GLN B 47 " --> pdb=" O VAL B 37 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 68 through 70 removed outlier: 3.626A pdb=" N ILE B 78 " --> pdb=" O SER B 70 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLU B 85 " --> pdb=" O THR B 81 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 68 through 70 removed outlier: 3.626A pdb=" N ILE B 78 " --> pdb=" O SER B 70 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N TYR B 90 " --> pdb=" O VAL B 77 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 96 through 100 removed outlier: 4.117A pdb=" N CYS B 98 " --> pdb=" O CYS B 111 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ASP B 115 " --> pdb=" O SER B 112 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 135 through 140 removed outlier: 6.713A pdb=" N GLY B 150 " --> pdb=" O ILE B 136 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N CYS B 138 " --> pdb=" O ALA B 148 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ALA B 148 " --> pdb=" O CYS B 138 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N TRP B 140 " --> pdb=" O TYR B 146 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N TYR B 146 " --> pdb=" O TRP B 140 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N MET B 151 " --> pdb=" O ILE B 155 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ILE B 155 " --> pdb=" O MET B 151 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL B 167 " --> pdb=" O ILE B 158 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N ASN B 160 " --> pdb=" O GLU B 165 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N GLU B 165 " --> pdb=" O ASN B 160 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 181 through 184 Processing sheet with id=AC4, first strand: chain 'B' and resid 303 through 304 removed outlier: 3.767A pdb=" N GLY B 318 " --> pdb=" O VAL B 304 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 356 through 358 Processing sheet with id=AC6, first strand: chain 'B' and resid 393 through 397 removed outlier: 3.629A pdb=" N LYS B 393 " --> pdb=" O GLN B 404 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N ILE B 409 " --> pdb=" O LYS B 429 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N LYS B 429 " --> pdb=" O ILE B 409 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N ILE B 411 " --> pdb=" O LYS B 427 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 438 through 442 Processing sheet with id=AC8, first strand: chain 'B' and resid 473 through 478 removed outlier: 4.483A pdb=" N GLN B 496 " --> pdb=" O LEU B 492 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ILE B 497 " --> pdb=" O LEU B 510 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 519 through 522 removed outlier: 6.623A pdb=" N CYS B 538 " --> pdb=" O GLN B 551 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N GLN B 551 " --> pdb=" O CYS B 538 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N VAL B 540 " --> pdb=" O LEU B 549 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 570 through 572 Processing sheet with id=AD2, first strand: chain 'B' and resid 593 through 598 removed outlier: 6.777A pdb=" N PHE B 603 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N TYR B 597 " --> pdb=" O LYS B 601 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N LYS B 601 " --> pdb=" O TYR B 597 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 966 through 967 removed outlier: 3.596A pdb=" N GLN I 50 " --> pdb=" O SER B 967 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 1093 through 1094 Processing sheet with id=AD5, first strand: chain 'B' and resid 1204 through 1206 Processing sheet with id=AD6, first strand: chain 'C' and resid 392 through 395 removed outlier: 3.526A pdb=" N PHE C 392 " --> pdb=" O GLY C 403 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLY C 403 " --> pdb=" O PHE C 392 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 434 through 435 removed outlier: 3.631A pdb=" N CYS C 434 " --> pdb=" O ALA C 441 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA C 441 " --> pdb=" O CYS C 434 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ALA C 442 " --> pdb=" O GLN C 449 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 498 through 501 removed outlier: 6.719A pdb=" N TYR C 499 " --> pdb=" O VAL C 508 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VAL C 508 " --> pdb=" O TYR C 499 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 519 through 522 removed outlier: 3.727A pdb=" N TYR C 549 " --> pdb=" O VAL C 540 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 560 through 563 removed outlier: 3.549A pdb=" N GLY C 560 " --> pdb=" O TYR C 576 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N TYR C 584 " --> pdb=" O PHE C 573 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 608 through 614 removed outlier: 6.723A pdb=" N THR C 619 " --> pdb=" O LEU C 611 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N LEU C 613 " --> pdb=" O GLU C 617 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N GLU C 617 " --> pdb=" O LEU C 613 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 1250 through 1252 Processing sheet with id=AE4, first strand: chain 'E' and resid 411 through 414 Processing sheet with id=AE5, first strand: chain 'E' and resid 448 through 451 Processing sheet with id=AE6, first strand: chain 'E' and resid 489 through 490 Processing sheet with id=AE7, first strand: chain 'E' and resid 496 through 498 Processing sheet with id=AE8, first strand: chain 'E' and resid 524 through 530 removed outlier: 4.857A pdb=" N HIS E 542 " --> pdb=" O THR E 538 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'E' and resid 524 through 530 removed outlier: 4.857A pdb=" N HIS E 542 " --> pdb=" O THR E 538 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N PHE E 543 " --> pdb=" O ARG E 560 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ARG E 560 " --> pdb=" O PHE E 543 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'E' and resid 583 through 584 removed outlier: 3.506A pdb=" N ILE E 584 " --> pdb=" O TYR E 602 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N TYR E 602 " --> pdb=" O ILE E 584 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLN E 618 " --> pdb=" O ASP E 613 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'E' and resid 646 through 653 removed outlier: 6.783A pdb=" N GLU E 664 " --> pdb=" O VAL E 649 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N HIS E 651 " --> pdb=" O VAL E 662 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N VAL E 662 " --> pdb=" O HIS E 651 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N TRP E 653 " --> pdb=" O LEU E 660 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N LEU E 660 " --> pdb=" O TRP E 653 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N VAL E 692 " --> pdb=" O PRO E 712 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ILE E 694 " --> pdb=" O SER E 710 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N SER E 710 " --> pdb=" O ILE E 694 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N SER E 696 " --> pdb=" O HIS E 708 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'E' and resid 717 through 724 removed outlier: 6.818A pdb=" N LEU E 720 " --> pdb=" O THR E 731 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N THR E 731 " --> pdb=" O LEU E 720 " (cutoff:3.500A) 1252 hydrogen bonds defined for protein. 3537 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: 12.43 Time building geometry restraints manager: 7.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 8628 1.33 - 1.46: 5473 1.46 - 1.58: 12967 1.58 - 1.70: 0 1.70 - 1.82: 250 Bond restraints: 27318 Sorted by residual: bond pdb=" CG1 ILE B 602 " pdb=" CD1 ILE B 602 " ideal model delta sigma weight residual 1.513 1.376 0.137 3.90e-02 6.57e+02 1.23e+01 bond pdb=" C TYR A 289 " pdb=" N THR A 290 " ideal model delta sigma weight residual 1.328 1.277 0.050 1.45e-02 4.76e+03 1.21e+01 bond pdb=" C CYS B1229 " pdb=" N PRO B1230 " ideal model delta sigma weight residual 1.337 1.299 0.038 1.24e-02 6.50e+03 9.26e+00 bond pdb=" CA ALA C 859 " pdb=" C ALA C 859 " ideal model delta sigma weight residual 1.524 1.488 0.036 1.27e-02 6.20e+03 8.12e+00 bond pdb=" CG LEU B 568 " pdb=" CD2 LEU B 568 " ideal model delta sigma weight residual 1.521 1.430 0.091 3.30e-02 9.18e+02 7.64e+00 ... (remaining 27313 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.02: 36911 4.02 - 8.05: 254 8.05 - 12.07: 20 12.07 - 16.10: 6 16.10 - 20.12: 2 Bond angle restraints: 37193 Sorted by residual: angle pdb=" N LYS A 723 " pdb=" CA LYS A 723 " pdb=" C LYS A 723 " ideal model delta sigma weight residual 109.96 90.66 19.30 1.49e+00 4.50e-01 1.68e+02 angle pdb=" C LYS A 723 " pdb=" CA LYS A 723 " pdb=" CB LYS A 723 " ideal model delta sigma weight residual 110.16 122.49 -12.33 1.44e+00 4.82e-01 7.33e+01 angle pdb=" N PRO B 223 " pdb=" CA PRO B 223 " pdb=" CB PRO B 223 " ideal model delta sigma weight residual 103.25 111.86 -8.61 1.05e+00 9.07e-01 6.73e+01 angle pdb=" C SER C 857 " pdb=" N GLU C 858 " pdb=" CA GLU C 858 " ideal model delta sigma weight residual 122.08 109.95 12.13 1.59e+00 3.96e-01 5.82e+01 angle pdb=" N ASN C 991 " pdb=" CA ASN C 991 " pdb=" C ASN C 991 " ideal model delta sigma weight residual 112.72 102.96 9.76 1.28e+00 6.10e-01 5.81e+01 ... (remaining 37188 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.78: 14944 16.78 - 33.56: 1053 33.56 - 50.34: 168 50.34 - 67.11: 20 67.11 - 83.89: 12 Dihedral angle restraints: 16197 sinusoidal: 5555 harmonic: 10642 Sorted by residual: dihedral pdb=" CA HIS C 990 " pdb=" C HIS C 990 " pdb=" N ASN C 991 " pdb=" CA ASN C 991 " ideal model delta harmonic sigma weight residual 180.00 139.99 40.01 0 5.00e+00 4.00e-02 6.40e+01 dihedral pdb=" CA GLN C 855 " pdb=" C GLN C 855 " pdb=" N PHE C 856 " pdb=" CA PHE C 856 " ideal model delta harmonic sigma weight residual 180.00 144.39 35.61 0 5.00e+00 4.00e-02 5.07e+01 dihedral pdb=" CA GLU C 858 " pdb=" C GLU C 858 " pdb=" N ALA C 859 " pdb=" CA ALA C 859 " ideal model delta harmonic sigma weight residual 180.00 145.14 34.86 0 5.00e+00 4.00e-02 4.86e+01 ... (remaining 16194 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 2970 0.052 - 0.105: 1038 0.105 - 0.157: 237 0.157 - 0.209: 32 0.209 - 0.261: 6 Chirality restraints: 4283 Sorted by residual: chirality pdb=" CA ILE B 602 " pdb=" N ILE B 602 " pdb=" C ILE B 602 " pdb=" CB ILE B 602 " both_signs ideal model delta sigma weight residual False 2.43 2.69 -0.26 2.00e-01 2.50e+01 1.71e+00 chirality pdb=" CA ASP B 533 " pdb=" N ASP B 533 " pdb=" C ASP B 533 " pdb=" CB ASP B 533 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" CB ILE C 897 " pdb=" CA ILE C 897 " pdb=" CG1 ILE C 897 " pdb=" CG2 ILE C 897 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.26 2.00e-01 2.50e+01 1.64e+00 ... (remaining 4280 not shown) Planarity restraints: 4800 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU B 806 " 0.119 5.00e-02 4.00e+02 1.84e-01 5.43e+01 pdb=" N PRO B 807 " -0.319 5.00e-02 4.00e+02 pdb=" CA PRO B 807 " 0.111 5.00e-02 4.00e+02 pdb=" CD PRO B 807 " 0.089 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 820 " 0.075 5.00e-02 4.00e+02 1.13e-01 2.05e+01 pdb=" N PRO B 821 " -0.196 5.00e-02 4.00e+02 pdb=" CA PRO B 821 " 0.059 5.00e-02 4.00e+02 pdb=" CD PRO B 821 " 0.062 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 380 " 0.073 5.00e-02 4.00e+02 1.12e-01 2.00e+01 pdb=" N PRO C 381 " -0.193 5.00e-02 4.00e+02 pdb=" CA PRO C 381 " 0.061 5.00e-02 4.00e+02 pdb=" CD PRO C 381 " 0.059 5.00e-02 4.00e+02 ... (remaining 4797 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 242 2.59 - 3.16: 24300 3.16 - 3.74: 40754 3.74 - 4.32: 57280 4.32 - 4.90: 93335 Nonbonded interactions: 215911 Sorted by model distance: nonbonded pdb=" O LEU B 815 " pdb=" OG SER B 820 " model vdw 2.008 3.040 nonbonded pdb=" O GLU B 534 " pdb=" ND2 ASN B 535 " model vdw 2.009 3.120 nonbonded pdb=" OD1 ASP A 808 " pdb=" OH TYR A 823 " model vdw 2.068 3.040 nonbonded pdb=" NZ LYS B 168 " pdb=" OE2 GLU B 170 " model vdw 2.070 3.120 nonbonded pdb=" O ASP C 826 " pdb=" N GLY C 830 " model vdw 2.083 3.120 ... (remaining 215906 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 143.220 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: 0.020 Extract box with map and model: 0.930 Check model and map are aligned: 0.180 Set scattering table: 0.220 Process input model: 67.960 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.120 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 216.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5736 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 : 0.010 0.137 27335 Z= 0.474 Angle : 1.019 23.156 37219 Z= 0.553 Chirality : 0.055 0.261 4283 Planarity : 0.007 0.184 4800 Dihedral : 11.988 83.892 9304 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 16.10 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.41 % Favored : 92.51 % Rotamer: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.93 (0.13), residues: 3592 helix: -0.95 (0.13), residues: 1356 sheet: -2.18 (0.18), residues: 719 loop : -2.69 (0.14), residues: 1517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.005 TRP A 898 HIS 0.014 0.002 HIS C 436 PHE 0.052 0.004 PHE B 570 TYR 0.036 0.004 TYR A 842 ARG 0.018 0.001 ARG A 148 Details of bonding type rmsd hydrogen bonds : bond 0.19720 ( 1238) hydrogen bonds : angle 7.86286 ( 3537) metal coordination : bond 0.01966 ( 16) metal coordination : angle 8.95209 ( 24) SS BOND : bond 0.00860 ( 1) SS BOND : angle 1.30482 ( 2) covalent geometry : bond 0.01043 (27318) covalent geometry : angle 0.99312 (37193) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7184 Ramachandran restraints generated. 3592 Oldfield, 0 Emsley, 3592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7184 Ramachandran restraints generated. 3592 Oldfield, 0 Emsley, 3592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 297 time to evaluate : 3.178 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 ASP cc_start: 0.3963 (t0) cc_final: 0.3728 (t0) REVERT: A 430 VAL cc_start: 0.6799 (t) cc_final: 0.6166 (m) REVERT: A 848 LEU cc_start: 0.6188 (tt) cc_final: 0.5745 (tp) REVERT: A 861 GLU cc_start: 0.6333 (tp30) cc_final: 0.6048 (tp30) REVERT: B 28 ILE cc_start: 0.8216 (mt) cc_final: 0.7714 (pt) REVERT: B 96 ILE cc_start: 0.5271 (mp) cc_final: 0.4959 (mm) REVERT: B 166 LYS cc_start: 0.7867 (mmtt) cc_final: 0.6902 (tptp) REVERT: B 195 MET cc_start: 0.8742 (mmm) cc_final: 0.8397 (mmp) REVERT: C 1163 HIS cc_start: 0.5673 (m-70) cc_final: 0.5350 (m170) REVERT: C 1175 MET cc_start: 0.5951 (mmm) cc_final: 0.5189 (mmm) REVERT: C 1291 VAL cc_start: 0.5507 (m) cc_final: 0.5261 (m) REVERT: C 1333 THR cc_start: 0.7379 (p) cc_final: 0.7119 (p) REVERT: E 489 MET cc_start: 0.2890 (mmt) cc_final: 0.2449 (mmm) REVERT: E 753 MET cc_start: 0.3286 (mmp) cc_final: 0.2991 (mmm) REVERT: E 788 MET cc_start: 0.6354 (ptt) cc_final: 0.5751 (mmm) REVERT: I 37 LYS cc_start: 0.8672 (pptt) cc_final: 0.8326 (tmmt) REVERT: I 41 LYS cc_start: 0.8369 (tttt) cc_final: 0.7858 (pttt) outliers start: 0 outliers final: 0 residues processed: 297 average time/residue: 0.4079 time to fit residues: 203.1024 Evaluate side-chains 192 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 192 time to evaluate : 4.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 305 optimal weight: 0.7980 chunk 274 optimal weight: 9.9990 chunk 152 optimal weight: 0.6980 chunk 93 optimal weight: 0.5980 chunk 185 optimal weight: 0.6980 chunk 146 optimal weight: 0.6980 chunk 283 optimal weight: 8.9990 chunk 109 optimal weight: 5.9990 chunk 172 optimal weight: 1.9990 chunk 211 optimal weight: 0.9980 chunk 328 optimal weight: 0.0980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 ASN A 246 ASN ** B 983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1063 ASN B1092 HIS B1193 GLN C 406 ASN ** C 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 608 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 757 GLN C 809 HIS C1283 HIS E 428 ASN E 880 GLN E 890 GLN ** E1009 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.061561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.052829 restraints weight = 126984.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.052526 restraints weight = 159448.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.052559 restraints weight = 147137.512| |-----------------------------------------------------------------------------| r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6067 moved from start: 0.2835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 27335 Z= 0.160 Angle : 0.700 20.760 37219 Z= 0.361 Chirality : 0.045 0.181 4283 Planarity : 0.005 0.084 4800 Dihedral : 5.547 65.455 3892 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 0.12 % Allowed : 5.35 % Favored : 94.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.65 % Cis-general : 0.00 % Twisted Proline : 0.83 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.83 (0.13), residues: 3592 helix: 0.06 (0.14), residues: 1423 sheet: -1.87 (0.19), residues: 686 loop : -2.09 (0.15), residues: 1483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.069 0.002 TRP A 898 HIS 0.012 0.001 HIS C1163 PHE 0.037 0.002 PHE A 879 TYR 0.031 0.002 TYR B 61 ARG 0.006 0.001 ARG A 148 Details of bonding type rmsd hydrogen bonds : bond 0.04119 ( 1238) hydrogen bonds : angle 5.13738 ( 3537) metal coordination : bond 0.00893 ( 16) metal coordination : angle 7.40251 ( 24) SS BOND : bond 0.00675 ( 1) SS BOND : angle 2.90980 ( 2) covalent geometry : bond 0.00338 (27318) covalent geometry : angle 0.67468 (37193) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7184 Ramachandran restraints generated. 3592 Oldfield, 0 Emsley, 3592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7184 Ramachandran restraints generated. 3592 Oldfield, 0 Emsley, 3592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 239 time to evaluate : 3.814 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 ASP cc_start: 0.5341 (t0) cc_final: 0.5053 (t0) REVERT: B 1 MET cc_start: 0.6808 (ppp) cc_final: 0.6175 (ppp) REVERT: B 28 ILE cc_start: 0.8783 (mt) cc_final: 0.8485 (pt) REVERT: B 58 CYS cc_start: 0.6204 (t) cc_final: 0.5421 (p) REVERT: B 105 THR cc_start: 0.5665 (p) cc_final: 0.5360 (p) REVERT: B 651 MET cc_start: 0.6736 (mmm) cc_final: 0.6365 (mmm) REVERT: B 706 PHE cc_start: 0.4044 (m-10) cc_final: 0.3788 (m-10) REVERT: C 1175 MET cc_start: 0.7527 (mmm) cc_final: 0.6819 (mmm) REVERT: C 1333 THR cc_start: 0.7038 (p) cc_final: 0.6836 (p) REVERT: E 420 MET cc_start: 0.1479 (mpp) cc_final: 0.0498 (mpp) REVERT: E 489 MET cc_start: 0.2737 (mmt) cc_final: 0.2382 (mmm) REVERT: I 20 MET cc_start: 0.7388 (pmm) cc_final: 0.7171 (pmm) REVERT: I 37 LYS cc_start: 0.8676 (pptt) cc_final: 0.8449 (tmmt) outliers start: 3 outliers final: 1 residues processed: 241 average time/residue: 0.4783 time to fit residues: 202.4877 Evaluate side-chains 173 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 172 time to evaluate : 5.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 294 optimal weight: 2.9990 chunk 192 optimal weight: 0.0010 chunk 144 optimal weight: 2.9990 chunk 80 optimal weight: 0.7980 chunk 83 optimal weight: 0.9980 chunk 116 optimal weight: 4.9990 chunk 340 optimal weight: 3.9990 chunk 338 optimal weight: 6.9990 chunk 117 optimal weight: 0.7980 chunk 324 optimal weight: 6.9990 chunk 21 optimal weight: 1.9990 overall best weight: 0.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 ASN A 112 ASN A 188 ASN A 214 HIS A 246 ASN ** B 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 145 GLN B 444 ASN ** B 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 551 GLN ** C 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 608 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 615 ASN ** E 708 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 890 GLN E 984 HIS ** E1009 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.061390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.052354 restraints weight = 131821.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.051808 restraints weight = 180020.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.052227 restraints weight = 154266.994| |-----------------------------------------------------------------------------| r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6889 moved from start: 0.5491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.111 27335 Z= 0.211 Angle : 0.758 22.550 37219 Z= 0.382 Chirality : 0.045 0.251 4283 Planarity : 0.006 0.099 4800 Dihedral : 5.292 55.744 3892 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 0.20 % Allowed : 3.45 % Favored : 96.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.65 % Cis-general : 0.00 % Twisted Proline : 0.83 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.14), residues: 3592 helix: 0.39 (0.14), residues: 1418 sheet: -1.70 (0.19), residues: 699 loop : -1.96 (0.15), residues: 1475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.070 0.003 TRP B 180 HIS 0.009 0.001 HIS B 787 PHE 0.033 0.002 PHE C1255 TYR 0.038 0.002 TYR E 729 ARG 0.017 0.001 ARG B 715 Details of bonding type rmsd hydrogen bonds : bond 0.04763 ( 1238) hydrogen bonds : angle 4.99119 ( 3537) metal coordination : bond 0.01062 ( 16) metal coordination : angle 8.98612 ( 24) SS BOND : bond 0.00587 ( 1) SS BOND : angle 2.41954 ( 2) covalent geometry : bond 0.00472 (27318) covalent geometry : angle 0.72300 (37193) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7184 Ramachandran restraints generated. 3592 Oldfield, 0 Emsley, 3592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7184 Ramachandran restraints generated. 3592 Oldfield, 0 Emsley, 3592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 204 time to evaluate : 3.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 ASP cc_start: 0.6451 (t0) cc_final: 0.6192 (t0) REVERT: A 865 MET cc_start: 0.6818 (mtp) cc_final: 0.6301 (mtm) REVERT: B 28 ILE cc_start: 0.8974 (mt) cc_final: 0.8526 (pt) REVERT: B 58 CYS cc_start: 0.7931 (t) cc_final: 0.7314 (t) REVERT: B 513 GLN cc_start: 0.8080 (pp30) cc_final: 0.7716 (pp30) REVERT: B 621 MET cc_start: 0.6585 (ttp) cc_final: 0.6369 (ttp) REVERT: B 706 PHE cc_start: 0.5997 (m-10) cc_final: 0.5507 (m-80) REVERT: C 1093 PHE cc_start: 0.4504 (t80) cc_final: 0.4292 (t80) REVERT: C 1132 MET cc_start: 0.7007 (mmt) cc_final: 0.6730 (mtt) REVERT: C 1175 MET cc_start: 0.7950 (mmm) cc_final: 0.7315 (mmm) REVERT: C 1307 MET cc_start: 0.7023 (tpt) cc_final: 0.6647 (tpt) REVERT: E 858 MET cc_start: 0.5726 (ptp) cc_final: 0.5352 (ptt) REVERT: I 20 MET cc_start: 0.7619 (pmm) cc_final: 0.7358 (pmm) REVERT: I 21 MET cc_start: 0.8153 (pmm) cc_final: 0.7766 (pmm) REVERT: I 41 LYS cc_start: 0.7493 (pttt) cc_final: 0.7217 (pttp) outliers start: 5 outliers final: 0 residues processed: 208 average time/residue: 0.3796 time to fit residues: 133.9613 Evaluate side-chains 150 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 150 time to evaluate : 3.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/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-5710/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-5710/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-5710/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-5710/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-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/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-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 61.9793 > 50: distance: 18 - 36: 13.376 distance: 23 - 41: 18.276 distance: 26 - 29: 11.266 distance: 27 - 46: 20.427 distance: 29 - 30: 25.910 distance: 30 - 31: 33.392 distance: 30 - 33: 10.231 distance: 31 - 32: 15.305 distance: 31 - 36: 35.284 distance: 32 - 51: 19.050 distance: 33 - 34: 6.827 distance: 33 - 35: 22.794 distance: 36 - 37: 23.727 distance: 37 - 38: 13.426 distance: 37 - 40: 17.405 distance: 38 - 39: 29.382 distance: 38 - 41: 34.965 distance: 41 - 42: 24.435 distance: 42 - 43: 34.163 distance: 42 - 45: 37.786 distance: 43 - 44: 20.976 distance: 43 - 46: 30.435 distance: 46 - 47: 13.623 distance: 47 - 48: 30.162 distance: 47 - 50: 6.276 distance: 48 - 49: 42.791 distance: 48 - 51: 15.601 distance: 51 - 52: 16.087 distance: 52 - 53: 22.711 distance: 52 - 55: 6.157 distance: 53 - 54: 22.485 distance: 53 - 56: 50.507 distance: 56 - 57: 51.795 distance: 57 - 58: 51.158 distance: 57 - 60: 55.692 distance: 58 - 59: 40.188 distance: 58 - 61: 35.031 distance: 61 - 62: 35.701 distance: 62 - 63: 13.672 distance: 62 - 65: 12.150 distance: 63 - 64: 20.253 distance: 63 - 66: 10.133 distance: 66 - 67: 13.659 distance: 67 - 68: 13.395 distance: 67 - 70: 27.782 distance: 68 - 69: 15.831 distance: 68 - 71: 16.916 distance: 69 - 87: 6.443 distance: 71 - 72: 6.061 distance: 72 - 73: 26.290 distance: 72 - 75: 26.603 distance: 73 - 74: 9.182 distance: 73 - 76: 18.940 distance: 74 - 94: 22.580 distance: 76 - 77: 15.241 distance: 77 - 78: 10.647 distance: 77 - 80: 20.008 distance: 78 - 79: 20.845 distance: 79 - 99: 21.122