Starting phenix.real_space_refine on Sun Jun 22 06:39:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vhn_32000/06_2025/7vhn_32000.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vhn_32000/06_2025/7vhn_32000.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7vhn_32000/06_2025/7vhn_32000.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vhn_32000/06_2025/7vhn_32000.map" model { file = "/net/cci-nas-00/data/ceres_data/7vhn_32000/06_2025/7vhn_32000.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vhn_32000/06_2025/7vhn_32000.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 117 5.16 5 C 16196 2.51 5 N 4195 2.21 5 O 4895 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 127 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: 25403 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 8323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1064, 8323 Classifications: {'peptide': 1064} Link IDs: {'PTRANS': 51, 'TRANS': 1012} Chain breaks: 6 Chain: "B" Number of atoms: 8323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1064, 8323 Classifications: {'peptide': 1064} Link IDs: {'PTRANS': 51, 'TRANS': 1012} Chain breaks: 6 Chain: "C" Number of atoms: 8323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1064, 8323 Classifications: {'peptide': 1064} Link IDs: {'PTRANS': 51, 'TRANS': 1012} Chain breaks: 6 Chain: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 14.03, per 1000 atoms: 0.55 Number of scatterers: 25403 At special positions: 0 Unit cell: (154.08, 151.94, 201.16, 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 117 16.00 O 4895 8.00 N 4195 7.00 C 16196 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.02 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.04 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.02 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " 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 Links applied NAG-ASN " NAG A1201 " - " ASN A 61 " " NAG A1202 " - " ASN A 122 " " NAG A1203 " - " ASN A 282 " " NAG A1204 " - " ASN A 331 " " NAG A1205 " - " ASN A 343 " " NAG A1206 " - " ASN A 603 " " NAG A1207 " - " ASN A 616 " " NAG A1208 " - " ASN A 657 " " NAG A1209 " - " ASN A 709 " " NAG A1210 " - " ASN A1074 " " NAG A1211 " - " ASN A 165 " " NAG B1201 " - " ASN B 61 " " NAG B1202 " - " ASN B 122 " " NAG B1203 " - " ASN B 282 " " NAG B1204 " - " ASN B 331 " " NAG B1205 " - " ASN B 343 " " NAG B1206 " - " ASN B 657 " " NAG B1207 " - " ASN B 709 " " NAG B1208 " - " ASN B1074 " " NAG B1209 " - " ASN B 165 " " NAG B1210 " - " ASN B 616 " " NAG C1201 " - " ASN C 282 " " NAG C1202 " - " ASN C 331 " " NAG C1203 " - " ASN C 343 " " NAG C1204 " - " ASN C 616 " " NAG C1205 " - " ASN C 657 " " NAG C1206 " - " ASN C 709 " " NAG C1207 " - " ASN C1074 " " NAG C1208 " - " ASN C 61 " " NAG C1209 " - " ASN C 122 " " NAG C1210 " - " ASN C 165 " Time building additional restraints: 5.73 Conformation dependent library (CDL) restraints added in 3.1 seconds 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5976 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 47 sheets defined 23.8% alpha, 22.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.55 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 383 through 387 Processing helix chain 'A' and resid 406 through 411 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 616 through 620 Processing helix chain 'A' and resid 737 through 743 removed outlier: 3.655A pdb=" N TYR A 741 " --> pdb=" O ASP A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.624A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 759 through 783 Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 850 through 855 removed outlier: 3.636A pdb=" N PHE A 855 " --> pdb=" O CYS A 851 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.798A pdb=" N ALA A 871 " --> pdb=" O ASP A 867 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N SER A 875 " --> pdb=" O ALA A 871 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 891 removed outlier: 4.084A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLY A 891 " --> pdb=" O THR A 887 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 886 through 891' Processing helix chain 'A' and resid 897 through 908 removed outlier: 3.903A pdb=" N ALA A 903 " --> pdb=" O ALA A 899 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N TYR A 904 " --> pdb=" O MET A 900 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 918 removed outlier: 3.900A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.652A pdb=" N ASN A 925 " --> pdb=" O LYS A 921 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLY A 932 " --> pdb=" O ASN A 928 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LEU A 938 " --> pdb=" O ILE A 934 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.923A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ALA A 958 " --> pdb=" O GLN A 954 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N LEU A 959 " --> pdb=" O ASN A 955 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASN A 960 " --> pdb=" O ALA A 956 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N THR A 961 " --> pdb=" O GLN A 957 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 979 through 983 removed outlier: 3.507A pdb=" N ARG A 983 " --> pdb=" O ILE A 980 " (cutoff:3.500A) Processing helix chain 'A' and resid 988 through 1019 removed outlier: 3.930A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE A 997 " --> pdb=" O ILE A 993 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLN A1002 " --> pdb=" O THR A 998 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR A1007 " --> pdb=" O SER A1003 " (cutoff:3.500A) Processing helix chain 'A' and resid 1021 through 1032 removed outlier: 3.519A pdb=" N ALA A1026 " --> pdb=" O ALA A1022 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N SER A1030 " --> pdb=" O ALA A1026 " (cutoff:3.500A) Processing helix chain 'A' and resid 1116 through 1118 No H-bonds generated for 'chain 'A' and resid 1116 through 1118' Processing helix chain 'A' and resid 1141 through 1148 removed outlier: 4.268A pdb=" N LEU A1145 " --> pdb=" O LEU A1141 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 349 through 353 Processing helix chain 'B' and resid 365 through 371 removed outlier: 3.932A pdb=" N SER B 371 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 387 removed outlier: 3.731A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 411 removed outlier: 4.200A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ALA B 411 " --> pdb=" O ARG B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 421 removed outlier: 3.954A pdb=" N TYR B 421 " --> pdb=" O LYS B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 616 through 620 Processing helix chain 'B' and resid 738 through 743 Processing helix chain 'B' and resid 746 through 754 removed outlier: 4.022A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 4.056A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N THR B 768 " --> pdb=" O ASN B 764 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N PHE B 782 " --> pdb=" O THR B 778 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 852 through 857 removed outlier: 4.176A pdb=" N ASN B 856 " --> pdb=" O ALA B 852 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N GLY B 857 " --> pdb=" O GLN B 853 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 852 through 857' Processing helix chain 'B' and resid 866 through 884 removed outlier: 4.027A pdb=" N ALA B 871 " --> pdb=" O ASP B 867 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N SER B 875 " --> pdb=" O ALA B 871 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU B 878 " --> pdb=" O THR B 874 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ILE B 882 " --> pdb=" O LEU B 878 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 891 removed outlier: 4.236A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLY B 891 " --> pdb=" O THR B 887 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 886 through 891' Processing helix chain 'B' and resid 898 through 907 removed outlier: 3.541A pdb=" N ALA B 903 " --> pdb=" O ALA B 899 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N TYR B 904 " --> pdb=" O MET B 900 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASN B 907 " --> pdb=" O ALA B 903 " (cutoff:3.500A) Processing helix chain 'B' and resid 908 through 910 No H-bonds generated for 'chain 'B' and resid 908 through 910' Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.670A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 940 removed outlier: 3.829A pdb=" N ASN B 925 " --> pdb=" O LYS B 921 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA B 930 " --> pdb=" O GLN B 926 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLY B 932 " --> pdb=" O ASN B 928 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYS B 933 " --> pdb=" O SER B 929 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N SER B 940 " --> pdb=" O ASP B 936 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.628A pdb=" N GLN B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA B 958 " --> pdb=" O GLN B 954 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU B 959 " --> pdb=" O ASN B 955 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASN B 960 " --> pdb=" O ALA B 956 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 989 through 1015 removed outlier: 3.543A pdb=" N GLY B 999 " --> pdb=" O ARG B 995 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N TYR B1007 " --> pdb=" O SER B1003 " (cutoff:3.500A) Processing helix chain 'B' and resid 1018 through 1026 removed outlier: 3.846A pdb=" N LEU B1024 " --> pdb=" O ALA B1020 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1148 removed outlier: 4.761A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU B1145 " --> pdb=" O LEU B1141 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER B1147 " --> pdb=" O PRO B1143 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 4.177A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.666A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 371 removed outlier: 4.324A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 387 Processing helix chain 'C' and resid 405 through 411 removed outlier: 4.637A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 421 Processing helix chain 'C' and resid 616 through 620 Processing helix chain 'C' and resid 737 through 743 removed outlier: 3.581A pdb=" N TYR C 741 " --> pdb=" O ASP C 737 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.955A pdb=" N SER C 750 " --> pdb=" O SER C 746 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 4.174A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 850 through 854 removed outlier: 3.656A pdb=" N LYS C 854 " --> pdb=" O ILE C 850 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 850 through 854' Processing helix chain 'C' and resid 869 through 885 removed outlier: 3.763A pdb=" N SER C 875 " --> pdb=" O ALA C 871 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 907 removed outlier: 4.030A pdb=" N ALA C 903 " --> pdb=" O ALA C 899 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N TYR C 904 " --> pdb=" O MET C 900 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.774A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 939 removed outlier: 3.587A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 941 through 944 removed outlier: 4.004A pdb=" N ALA C 944 " --> pdb=" O THR C 941 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 941 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.585A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU C 959 " --> pdb=" O ASN C 955 " (cutoff:3.500A) Processing helix chain 'C' and resid 989 through 1018 removed outlier: 3.516A pdb=" N GLN C1002 " --> pdb=" O THR C 998 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA C1016 " --> pdb=" O LEU C1012 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ILE C1018 " --> pdb=" O ARG C1014 " (cutoff:3.500A) Processing helix chain 'C' and resid 1018 through 1032 removed outlier: 3.532A pdb=" N ASN C1023 " --> pdb=" O ARG C1019 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N LEU C1024 " --> pdb=" O ALA C1020 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N THR C1027 " --> pdb=" O ASN C1023 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N SER C1030 " --> pdb=" O ALA C1026 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 4.708A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N LEU C1145 " --> pdb=" O LEU C1141 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 31 removed outlier: 3.501A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ASN A 188 " --> pdb=" O GLU A 96 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 50 through 55 removed outlier: 3.703A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 5.891A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N TRP A 104 " --> pdb=" O ILE A 119 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 134 through 135 removed outlier: 6.338A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 314 Processing sheet with id=AA6, first strand: chain 'A' and resid 318 through 319 Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 326 Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA9, first strand: chain 'A' and resid 448 through 454 removed outlier: 6.687A pdb=" N TYR A 449 " --> pdb=" O PHE A 497 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N PHE A 497 " --> pdb=" O TYR A 449 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N TYR A 451 " --> pdb=" O TYR A 495 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 Processing sheet with id=AB2, first strand: chain 'A' and resid 701 through 702 removed outlier: 7.058A pdb=" N ALA A 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 712 through 722 removed outlier: 6.629A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TYR A1047 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 712 through 722 removed outlier: 6.629A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL A1094 " --> pdb=" O THR A1105 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 725 through 727 removed outlier: 3.655A pdb=" N GLU A 725 " --> pdb=" O PHE A1062 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLY A1059 " --> pdb=" O ALA A1056 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ALA A1056 " --> pdb=" O GLY A1059 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 735 through 736 Processing sheet with id=AB7, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AB8, first strand: chain 'A' and resid 1081 through 1082 removed outlier: 4.036A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 27 through 30 removed outlier: 3.951A pdb=" N ASN B 188 " --> pdb=" O GLU B 96 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.755A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 removed outlier: 11.131A pdb=" N ILE B 128 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 8.148A pdb=" N THR B 167 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N VAL B 130 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N ASN B 165 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N GLU B 132 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N ALA B 163 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N GLN B 134 " --> pdb=" O SER B 161 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 319 removed outlier: 3.664A pdb=" N THR B 315 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU B 650 " --> pdb=" O PHE B 643 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AC5, first strand: chain 'B' and resid 361 through 362 removed outlier: 4.147A pdb=" N CYS B 525 " --> pdb=" O CYS B 361 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC7, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC8, first strand: chain 'B' and resid 539 through 540 Processing sheet with id=AC9, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.767A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.300A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 715 Processing sheet with id=AD2, first strand: chain 'B' and resid 721 through 727 removed outlier: 3.683A pdb=" N GLU B 725 " --> pdb=" O PHE B1062 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 721 through 727 removed outlier: 3.683A pdb=" N GLU B 725 " --> pdb=" O PHE B1062 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLY B1059 " --> pdb=" O ALA B1056 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ALA B1056 " --> pdb=" O GLY B1059 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 734 through 736 removed outlier: 4.081A pdb=" N SER B 735 " --> pdb=" O ASN B 859 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 1081 through 1082 removed outlier: 5.364A pdb=" N GLY B1124 " --> pdb=" O ALA B1087 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N PHE B1089 " --> pdb=" O VAL B1122 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N VAL B1122 " --> pdb=" O PHE B1089 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 27 through 31 removed outlier: 3.612A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.745A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.790A pdb=" N LEU C 84 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ARG C 237 " --> pdb=" O PHE C 106 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N PHE C 106 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N GLN C 239 " --> pdb=" O TRP C 104 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N TRP C 104 " --> pdb=" O GLN C 239 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N LEU C 241 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N TRP C 104 " --> pdb=" O ILE C 119 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N VAL C 120 " --> pdb=" O VAL C 127 " (cutoff:3.500A) removed outlier: 11.636A pdb=" N VAL C 126 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 10.470A pdb=" N GLU C 169 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 11.926A pdb=" N ILE C 128 " --> pdb=" O THR C 167 " (cutoff:3.500A) removed outlier: 8.739A pdb=" N THR C 167 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N VAL C 130 " --> pdb=" O ASN C 165 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N ASN C 165 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N GLU C 132 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ALA C 163 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 311 through 314 Processing sheet with id=AE1, first strand: chain 'C' and resid 311 through 314 removed outlier: 4.064A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 325 through 326 removed outlier: 7.302A pdb=" N ILE C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AE4, first strand: chain 'C' and resid 453 through 454 Processing sheet with id=AE5, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE6, first strand: chain 'C' and resid 654 through 655 Processing sheet with id=AE7, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.600A pdb=" N LYS C1073 " --> pdb=" O ILE C 714 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL C1094 " --> pdb=" O THR C1105 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 718 through 722 removed outlier: 7.080A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N TYR C1047 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 725 through 728 removed outlier: 3.803A pdb=" N GLU C 725 " --> pdb=" O PHE C1062 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLY C1059 " --> pdb=" O ALA C1056 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ALA C1056 " --> pdb=" O GLY C1059 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 735 through 736 Processing sheet with id=AF2, first strand: chain 'C' and resid 1081 through 1082 removed outlier: 4.130A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N SER C1123 " --> pdb=" O ALA C1087 " (cutoff:3.500A) 853 hydrogen bonds defined for protein. 2283 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: 10.96 Time building geometry restraints manager: 6.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 5556 1.33 - 1.45: 6794 1.45 - 1.58: 13476 1.58 - 1.71: 0 1.71 - 1.83: 147 Bond restraints: 25973 Sorted by residual: bond pdb=" N ILE A 714 " pdb=" CA ILE A 714 " ideal model delta sigma weight residual 1.458 1.488 -0.030 7.70e-03 1.69e+04 1.55e+01 bond pdb=" N PHE A 329 " pdb=" CA PHE A 329 " ideal model delta sigma weight residual 1.453 1.484 -0.031 8.30e-03 1.45e+04 1.43e+01 bond pdb=" N PHE C 329 " pdb=" CA PHE C 329 " ideal model delta sigma weight residual 1.453 1.488 -0.034 9.20e-03 1.18e+04 1.41e+01 bond pdb=" N ASP B 578 " pdb=" CA ASP B 578 " ideal model delta sigma weight residual 1.453 1.486 -0.033 9.20e-03 1.18e+04 1.28e+01 bond pdb=" N VAL B 126 " pdb=" CA VAL B 126 " ideal model delta sigma weight residual 1.457 1.496 -0.039 1.22e-02 6.72e+03 1.01e+01 ... (remaining 25968 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.28: 34213 2.28 - 4.57: 1032 4.57 - 6.85: 67 6.85 - 9.13: 8 9.13 - 11.42: 3 Bond angle restraints: 35323 Sorted by residual: angle pdb=" C LYS C 528 " pdb=" N LYS C 529 " pdb=" CA LYS C 529 " ideal model delta sigma weight residual 121.54 132.96 -11.42 1.91e+00 2.74e-01 3.57e+01 angle pdb=" CA PHE B 133 " pdb=" CB PHE B 133 " pdb=" CG PHE B 133 " ideal model delta sigma weight residual 113.80 118.38 -4.58 1.00e+00 1.00e+00 2.09e+01 angle pdb=" N GLY C 103 " pdb=" CA GLY C 103 " pdb=" C GLY C 103 " ideal model delta sigma weight residual 110.73 119.29 -8.56 1.90e+00 2.77e-01 2.03e+01 angle pdb=" C PHE A 559 " pdb=" CA PHE A 559 " pdb=" CB PHE A 559 " ideal model delta sigma weight residual 113.15 102.57 10.58 2.38e+00 1.77e-01 1.98e+01 angle pdb=" CA THR B 124 " pdb=" C THR B 124 " pdb=" O THR B 124 " ideal model delta sigma weight residual 120.82 116.24 4.58 1.05e+00 9.07e-01 1.91e+01 ... (remaining 35318 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 14383 17.83 - 35.66: 1243 35.66 - 53.49: 212 53.49 - 71.32: 32 71.32 - 89.15: 18 Dihedral angle restraints: 15888 sinusoidal: 6603 harmonic: 9285 Sorted by residual: dihedral pdb=" CB CYS A 538 " pdb=" SG CYS A 538 " pdb=" SG CYS A 590 " pdb=" CB CYS A 590 " ideal model delta sinusoidal sigma weight residual -86.00 -8.13 -77.87 1 1.00e+01 1.00e-02 7.58e+01 dihedral pdb=" CB CYS B 480 " pdb=" SG CYS B 480 " pdb=" SG CYS B 488 " pdb=" CB CYS B 488 " ideal model delta sinusoidal sigma weight residual 93.00 169.15 -76.15 1 1.00e+01 1.00e-02 7.30e+01 dihedral pdb=" CB CYS B1082 " pdb=" SG CYS B1082 " pdb=" SG CYS B1126 " pdb=" CB CYS B1126 " ideal model delta sinusoidal sigma weight residual -86.00 -23.81 -62.19 1 1.00e+01 1.00e-02 5.12e+01 ... (remaining 15885 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.104: 3780 0.104 - 0.208: 266 0.208 - 0.313: 33 0.313 - 0.417: 4 0.417 - 0.521: 5 Chirality restraints: 4088 Sorted by residual: chirality pdb=" C1 NAG C1203 " pdb=" ND2 ASN C 343 " pdb=" C2 NAG C1203 " pdb=" O5 NAG C1203 " both_signs ideal model delta sigma weight residual False -2.40 -1.88 -0.52 2.00e-01 2.50e+01 6.79e+00 chirality pdb=" C1 NAG C1207 " pdb=" ND2 ASN C1074 " pdb=" C2 NAG C1207 " pdb=" O5 NAG C1207 " both_signs ideal model delta sigma weight residual False -2.40 -1.92 -0.48 2.00e-01 2.50e+01 5.85e+00 chirality pdb=" C1 NAG B1203 " pdb=" ND2 ASN B 282 " pdb=" C2 NAG B1203 " pdb=" O5 NAG B1203 " both_signs ideal model delta sigma weight residual False -2.40 -1.94 -0.46 2.00e-01 2.50e+01 5.34e+00 ... (remaining 4085 not shown) Planarity restraints: 4568 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1205 " 0.349 2.00e-02 2.50e+03 3.00e-01 1.13e+03 pdb=" C7 NAG B1205 " -0.085 2.00e-02 2.50e+03 pdb=" C8 NAG B1205 " 0.148 2.00e-02 2.50e+03 pdb=" N2 NAG B1205 " -0.534 2.00e-02 2.50e+03 pdb=" O7 NAG B1205 " 0.121 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1208 " -0.326 2.00e-02 2.50e+03 2.82e-01 9.95e+02 pdb=" C7 NAG C1208 " 0.075 2.00e-02 2.50e+03 pdb=" C8 NAG C1208 " -0.045 2.00e-02 2.50e+03 pdb=" N2 NAG C1208 " 0.495 2.00e-02 2.50e+03 pdb=" O7 NAG C1208 " -0.199 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1208 " -0.316 2.00e-02 2.50e+03 2.76e-01 9.53e+02 pdb=" C7 NAG B1208 " 0.067 2.00e-02 2.50e+03 pdb=" C8 NAG B1208 " -0.082 2.00e-02 2.50e+03 pdb=" N2 NAG B1208 " 0.494 2.00e-02 2.50e+03 pdb=" O7 NAG B1208 " -0.162 2.00e-02 2.50e+03 ... (remaining 4565 not shown) Histogram of nonbonded interaction distances: 1.47 - 2.16: 4 2.16 - 2.84: 9031 2.84 - 3.53: 33847 3.53 - 4.21: 55697 4.21 - 4.90: 95836 Nonbonded interactions: 194415 Sorted by model distance: nonbonded pdb=" ND2 ASN A 164 " pdb=" C1 NAG A1211 " model vdw 1.473 3.550 nonbonded pdb=" O GLU C 661 " pdb=" OH TYR C 695 " model vdw 2.029 3.040 nonbonded pdb=" OG1 THR A 393 " pdb=" O GLU A 516 " model vdw 2.128 3.040 nonbonded pdb=" OG1 THR B 22 " pdb=" O LYS B 77 " model vdw 2.147 3.040 nonbonded pdb=" O ASP C 442 " pdb=" ND2 ASN C 448 " model vdw 2.172 3.120 ... (remaining 194410 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' and (resid 14 through 1148 or resid 1201 through 1210)) selection = chain 'B' selection = chain 'C' } 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: 2.360 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: 0.940 Check model and map are aligned: 0.190 Set scattering table: 0.230 Process input model: 55.960 Find NCS groups from input model: 1.180 Set up NCS constraints: 0.090 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 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 : 0.006 0.066 26046 Z= 0.357 Angle : 0.888 12.540 35500 Z= 0.528 Chirality : 0.062 0.521 4088 Planarity : 0.015 0.300 4537 Dihedral : 13.367 89.150 9786 Min Nonbonded Distance : 1.473 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.71 % Favored : 92.22 % Rotamer: Outliers : 0.72 % Allowed : 1.47 % Favored : 97.81 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -2.94 (0.13), residues: 3150 helix: -1.45 (0.19), residues: 639 sheet: -1.15 (0.19), residues: 646 loop : -2.54 (0.13), residues: 1865 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 64 HIS 0.006 0.001 HIS C1048 PHE 0.029 0.002 PHE B 201 TYR 0.023 0.002 TYR A 453 ARG 0.006 0.001 ARG B 815 Details of bonding type rmsd link_NAG-ASN : bond 0.01499 ( 31) link_NAG-ASN : angle 5.23912 ( 93) hydrogen bonds : bond 0.21830 ( 837) hydrogen bonds : angle 8.83993 ( 2283) SS BOND : bond 0.00426 ( 42) SS BOND : angle 1.44841 ( 84) covalent geometry : bond 0.00607 (25973) covalent geometry : angle 0.84573 (35323) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 193 time to evaluate : 2.613 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 PHE cc_start: 0.8205 (m-80) cc_final: 0.7616 (m-80) REVERT: A 374 PHE cc_start: 0.5230 (m-80) cc_final: 0.4898 (m-80) REVERT: A 855 PHE cc_start: 0.8341 (m-10) cc_final: 0.8104 (m-80) REVERT: B 118 LEU cc_start: 0.8960 (tt) cc_final: 0.8320 (mp) REVERT: B 129 LYS cc_start: 0.7421 (mttt) cc_final: 0.7039 (mttt) REVERT: B 177 MET cc_start: -0.0844 (tpp) cc_final: -0.1841 (ttp) REVERT: B 708 SER cc_start: 0.9021 (OUTLIER) cc_final: 0.8808 (p) REVERT: B 900 MET cc_start: 0.8416 (mtt) cc_final: 0.8215 (mtt) REVERT: B 1029 MET cc_start: 0.9359 (tpp) cc_final: 0.9047 (tpp) REVERT: C 904 TYR cc_start: 0.7625 (m-10) cc_final: 0.7285 (m-10) REVERT: C 1050 MET cc_start: 0.8370 (ptm) cc_final: 0.8137 (ptm) outliers start: 20 outliers final: 7 residues processed: 207 average time/residue: 0.3641 time to fit residues: 121.6593 Evaluate side-chains 132 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 124 time to evaluate : 2.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 342 PHE Chi-restraints excluded: chain C residue 709 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 268 optimal weight: 0.7980 chunk 241 optimal weight: 0.8980 chunk 133 optimal weight: 6.9990 chunk 82 optimal weight: 0.5980 chunk 162 optimal weight: 0.9990 chunk 128 optimal weight: 0.8980 chunk 249 optimal weight: 0.8980 chunk 96 optimal weight: 1.9990 chunk 151 optimal weight: 6.9990 chunk 185 optimal weight: 1.9990 chunk 288 optimal weight: 6.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 ASN B 66 HIS B 125 ASN B 134 GLN B 655 HIS B 774 GLN B 859 ASN B 901 GLN C 81 ASN C 134 GLN C 872 GLN C 957 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.108755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.079914 restraints weight = 65644.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.078438 restraints weight = 42000.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.079280 restraints weight = 39929.909| |-----------------------------------------------------------------------------| r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.1337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 26046 Z= 0.130 Angle : 0.658 10.938 35500 Z= 0.332 Chirality : 0.046 0.338 4088 Planarity : 0.004 0.051 4537 Dihedral : 5.943 58.314 4078 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 0.97 % Allowed : 7.25 % Favored : 91.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.34 (0.14), residues: 3150 helix: -0.46 (0.20), residues: 652 sheet: -0.87 (0.19), residues: 641 loop : -2.31 (0.13), residues: 1857 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP B 436 HIS 0.006 0.001 HIS C1118 PHE 0.031 0.002 PHE B 338 TYR 0.018 0.001 TYR C 204 ARG 0.005 0.001 ARG B 21 Details of bonding type rmsd link_NAG-ASN : bond 0.00499 ( 31) link_NAG-ASN : angle 2.50227 ( 93) hydrogen bonds : bond 0.05136 ( 837) hydrogen bonds : angle 6.12881 ( 2283) SS BOND : bond 0.00332 ( 42) SS BOND : angle 1.32071 ( 84) covalent geometry : bond 0.00279 (25973) covalent geometry : angle 0.64408 (35323) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 162 time to evaluate : 2.671 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 PHE cc_start: 0.7327 (m-80) cc_final: 0.6112 (m-10) REVERT: A 135 PHE cc_start: 0.7987 (m-80) cc_final: 0.7211 (m-80) REVERT: A 392 PHE cc_start: 0.6484 (m-10) cc_final: 0.6205 (m-80) REVERT: A 529 LYS cc_start: 0.7916 (tppt) cc_final: 0.7584 (tppt) REVERT: A 570 ASP cc_start: 0.8083 (p0) cc_final: 0.7675 (p0) REVERT: B 118 LEU cc_start: 0.8869 (tt) cc_final: 0.8172 (mp) REVERT: B 129 LYS cc_start: 0.7186 (mttt) cc_final: 0.6826 (mttt) REVERT: B 177 MET cc_start: -0.0419 (tpp) cc_final: -0.2054 (mtm) REVERT: B 1029 MET cc_start: 0.9342 (tpp) cc_final: 0.8984 (tpp) REVERT: C 238 PHE cc_start: 0.8446 (p90) cc_final: 0.7929 (p90) REVERT: C 327 VAL cc_start: 0.9259 (OUTLIER) cc_final: 0.9038 (t) REVERT: C 396 TYR cc_start: 0.7617 (m-10) cc_final: 0.7414 (m-10) REVERT: C 529 LYS cc_start: 0.6548 (mmmt) cc_final: 0.6229 (mmmt) REVERT: C 773 GLU cc_start: 0.7525 (tp30) cc_final: 0.7219 (tp30) REVERT: C 904 TYR cc_start: 0.7418 (m-10) cc_final: 0.6922 (m-10) outliers start: 27 outliers final: 17 residues processed: 183 average time/residue: 0.3422 time to fit residues: 104.5076 Evaluate side-chains 146 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 128 time to evaluate : 2.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 342 PHE Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 1074 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 96 optimal weight: 0.4980 chunk 127 optimal weight: 8.9990 chunk 188 optimal weight: 4.9990 chunk 135 optimal weight: 7.9990 chunk 181 optimal weight: 3.9990 chunk 124 optimal weight: 3.9990 chunk 100 optimal weight: 4.9990 chunk 17 optimal weight: 4.9990 chunk 273 optimal weight: 0.0030 chunk 132 optimal weight: 4.9990 chunk 305 optimal weight: 2.9990 overall best weight: 2.2996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 859 ASN C 30 ASN C 81 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.106563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.077184 restraints weight = 66345.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.075724 restraints weight = 46035.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.076161 restraints weight = 59339.799| |-----------------------------------------------------------------------------| r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.1542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 26046 Z= 0.203 Angle : 0.657 11.361 35500 Z= 0.333 Chirality : 0.046 0.284 4088 Planarity : 0.004 0.058 4537 Dihedral : 5.818 59.956 4073 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 1.51 % Allowed : 10.12 % Favored : 88.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.26 (0.14), residues: 3150 helix: -0.30 (0.20), residues: 644 sheet: -0.93 (0.19), residues: 645 loop : -2.24 (0.13), residues: 1861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP B 436 HIS 0.005 0.001 HIS C1118 PHE 0.023 0.002 PHE C 429 TYR 0.018 0.001 TYR C 204 ARG 0.005 0.000 ARG B 509 Details of bonding type rmsd link_NAG-ASN : bond 0.00334 ( 31) link_NAG-ASN : angle 2.21005 ( 93) hydrogen bonds : bond 0.05307 ( 837) hydrogen bonds : angle 5.88944 ( 2283) SS BOND : bond 0.00417 ( 42) SS BOND : angle 1.43412 ( 84) covalent geometry : bond 0.00476 (25973) covalent geometry : angle 0.64511 (35323) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 135 time to evaluate : 3.233 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 392 PHE cc_start: 0.6651 (m-10) cc_final: 0.6282 (m-80) REVERT: A 570 ASP cc_start: 0.8169 (p0) cc_final: 0.7687 (p0) REVERT: B 129 LYS cc_start: 0.7110 (mttt) cc_final: 0.6871 (mttt) REVERT: B 177 MET cc_start: -0.0506 (tpp) cc_final: -0.1909 (mtm) REVERT: B 515 PHE cc_start: 0.8632 (OUTLIER) cc_final: 0.7857 (p90) REVERT: B 1029 MET cc_start: 0.9279 (tpp) cc_final: 0.8910 (tpp) REVERT: C 238 PHE cc_start: 0.8554 (p90) cc_final: 0.8342 (p90) REVERT: C 378 LYS cc_start: 0.7891 (OUTLIER) cc_final: 0.7588 (ttmt) REVERT: C 519 HIS cc_start: 0.6239 (OUTLIER) cc_final: 0.5994 (m90) REVERT: C 904 TYR cc_start: 0.7667 (m-10) cc_final: 0.7170 (m-10) outliers start: 42 outliers final: 26 residues processed: 167 average time/residue: 0.4130 time to fit residues: 115.4906 Evaluate side-chains 160 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 131 time to evaluate : 5.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 1104 VAL 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: 55.6353 > 50: distance: 58 - 62: 23.243 distance: 62 - 63: 35.590 distance: 63 - 64: 50.141 distance: 63 - 66: 9.327 distance: 64 - 65: 26.990 distance: 64 - 69: 44.650 distance: 66 - 67: 54.573 distance: 66 - 68: 42.973 distance: 69 - 70: 12.296 distance: 70 - 71: 30.471 distance: 70 - 73: 15.396 distance: 71 - 72: 31.063 distance: 71 - 77: 22.568 distance: 73 - 74: 10.058 distance: 74 - 75: 11.724 distance: 74 - 76: 12.924 distance: 77 - 78: 26.636 distance: 78 - 79: 25.760 distance: 78 - 81: 17.695 distance: 79 - 80: 24.452 distance: 79 - 85: 26.826 distance: 81 - 82: 14.326 distance: 82 - 83: 22.622 distance: 82 - 84: 16.090 distance: 85 - 86: 3.031 distance: 86 - 87: 33.132 distance: 86 - 89: 10.822 distance: 87 - 88: 14.902 distance: 87 - 92: 37.214 distance: 89 - 90: 9.074 distance: 89 - 91: 25.195 distance: 92 - 93: 8.934 distance: 93 - 94: 21.351 distance: 93 - 96: 9.274 distance: 94 - 95: 12.304 distance: 94 - 101: 27.740 distance: 96 - 97: 38.888 distance: 97 - 98: 11.901 distance: 98 - 99: 41.960 distance: 99 - 100: 11.455 distance: 101 - 102: 18.988 distance: 102 - 103: 14.401 distance: 102 - 105: 34.202 distance: 103 - 104: 8.497 distance: 103 - 109: 17.433 distance: 105 - 106: 6.821 distance: 106 - 107: 26.278 distance: 106 - 108: 17.209 distance: 109 - 110: 26.818 distance: 110 - 111: 15.068 distance: 110 - 113: 11.171 distance: 111 - 112: 28.358 distance: 111 - 118: 22.256 distance: 113 - 114: 15.860 distance: 114 - 115: 17.155 distance: 115 - 116: 32.305 distance: 116 - 117: 25.934 distance: 118 - 119: 9.646 distance: 119 - 120: 14.963 distance: 119 - 122: 16.502 distance: 120 - 121: 17.803 distance: 122 - 123: 11.618 distance: 123 - 195: 18.562 distance: 124 - 125: 17.627 distance: 124 - 161: 10.325 distance: 125 - 126: 26.701 distance: 125 - 128: 5.510 distance: 126 - 127: 17.432 distance: 126 - 131: 22.265 distance: 127 - 158: 16.820 distance: 128 - 129: 27.404 distance: 128 - 130: 29.616 distance: 131 - 132: 8.328 distance: 132 - 133: 11.727 distance: 132 - 135: 19.829 distance: 133 - 134: 5.107 distance: 133 - 139: 7.351 distance: 135 - 136: 19.048 distance: 136 - 137: 11.429 distance: 136 - 138: 20.607