Starting phenix.real_space_refine on Sat Jul 4 17:07:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6x79_22083/07_2026/6x79_22083.cif Found real_map, /net/cci-nas-00/data/ceres_data/6x79_22083/07_2026/6x79_22083.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6x79_22083/07_2026/6x79_22083.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6x79_22083/07_2026/6x79_22083.map" model { file = "/net/cci-nas-00/data/ceres_data/6x79_22083/07_2026/6x79_22083.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6x79_22083/07_2026/6x79_22083.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6x79_22083/07_2026/6x79_22083.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6x79_22083/07_2026/6x79_22083.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.106 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 102 5.16 5 C 14187 2.51 5 N 3660 2.21 5 O 4302 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 117 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 22251 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 7179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 950, 7179 Classifications: {'peptide': 950} Incomplete info: {'truncation_to_alanine': 67} Link IDs: {'PTRANS': 45, 'TRANS': 904} Chain breaks: 14 Unresolved non-hydrogen bonds: 260 Unresolved non-hydrogen angles: 334 Unresolved non-hydrogen dihedrals: 214 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'ASP:plan': 13, 'ASN:plan1': 6, 'GLU:plan': 6, 'GLN:plan1': 5, 'PHE:plan': 3, 'ARG:plan': 3, 'HIS:plan': 2, 'TYR:plan': 6} Unresolved non-hydrogen planarities: 186 Chain: "B" Number of atoms: 7179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 950, 7179 Classifications: {'peptide': 950} Incomplete info: {'truncation_to_alanine': 67} Link IDs: {'PTRANS': 45, 'TRANS': 904} Chain breaks: 14 Unresolved non-hydrogen bonds: 260 Unresolved non-hydrogen angles: 334 Unresolved non-hydrogen dihedrals: 214 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'ASP:plan': 13, 'ASN:plan1': 6, 'GLU:plan': 6, 'GLN:plan1': 5, 'PHE:plan': 3, 'ARG:plan': 3, 'HIS:plan': 2, 'TYR:plan': 6} Unresolved non-hydrogen planarities: 186 Chain: "C" Number of atoms: 7179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 950, 7179 Classifications: {'peptide': 950} Incomplete info: {'truncation_to_alanine': 67} Link IDs: {'PTRANS': 45, 'TRANS': 904} Chain breaks: 14 Unresolved non-hydrogen bonds: 260 Unresolved non-hydrogen angles: 334 Unresolved non-hydrogen dihedrals: 214 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'ASP:plan': 13, 'ASN:plan1': 6, 'GLU:plan': 6, 'GLN:plan1': 5, 'PHE:plan': 3, 'ARG:plan': 3, 'HIS:plan': 2, 'TYR:plan': 6} Unresolved non-hydrogen planarities: 186 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 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 chiralities: 11 Chain: "B" 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 chiralities: 11 Chain: "C" 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 chiralities: 11 Time building chain proxies: 4.60, per 1000 atoms: 0.21 Number of scatterers: 22251 At special positions: 0 Unit cell: (128.76, 128.76, 162.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 102 16.00 O 4302 8.00 N 3660 7.00 C 14187 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.02 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.06 Simple disulfide: pdb=" SG CYS A 383 " - pdb=" SG CYS B 985 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.02 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.04 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 A 985 " - pdb=" SG CYS C 383 " distance=2.04 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.02 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.02 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.02 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.06 Simple disulfide: pdb=" SG CYS B 383 " - pdb=" SG CYS C 985 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.02 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.04 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=2.03 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=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.02 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 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=2.02 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.06 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.02 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.04 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=2.03 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=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.02 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 BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " NAG-ASN " NAG A1301 " - " ASN A 122 " " NAG A1302 " - " ASN A 282 " " NAG A1303 " - " ASN A 331 " " NAG A1304 " - " ASN A 343 " " NAG A1305 " - " ASN A 616 " " NAG A1306 " - " ASN A 657 " " NAG A1307 " - " ASN A 709 " " NAG A1308 " - " ASN A1074 " " NAG A1309 " - " ASN A1098 " " NAG A1310 " - " ASN A1134 " " NAG A1311 " - " ASN A 603 " " NAG B1301 " - " ASN B 122 " " NAG B1302 " - " ASN B 282 " " NAG B1303 " - " ASN B 331 " " NAG B1304 " - " ASN B 343 " " NAG B1305 " - " ASN B 616 " " NAG B1306 " - " ASN B 657 " " NAG B1307 " - " ASN B 709 " " NAG B1308 " - " ASN B1074 " " NAG B1309 " - " ASN B1098 " " NAG B1310 " - " ASN B1134 " " NAG B1311 " - " ASN B 603 " " NAG C1301 " - " ASN C 122 " " NAG C1302 " - " ASN C 282 " " NAG C1303 " - " ASN C 331 " " NAG C1304 " - " ASN C 343 " " NAG C1305 " - " ASN C 616 " " NAG C1306 " - " ASN C 657 " " NAG C1307 " - " ASN C 709 " " NAG C1308 " - " ASN C1074 " " NAG C1309 " - " ASN C1098 " " NAG C1310 " - " ASN C1134 " " NAG C1311 " - " ASN C 603 " " NAG D 1 " - " ASN A 234 " " NAG E 1 " - " ASN A 717 " " NAG F 1 " - " ASN A 801 " " NAG G 1 " - " ASN B 234 " " NAG H 1 " - " ASN B 717 " " NAG I 1 " - " ASN B 801 " " NAG J 1 " - " ASN C 234 " " NAG K 1 " - " ASN C 717 " " NAG L 1 " - " ASN C 801 " Time building additional restraints: 1.32 Conformation dependent library (CDL) restraints added in 880.0 milliseconds 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5352 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 45 sheets defined 25.5% alpha, 32.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.79 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 351 through 353 No H-bonds generated for 'chain 'A' and resid 351 through 353' Processing helix chain 'A' and resid 365 through 371 Processing helix chain 'A' and resid 383 through 388 removed outlier: 4.465A pdb=" N ASN A 388 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.371A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 4.112A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (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 758 through 783 removed outlier: 3.805A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 823 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.512A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 919 Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.634A pdb=" N SER A 940 " --> pdb=" O ASP A 936 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.947A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (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 976 through 982 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.302A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 351 through 353 No H-bonds generated for 'chain 'B' and resid 351 through 353' Processing helix chain 'B' and resid 365 through 371 Processing helix chain 'B' and resid 383 through 388 removed outlier: 4.465A pdb=" N ASN B 388 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.371A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 removed outlier: 4.112A 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: 3.805A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 823 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.512A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 913 through 919 Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.635A pdb=" N SER B 940 " --> pdb=" O ASP B 936 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.948A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (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 976 through 982 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.454A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 351 through 353 No H-bonds generated for 'chain 'C' and resid 351 through 353' Processing helix chain 'C' and resid 365 through 371 Processing helix chain 'C' and resid 383 through 388 removed outlier: 4.466A pdb=" N ASN C 388 " --> pdb=" O PRO C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.371A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 removed outlier: 4.113A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (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: 3.805A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 823 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.512A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 919 Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.635A pdb=" N SER C 940 " --> pdb=" O ASP C 936 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.948A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 982 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.298A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.382A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 55 removed outlier: 7.486A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 83 through 85 Processing sheet with id=AA4, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.280A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 324 through 328 removed outlier: 4.329A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 348 through 349 removed outlier: 7.172A pdb=" N ALA A 348 " --> pdb=" O VAL A 401 " (cutoff:3.500A) removed outlier: 9.376A pdb=" N ARG A 403 " --> pdb=" O ALA A 348 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 348 through 349 removed outlier: 7.172A pdb=" N ALA A 348 " --> pdb=" O VAL A 401 " (cutoff:3.500A) removed outlier: 9.376A pdb=" N ARG A 403 " --> pdb=" O ALA A 348 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.819A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 448 through 453 removed outlier: 5.829A pdb=" N TYR A 449 " --> pdb=" O PHE A 497 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N PHE A 497 " --> pdb=" O TYR A 449 " (cutoff:3.500A) removed outlier: 4.842A 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 removed outlier: 6.139A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.512A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.933A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.461A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.461A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.394A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.854A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.381A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 47 through 55 removed outlier: 7.487A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 83 through 85 Processing sheet with id=AC2, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.280A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.728A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 324 through 328 removed outlier: 4.329A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 348 through 349 removed outlier: 7.171A pdb=" N ALA B 348 " --> pdb=" O VAL B 401 " (cutoff:3.500A) removed outlier: 9.376A pdb=" N ARG B 403 " --> pdb=" O ALA B 348 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 348 through 349 removed outlier: 7.171A pdb=" N ALA B 348 " --> pdb=" O VAL B 401 " (cutoff:3.500A) removed outlier: 9.376A pdb=" N ARG B 403 " --> pdb=" O ALA B 348 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.820A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 448 through 453 removed outlier: 5.829A pdb=" N TYR B 449 " --> pdb=" O PHE B 497 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N PHE B 497 " --> pdb=" O TYR B 449 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N TYR B 451 " --> pdb=" O TYR B 495 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.139A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.512A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 701 through 702 removed outlier: 6.934A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.461A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.461A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.394A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.853A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.382A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 47 through 55 removed outlier: 7.486A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 83 through 85 Processing sheet with id=AD8, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.279A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 324 through 328 removed outlier: 4.329A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 348 through 349 removed outlier: 7.172A pdb=" N ALA C 348 " --> pdb=" O VAL C 401 " (cutoff:3.500A) removed outlier: 9.377A pdb=" N ARG C 403 " --> pdb=" O ALA C 348 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 348 through 349 removed outlier: 7.172A pdb=" N ALA C 348 " --> pdb=" O VAL C 401 " (cutoff:3.500A) removed outlier: 9.377A pdb=" N ARG C 403 " --> pdb=" O ALA C 348 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.820A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 448 through 453 removed outlier: 5.829A pdb=" N TYR C 449 " --> pdb=" O PHE C 497 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N PHE C 497 " --> pdb=" O TYR C 449 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N TYR C 451 " --> pdb=" O TYR C 495 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.140A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.512A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.460A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.460A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.394A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.853A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) 1006 hydrogen bonds defined for protein. 2802 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: 5.43 Time building geometry restraints manager: 1.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 3922 1.32 - 1.45: 6780 1.45 - 1.59: 11860 1.59 - 1.72: 7 1.72 - 1.86: 126 Bond restraints: 22695 Sorted by residual: bond pdb=" NE ARG C 454 " pdb=" CZ ARG C 454 " ideal model delta sigma weight residual 1.326 1.383 -0.057 1.10e-02 8.26e+03 2.66e+01 bond pdb=" NE ARG B 454 " pdb=" CZ ARG B 454 " ideal model delta sigma weight residual 1.326 1.382 -0.056 1.10e-02 8.26e+03 2.62e+01 bond pdb=" NE ARG A 454 " pdb=" CZ ARG A 454 " ideal model delta sigma weight residual 1.326 1.382 -0.056 1.10e-02 8.26e+03 2.60e+01 bond pdb=" C ALA A 989 " pdb=" O ALA A 989 " ideal model delta sigma weight residual 1.236 1.183 0.053 1.15e-02 7.56e+03 2.13e+01 bond pdb=" CA ALA B 989 " pdb=" C ALA B 989 " ideal model delta sigma weight residual 1.524 1.464 0.060 1.32e-02 5.74e+03 2.05e+01 ... (remaining 22690 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.65: 25653 1.65 - 3.31: 4354 3.31 - 4.96: 603 4.96 - 6.61: 250 6.61 - 8.27: 43 Bond angle restraints: 30903 Sorted by residual: angle pdb=" C PRO B 862 " pdb=" N PRO B 863 " pdb=" CA PRO B 863 " ideal model delta sigma weight residual 120.03 127.41 -7.38 9.90e-01 1.02e+00 5.56e+01 angle pdb=" C PRO A 862 " pdb=" N PRO A 863 " pdb=" CA PRO A 863 " ideal model delta sigma weight residual 120.03 127.41 -7.38 9.90e-01 1.02e+00 5.56e+01 angle pdb=" C PRO C 862 " pdb=" N PRO C 863 " pdb=" CA PRO C 863 " ideal model delta sigma weight residual 120.03 127.37 -7.34 9.90e-01 1.02e+00 5.50e+01 angle pdb=" C GLN A 498 " pdb=" N PRO A 499 " pdb=" CA PRO A 499 " ideal model delta sigma weight residual 119.56 126.89 -7.33 1.02e+00 9.61e-01 5.16e+01 angle pdb=" C GLN B 498 " pdb=" N PRO B 499 " pdb=" CA PRO B 499 " ideal model delta sigma weight residual 119.56 126.87 -7.31 1.02e+00 9.61e-01 5.13e+01 ... (remaining 30898 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.69: 12563 17.69 - 35.38: 374 35.38 - 53.07: 71 53.07 - 70.76: 60 70.76 - 88.45: 15 Dihedral angle restraints: 13083 sinusoidal: 4821 harmonic: 8262 Sorted by residual: dihedral pdb=" CB CYS B 743 " pdb=" SG CYS B 743 " pdb=" SG CYS B 749 " pdb=" CB CYS B 749 " ideal model delta sinusoidal sigma weight residual -86.00 -160.35 74.35 1 1.00e+01 1.00e-02 7.01e+01 dihedral pdb=" CB CYS A 743 " pdb=" SG CYS A 743 " pdb=" SG CYS A 749 " pdb=" CB CYS A 749 " ideal model delta sinusoidal sigma weight residual -86.00 -160.35 74.35 1 1.00e+01 1.00e-02 7.01e+01 dihedral pdb=" CB CYS C 743 " pdb=" SG CYS C 743 " pdb=" SG CYS C 749 " pdb=" CB CYS C 749 " ideal model delta sinusoidal sigma weight residual -86.00 -160.35 74.35 1 1.00e+01 1.00e-02 7.01e+01 ... (remaining 13080 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 2733 0.084 - 0.168: 759 0.168 - 0.252: 162 0.252 - 0.336: 68 0.336 - 0.420: 46 Chirality restraints: 3768 Sorted by residual: chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.53 0.13 2.00e-02 2.50e+03 4.54e+01 chirality pdb=" C1 NAG L 2 " pdb=" O4 NAG L 1 " pdb=" C2 NAG L 2 " pdb=" O5 NAG L 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.53 0.13 2.00e-02 2.50e+03 4.46e+01 chirality pdb=" C1 NAG J 2 " pdb=" O4 NAG J 1 " pdb=" C2 NAG J 2 " pdb=" O5 NAG J 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.53 0.13 2.00e-02 2.50e+03 4.34e+01 ... (remaining 3765 not shown) Planarity restraints: 3948 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 331 " -0.051 2.00e-02 2.50e+03 5.19e-02 3.37e+01 pdb=" CG ASN B 331 " 0.027 2.00e-02 2.50e+03 pdb=" OD1 ASN B 331 " 0.010 2.00e-02 2.50e+03 pdb=" ND2 ASN B 331 " 0.077 2.00e-02 2.50e+03 pdb=" C1 NAG B1303 " -0.063 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 331 " 0.051 2.00e-02 2.50e+03 5.18e-02 3.36e+01 pdb=" CG ASN A 331 " -0.028 2.00e-02 2.50e+03 pdb=" OD1 ASN A 331 " -0.010 2.00e-02 2.50e+03 pdb=" ND2 ASN A 331 " -0.077 2.00e-02 2.50e+03 pdb=" C1 NAG A1303 " 0.063 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 331 " 0.051 2.00e-02 2.50e+03 5.16e-02 3.33e+01 pdb=" CG ASN C 331 " -0.027 2.00e-02 2.50e+03 pdb=" OD1 ASN C 331 " -0.010 2.00e-02 2.50e+03 pdb=" ND2 ASN C 331 " -0.077 2.00e-02 2.50e+03 pdb=" C1 NAG C1303 " 0.063 2.00e-02 2.50e+03 ... (remaining 3945 not shown) Histogram of nonbonded interaction distances: 2.38 - 2.89: 7957 2.89 - 3.39: 19584 3.39 - 3.89: 36598 3.89 - 4.40: 41744 4.40 - 4.90: 70192 Nonbonded interactions: 176075 Sorted by model distance: nonbonded pdb=" NZ LYS C 811 " pdb=" OD2 ASP C 820 " model vdw 2.382 3.120 nonbonded pdb=" NZ LYS A 811 " pdb=" OD2 ASP A 820 " model vdw 2.382 3.120 nonbonded pdb=" NZ LYS B 811 " pdb=" OD2 ASP B 820 " model vdw 2.383 3.120 nonbonded pdb=" N PRO C 600 " pdb=" O PRO C 600 " model vdw 2.495 2.496 nonbonded pdb=" N PRO B 600 " pdb=" O PRO B 600 " model vdw 2.495 2.496 ... (remaining 176070 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: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 20.200 Find NCS groups from input model: 0.930 Set up NCS constraints: 0.080 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: 0.000 Load rotamer database and sin/cos tables:9.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 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 : 0.014 0.088 22785 Z= 0.742 Angle : 1.373 10.181 31134 Z= 0.907 Chirality : 0.096 0.420 3768 Planarity : 0.005 0.042 3906 Dihedral : 10.438 88.451 7614 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 0.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 0.26 % Allowed : 0.39 % Favored : 99.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.14), residues: 2760 helix: 0.27 (0.18), residues: 654 sheet: 1.47 (0.19), residues: 603 loop : 0.09 (0.14), residues: 1503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C1000 TYR 0.027 0.004 TYR B 170 PHE 0.018 0.003 PHE A 58 TRP 0.032 0.006 TRP B 886 HIS 0.003 0.001 HIS C1083 Details of bonding type rmsd/Z covalent geometry : bond 0.01372 / 0.73 (22695) covalent geometry : angle 1.34636 / 0.90 (30903) SS BOND : bond 0.01009 / 0.52 ( 39) SS BOND : angle 4.64275 / 2.84 ( 78) hydrogen bonds : bond 0.18023 / 11.88 ( 973) hydrogen bonds : angle 7.88903 / 5.54 ( 2802) link_BETA1-4 : bond 0.06457 / 4.11 ( 9) link_BETA1-4 : angle 3.66143 / 2.29 ( 27) link_NAG-ASN : bond 0.06728 / 4.19 ( 42) link_NAG-ASN : angle 2.19903 / 1.47 ( 126) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 484 time to evaluate : 1.060 Fit side-chains revert: symmetry clash REVERT: A 306 PHE cc_start: 0.7828 (m-10) cc_final: 0.7606 (m-80) REVERT: A 787 GLN cc_start: 0.6897 (mt0) cc_final: 0.6660 (mt0) REVERT: A 856 ASN cc_start: 0.7091 (m-40) cc_final: 0.6867 (m-40) REVERT: B 523 THR cc_start: 0.7236 (p) cc_final: 0.6922 (t) REVERT: B 773 GLU cc_start: 0.7178 (tt0) cc_final: 0.6886 (tt0) REVERT: B 786 LYS cc_start: 0.7222 (mtmm) cc_final: 0.7000 (mmtt) REVERT: B 856 ASN cc_start: 0.7135 (m-40) cc_final: 0.6902 (m-40) REVERT: C 731 MET cc_start: 0.8803 (ptm) cc_final: 0.8483 (ptm) REVERT: C 856 ASN cc_start: 0.6953 (m-40) cc_final: 0.6729 (m110) outliers start: 6 outliers final: 4 residues processed: 490 average time/residue: 0.5714 time to fit residues: 325.3119 Evaluate side-chains 254 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 250 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 985 CYS Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain C residue 651 ILE Chi-restraints excluded: chain C residue 985 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 197 optimal weight: 0.8980 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 0.6980 chunk 248 optimal weight: 0.2980 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 0.5980 chunk 244 optimal weight: 0.5980 chunk 183 optimal weight: 0.9990 chunk 111 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 580 GLN A 675 GLN A 935 GLN A1010 GLN A1113 GLN A1119 ASN B 207 HIS B 580 GLN B 675 GLN B 919 ASN B 935 GLN B 965 GLN B1113 GLN B1119 ASN C 580 GLN C 675 GLN C 762 GLN C 804 GLN C 919 ASN C 935 GLN C 954 GLN C 965 GLN C 978 ASN C1010 GLN C1113 GLN C1119 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.205601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.160915 restraints weight = 26346.808| |-----------------------------------------------------------------------------| r_work (start): 0.3895 rms_B_bonded: 2.46 r_work: 0.3635 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3497 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.2184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 22785 Z= 0.156 Angle : 0.666 17.940 31134 Z= 0.345 Chirality : 0.047 0.214 3768 Planarity : 0.004 0.037 3906 Dihedral : 4.499 35.025 3000 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Rotamer: Outliers : 2.57 % Allowed : 9.50 % Favored : 87.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.15), residues: 2760 helix: 1.44 (0.21), residues: 633 sheet: 1.07 (0.18), residues: 687 loop : -0.03 (0.15), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 567 TYR 0.020 0.001 TYR A1067 PHE 0.025 0.002 PHE B 92 TRP 0.016 0.002 TRP A 353 HIS 0.004 0.001 HIS B1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.16 (22695) covalent geometry : angle 0.60916 / 0.33 (30903) SS BOND : bond 0.00388 / 0.25 ( 39) SS BOND : angle 2.20870 / 1.28 ( 78) hydrogen bonds : bond 0.06226 / 4.08 ( 973) hydrogen bonds : angle 6.21253 / 4.41 ( 2802) link_BETA1-4 : bond 0.00486 / 0.31 ( 9) link_BETA1-4 : angle 1.77177 / 1.08 ( 27) link_NAG-ASN : bond 0.00588 / 0.30 ( 42) link_NAG-ASN : angle 3.85584 / 2.87 ( 126) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 285 time to evaluate : 0.821 Fit side-chains revert: symmetry clash REVERT: A 28 TYR cc_start: 0.5985 (m-80) cc_final: 0.5748 (m-10) REVERT: A 61 ASN cc_start: 0.4787 (m-40) cc_final: 0.3943 (p0) REVERT: A 195 LYS cc_start: 0.8239 (ptpp) cc_final: 0.8014 (ptpp) REVERT: A 357 ARG cc_start: 0.8028 (ptm160) cc_final: 0.7769 (ttp80) REVERT: A 513 LEU cc_start: 0.7514 (mt) cc_final: 0.7293 (mt) REVERT: A 558 LYS cc_start: 0.7954 (ttpp) cc_final: 0.7265 (mptt) REVERT: A 591 SER cc_start: 0.7868 (OUTLIER) cc_final: 0.7373 (m) REVERT: A 645 THR cc_start: 0.7555 (p) cc_final: 0.7074 (t) REVERT: A 780 GLU cc_start: 0.8122 (mm-30) cc_final: 0.7867 (pt0) REVERT: A 856 ASN cc_start: 0.8115 (m-40) cc_final: 0.7788 (m-40) REVERT: A 918 GLU cc_start: 0.8395 (OUTLIER) cc_final: 0.7048 (mp0) REVERT: A 995 ARG cc_start: 0.8045 (OUTLIER) cc_final: 0.7755 (mmm-85) REVERT: A 1138 TYR cc_start: 0.6925 (t80) cc_final: 0.6172 (m-10) REVERT: B 319 ARG cc_start: 0.7559 (ttm110) cc_final: 0.6378 (tpt170) REVERT: B 353 TRP cc_start: 0.8735 (p-90) cc_final: 0.8075 (p-90) REVERT: B 368 LEU cc_start: 0.7212 (mp) cc_final: 0.6843 (mp) REVERT: B 523 THR cc_start: 0.7515 (p) cc_final: 0.6872 (t) REVERT: B 773 GLU cc_start: 0.7812 (tt0) cc_final: 0.7457 (tt0) REVERT: B 786 LYS cc_start: 0.7613 (mtmm) cc_final: 0.6916 (mmtt) REVERT: B 983 ARG cc_start: 0.7870 (mtp180) cc_final: 0.7534 (mtp85) REVERT: B 995 ARG cc_start: 0.8089 (OUTLIER) cc_final: 0.7264 (mpp80) REVERT: B 1010 GLN cc_start: 0.8141 (OUTLIER) cc_final: 0.7672 (pt0) REVERT: B 1138 TYR cc_start: 0.7111 (t80) cc_final: 0.6356 (m-10) REVERT: C 28 TYR cc_start: 0.6063 (m-10) cc_final: 0.5766 (m-10) REVERT: C 303 LEU cc_start: 0.7163 (OUTLIER) cc_final: 0.6871 (mt) REVERT: C 319 ARG cc_start: 0.7308 (ttm110) cc_final: 0.7097 (mtp-110) REVERT: C 428 ASP cc_start: 0.7742 (p0) cc_final: 0.7462 (p0) REVERT: C 567 ARG cc_start: 0.6939 (mtt90) cc_final: 0.6268 (mpt180) REVERT: C 612 TYR cc_start: 0.8578 (m-80) cc_final: 0.8312 (m-80) REVERT: C 645 THR cc_start: 0.7364 (p) cc_final: 0.7079 (t) REVERT: C 731 MET cc_start: 0.8973 (ptm) cc_final: 0.8590 (ptm) REVERT: C 979 ASP cc_start: 0.8425 (m-30) cc_final: 0.8223 (m-30) REVERT: C 1119 ASN cc_start: 0.7669 (m-40) cc_final: 0.7214 (m110) REVERT: C 1138 TYR cc_start: 0.7016 (t80) cc_final: 0.6312 (m-10) outliers start: 59 outliers final: 24 residues processed: 324 average time/residue: 0.5398 time to fit residues: 205.1984 Evaluate side-chains 246 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 216 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 995 ARG Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 985 CYS Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 995 ARG Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 651 ILE Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 776 LYS Chi-restraints excluded: chain C residue 985 CYS Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 995 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 142 optimal weight: 0.9980 chunk 98 optimal weight: 0.6980 chunk 3 optimal weight: 0.0270 chunk 263 optimal weight: 1.9990 chunk 36 optimal weight: 6.9990 chunk 201 optimal weight: 3.9990 chunk 202 optimal weight: 0.9980 chunk 273 optimal weight: 0.7980 chunk 248 optimal weight: 0.8980 chunk 68 optimal weight: 0.9980 chunk 29 optimal weight: 4.9990 overall best weight: 0.6838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 196 ASN A 207 HIS A 935 GLN A 955 ASN A 965 GLN A1010 GLN ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 675 GLN B 955 ASN B1071 GLN B1101 HIS C 87 ASN C 544 ASN C 644 GLN C 675 GLN C1010 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.203258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.149111 restraints weight = 26241.996| |-----------------------------------------------------------------------------| r_work (start): 0.3727 rms_B_bonded: 2.17 r_work: 0.3602 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3467 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.2768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 22785 Z= 0.142 Angle : 0.583 17.074 31134 Z= 0.297 Chirality : 0.045 0.199 3768 Planarity : 0.004 0.033 3906 Dihedral : 4.283 40.071 3000 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 3.53 % Allowed : 10.76 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.15), residues: 2760 helix: 1.46 (0.20), residues: 675 sheet: 0.78 (0.18), residues: 702 loop : -0.19 (0.15), residues: 1383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 567 TYR 0.019 0.001 TYR A1067 PHE 0.024 0.002 PHE B 55 TRP 0.015 0.002 TRP A 353 HIS 0.004 0.001 HIS C1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 (22695) covalent geometry : angle 0.53164 / 0.29 (30903) SS BOND : bond 0.00265 / 0.16 ( 39) SS BOND : angle 1.80829 / 1.05 ( 78) hydrogen bonds : bond 0.05336 / 3.47 ( 973) hydrogen bonds : angle 5.79362 / 4.13 ( 2802) link_BETA1-4 : bond 0.00419 / 0.25 ( 9) link_BETA1-4 : angle 1.19237 / 0.72 ( 27) link_NAG-ASN : bond 0.00650 / 0.29 ( 42) link_NAG-ASN : angle 3.50001 / 2.67 ( 126) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 250 time to evaluate : 0.855 Fit side-chains REVERT: A 40 ASP cc_start: 0.6813 (OUTLIER) cc_final: 0.6575 (m-30) REVERT: A 50 SER cc_start: 0.8467 (t) cc_final: 0.8110 (t) REVERT: A 61 ASN cc_start: 0.4754 (m-40) cc_final: 0.4013 (p0) REVERT: A 195 LYS cc_start: 0.8205 (ptpp) cc_final: 0.7921 (ptpp) REVERT: A 357 ARG cc_start: 0.8024 (ptm160) cc_final: 0.7761 (ttp80) REVERT: A 513 LEU cc_start: 0.7794 (mt) cc_final: 0.7408 (mt) REVERT: A 558 LYS cc_start: 0.8148 (ttpp) cc_final: 0.7405 (mptt) REVERT: A 576 VAL cc_start: 0.8801 (t) cc_final: 0.8410 (p) REVERT: A 645 THR cc_start: 0.7545 (p) cc_final: 0.6850 (t) REVERT: A 787 GLN cc_start: 0.7967 (mt0) cc_final: 0.7525 (mt0) REVERT: A 918 GLU cc_start: 0.8289 (OUTLIER) cc_final: 0.6908 (mp0) REVERT: A 1119 ASN cc_start: 0.7645 (m110) cc_final: 0.7251 (m-40) REVERT: A 1138 TYR cc_start: 0.7064 (t80) cc_final: 0.6296 (m-10) REVERT: B 40 ASP cc_start: 0.6485 (OUTLIER) cc_final: 0.6221 (m-30) REVERT: B 353 TRP cc_start: 0.8716 (p-90) cc_final: 0.8160 (p-90) REVERT: B 584 ILE cc_start: 0.6810 (OUTLIER) cc_final: 0.6056 (mm) REVERT: B 784 GLN cc_start: 0.8308 (OUTLIER) cc_final: 0.8054 (mt0) REVERT: B 786 LYS cc_start: 0.7738 (mtmm) cc_final: 0.7110 (mmtt) REVERT: B 983 ARG cc_start: 0.7971 (mtp180) cc_final: 0.7610 (mtp85) REVERT: B 995 ARG cc_start: 0.8019 (OUTLIER) cc_final: 0.7143 (mpp80) REVERT: B 1010 GLN cc_start: 0.8183 (OUTLIER) cc_final: 0.7661 (pt0) REVERT: B 1138 TYR cc_start: 0.7081 (t80) cc_final: 0.6339 (m-10) REVERT: C 28 TYR cc_start: 0.5959 (m-10) cc_final: 0.5746 (m-10) REVERT: C 303 LEU cc_start: 0.7144 (OUTLIER) cc_final: 0.6849 (mt) REVERT: C 368 LEU cc_start: 0.7273 (mp) cc_final: 0.6874 (mp) REVERT: C 428 ASP cc_start: 0.7646 (p0) cc_final: 0.7379 (p0) REVERT: C 567 ARG cc_start: 0.7024 (mtt90) cc_final: 0.6303 (mpt180) REVERT: C 645 THR cc_start: 0.7355 (p) cc_final: 0.6812 (t) REVERT: C 731 MET cc_start: 0.9022 (ptm) cc_final: 0.8688 (ptm) REVERT: C 790 LYS cc_start: 0.8594 (OUTLIER) cc_final: 0.8388 (mtmt) REVERT: C 856 ASN cc_start: 0.7980 (m-40) cc_final: 0.7531 (m-40) REVERT: C 979 ASP cc_start: 0.8469 (m-30) cc_final: 0.8213 (m-30) REVERT: C 1138 TYR cc_start: 0.6963 (t80) cc_final: 0.6462 (m-10) outliers start: 81 outliers final: 29 residues processed: 306 average time/residue: 0.5117 time to fit residues: 185.3645 Evaluate side-chains 261 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 223 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 995 ARG Chi-restraints excluded: chain B residue 40 ASP Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 383 CYS Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 784 GLN Chi-restraints excluded: chain B residue 985 CYS Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 995 ARG Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 651 ILE Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 790 LYS Chi-restraints excluded: chain C residue 985 CYS Chi-restraints excluded: chain C residue 995 ARG Chi-restraints excluded: chain C residue 1077 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 173 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 190 optimal weight: 6.9990 chunk 84 optimal weight: 0.8980 chunk 74 optimal weight: 0.5980 chunk 21 optimal weight: 0.5980 chunk 142 optimal weight: 0.9980 chunk 248 optimal weight: 0.8980 chunk 20 optimal weight: 0.6980 chunk 168 optimal weight: 1.9990 chunk 101 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 856 ASN A1010 GLN ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 675 GLN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 965 GLN ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 675 GLN C1010 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.201941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.148987 restraints weight = 26294.277| |-----------------------------------------------------------------------------| r_work (start): 0.3718 rms_B_bonded: 2.49 r_work: 0.3503 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.3108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 22785 Z= 0.143 Angle : 0.565 16.636 31134 Z= 0.287 Chirality : 0.045 0.188 3768 Planarity : 0.004 0.031 3906 Dihedral : 4.275 47.301 3000 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 3.53 % Allowed : 12.16 % Favored : 84.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.15), residues: 2760 helix: 1.53 (0.21), residues: 675 sheet: 0.71 (0.18), residues: 690 loop : -0.30 (0.15), residues: 1395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 319 TYR 0.019 0.001 TYR A1067 PHE 0.019 0.001 PHE B 92 TRP 0.015 0.002 TRP A 353 HIS 0.004 0.001 HIS C1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.14 (22695) covalent geometry : angle 0.52040 / 0.28 (30903) SS BOND : bond 0.00468 / 0.30 ( 39) SS BOND : angle 1.92257 / 1.11 ( 78) hydrogen bonds : bond 0.05114 / 3.33 ( 973) hydrogen bonds : angle 5.63387 / 4.01 ( 2802) link_BETA1-4 : bond 0.00289 / 0.18 ( 9) link_BETA1-4 : angle 1.15950 / 0.70 ( 27) link_NAG-ASN : bond 0.00526 / 0.24 ( 42) link_NAG-ASN : angle 3.16537 / 2.44 ( 126) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 242 time to evaluate : 0.787 Fit side-chains revert: symmetry clash REVERT: A 50 SER cc_start: 0.8318 (t) cc_final: 0.8099 (t) REVERT: A 61 ASN cc_start: 0.4918 (m-40) cc_final: 0.4012 (p0) REVERT: A 195 LYS cc_start: 0.8081 (ptpp) cc_final: 0.7836 (ptpp) REVERT: A 357 ARG cc_start: 0.8052 (ptm160) cc_final: 0.7670 (ttp-170) REVERT: A 368 LEU cc_start: 0.7102 (mp) cc_final: 0.6699 (mp) REVERT: A 513 LEU cc_start: 0.7764 (mt) cc_final: 0.7456 (mt) REVERT: A 558 LYS cc_start: 0.8162 (ttpp) cc_final: 0.7390 (mptt) REVERT: A 576 VAL cc_start: 0.8725 (OUTLIER) cc_final: 0.8389 (p) REVERT: A 644 GLN cc_start: 0.8020 (tp-100) cc_final: 0.7771 (tp40) REVERT: A 645 THR cc_start: 0.7512 (p) cc_final: 0.6876 (t) REVERT: A 787 GLN cc_start: 0.7810 (mt0) cc_final: 0.7379 (mt0) REVERT: A 918 GLU cc_start: 0.8143 (OUTLIER) cc_final: 0.6736 (mp0) REVERT: A 1038 LYS cc_start: 0.8884 (OUTLIER) cc_final: 0.8378 (mptt) REVERT: A 1119 ASN cc_start: 0.7645 (m110) cc_final: 0.7248 (m-40) REVERT: A 1138 TYR cc_start: 0.7072 (t80) cc_final: 0.6363 (m-10) REVERT: B 40 ASP cc_start: 0.6449 (OUTLIER) cc_final: 0.5953 (p0) REVERT: B 353 TRP cc_start: 0.8709 (p-90) cc_final: 0.8138 (p-90) REVERT: B 513 LEU cc_start: 0.7680 (mt) cc_final: 0.7337 (mt) REVERT: B 584 ILE cc_start: 0.6817 (OUTLIER) cc_final: 0.6012 (mm) REVERT: B 784 GLN cc_start: 0.8280 (OUTLIER) cc_final: 0.7895 (mt0) REVERT: B 786 LYS cc_start: 0.7936 (mtmm) cc_final: 0.7293 (mmtt) REVERT: B 983 ARG cc_start: 0.7888 (mtp180) cc_final: 0.7531 (mtp85) REVERT: B 995 ARG cc_start: 0.7952 (OUTLIER) cc_final: 0.7213 (mpp80) REVERT: B 1010 GLN cc_start: 0.8123 (OUTLIER) cc_final: 0.7667 (pt0) REVERT: B 1138 TYR cc_start: 0.7130 (t80) cc_final: 0.6490 (m-10) REVERT: C 303 LEU cc_start: 0.7060 (OUTLIER) cc_final: 0.6784 (mt) REVERT: C 360 ASN cc_start: 0.7836 (t0) cc_final: 0.7088 (p0) REVERT: C 403 ARG cc_start: 0.6483 (ttp-170) cc_final: 0.5144 (mpt180) REVERT: C 428 ASP cc_start: 0.7677 (p0) cc_final: 0.7385 (p0) REVERT: C 584 ILE cc_start: 0.7125 (OUTLIER) cc_final: 0.6279 (mm) REVERT: C 645 THR cc_start: 0.7337 (p) cc_final: 0.7047 (t) REVERT: C 731 MET cc_start: 0.9004 (ptm) cc_final: 0.8634 (ptm) REVERT: C 784 GLN cc_start: 0.8096 (OUTLIER) cc_final: 0.7545 (mt0) REVERT: C 979 ASP cc_start: 0.8399 (m-30) cc_final: 0.8192 (m-30) REVERT: C 1138 TYR cc_start: 0.6982 (t80) cc_final: 0.6576 (m-10) outliers start: 81 outliers final: 44 residues processed: 301 average time/residue: 0.4668 time to fit residues: 168.5647 Evaluate side-chains 281 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 226 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 995 ARG Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain B residue 40 ASP Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 383 CYS Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 784 GLN Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 985 CYS Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 995 ARG Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 383 CYS Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 596 SER Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 784 GLN Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 985 CYS Chi-restraints excluded: chain C residue 995 ARG Chi-restraints excluded: chain C residue 1077 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 92 optimal weight: 1.9990 chunk 229 optimal weight: 0.9980 chunk 173 optimal weight: 2.9990 chunk 209 optimal weight: 0.9980 chunk 277 optimal weight: 1.9990 chunk 280 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 261 optimal weight: 0.2980 chunk 123 optimal weight: 7.9990 chunk 98 optimal weight: 0.2980 chunk 246 optimal weight: 0.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 965 GLN A1010 GLN A1071 GLN ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 658 ASN B 675 GLN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 644 GLN C 675 GLN C1010 GLN C1071 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.201467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.147382 restraints weight = 26039.316| |-----------------------------------------------------------------------------| r_work (start): 0.3738 rms_B_bonded: 2.15 r_work: 0.3591 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3455 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.3354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 22785 Z= 0.139 Angle : 0.550 14.569 31134 Z= 0.280 Chirality : 0.045 0.161 3768 Planarity : 0.004 0.034 3906 Dihedral : 4.189 49.452 2998 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 3.62 % Allowed : 12.94 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.15), residues: 2760 helix: 1.57 (0.21), residues: 675 sheet: 0.67 (0.19), residues: 690 loop : -0.36 (0.15), residues: 1395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 319 TYR 0.019 0.001 TYR A1067 PHE 0.026 0.001 PHE B 55 TRP 0.020 0.002 TRP A 353 HIS 0.004 0.001 HIS C1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.14 (22695) covalent geometry : angle 0.51206 / 0.27 (30903) SS BOND : bond 0.00273 / 0.17 ( 39) SS BOND : angle 1.86105 / 1.08 ( 78) hydrogen bonds : bond 0.04957 / 3.22 ( 973) hydrogen bonds : angle 5.51694 / 3.92 ( 2802) link_BETA1-4 : bond 0.00276 / 0.18 ( 9) link_BETA1-4 : angle 1.13054 / 0.68 ( 27) link_NAG-ASN : bond 0.00475 / 0.21 ( 42) link_NAG-ASN : angle 2.81865 / 2.18 ( 126) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 236 time to evaluate : 0.852 Fit side-chains revert: symmetry clash REVERT: A 40 ASP cc_start: 0.6972 (OUTLIER) cc_final: 0.6264 (p0) REVERT: A 50 SER cc_start: 0.8391 (t) cc_final: 0.8155 (t) REVERT: A 61 ASN cc_start: 0.5026 (m-40) cc_final: 0.4107 (p0) REVERT: A 195 LYS cc_start: 0.8116 (ptpp) cc_final: 0.7871 (ptpp) REVERT: A 319 ARG cc_start: 0.7249 (ttm110) cc_final: 0.6248 (tpt170) REVERT: A 357 ARG cc_start: 0.8171 (ptm160) cc_final: 0.7850 (ttp-170) REVERT: A 576 VAL cc_start: 0.8754 (t) cc_final: 0.8439 (p) REVERT: A 645 THR cc_start: 0.7490 (p) cc_final: 0.6957 (t) REVERT: A 787 GLN cc_start: 0.7947 (mt0) cc_final: 0.7530 (mt0) REVERT: A 918 GLU cc_start: 0.8259 (OUTLIER) cc_final: 0.6870 (mp0) REVERT: A 1119 ASN cc_start: 0.7698 (m110) cc_final: 0.7133 (m-40) REVERT: A 1138 TYR cc_start: 0.7085 (t80) cc_final: 0.6355 (m-10) REVERT: B 40 ASP cc_start: 0.6562 (OUTLIER) cc_final: 0.6054 (p0) REVERT: B 353 TRP cc_start: 0.8727 (p-90) cc_final: 0.8070 (p-90) REVERT: B 360 ASN cc_start: 0.7525 (t0) cc_final: 0.6582 (t0) REVERT: B 513 LEU cc_start: 0.7756 (mt) cc_final: 0.7480 (mt) REVERT: B 584 ILE cc_start: 0.6893 (OUTLIER) cc_final: 0.6061 (mm) REVERT: B 784 GLN cc_start: 0.8289 (OUTLIER) cc_final: 0.7972 (mt0) REVERT: B 786 LYS cc_start: 0.8092 (mtmm) cc_final: 0.7384 (mmtt) REVERT: B 804 GLN cc_start: 0.8359 (mt0) cc_final: 0.8137 (mp10) REVERT: B 886 TRP cc_start: 0.7646 (p90) cc_final: 0.7323 (p90) REVERT: B 983 ARG cc_start: 0.7975 (mtp180) cc_final: 0.7634 (mtp85) REVERT: B 995 ARG cc_start: 0.8056 (OUTLIER) cc_final: 0.7139 (mpp80) REVERT: B 1010 GLN cc_start: 0.8246 (OUTLIER) cc_final: 0.7738 (pt0) REVERT: B 1138 TYR cc_start: 0.7218 (t80) cc_final: 0.6598 (m-10) REVERT: C 40 ASP cc_start: 0.6459 (OUTLIER) cc_final: 0.5980 (p0) REVERT: C 303 LEU cc_start: 0.7155 (OUTLIER) cc_final: 0.6849 (mt) REVERT: C 360 ASN cc_start: 0.7701 (t0) cc_final: 0.6963 (p0) REVERT: C 428 ASP cc_start: 0.7642 (p0) cc_final: 0.7319 (p0) REVERT: C 584 ILE cc_start: 0.7141 (OUTLIER) cc_final: 0.6241 (mm) REVERT: C 645 THR cc_start: 0.7549 (p) cc_final: 0.7077 (t) REVERT: C 731 MET cc_start: 0.9061 (ptm) cc_final: 0.8688 (ptm) REVERT: C 784 GLN cc_start: 0.8153 (OUTLIER) cc_final: 0.7621 (mt0) outliers start: 83 outliers final: 41 residues processed: 293 average time/residue: 0.4573 time to fit residues: 161.4093 Evaluate side-chains 268 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 216 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 995 ARG Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain B residue 40 ASP Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 383 CYS Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 784 GLN Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 985 CYS Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 995 ARG Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain C residue 40 ASP Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 383 CYS Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 596 SER Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 784 GLN Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 995 ARG Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1077 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 93 optimal weight: 2.9990 chunk 262 optimal weight: 1.9990 chunk 201 optimal weight: 0.9990 chunk 230 optimal weight: 5.9990 chunk 196 optimal weight: 6.9990 chunk 42 optimal weight: 0.0980 chunk 265 optimal weight: 2.9990 chunk 162 optimal weight: 0.0040 chunk 22 optimal weight: 4.9990 chunk 89 optimal weight: 0.8980 chunk 182 optimal weight: 0.6980 overall best weight: 0.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1010 GLN ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 675 GLN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 675 GLN C1010 GLN C1119 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.202198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.148266 restraints weight = 26270.165| |-----------------------------------------------------------------------------| r_work (start): 0.3749 rms_B_bonded: 2.15 r_work: 0.3610 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3474 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.3522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 22785 Z= 0.120 Angle : 0.525 12.771 31134 Z= 0.268 Chirality : 0.044 0.169 3768 Planarity : 0.004 0.034 3906 Dihedral : 4.006 48.397 2997 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 3.22 % Allowed : 13.94 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.15), residues: 2760 helix: 1.69 (0.21), residues: 675 sheet: 0.67 (0.19), residues: 690 loop : -0.35 (0.15), residues: 1395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 319 TYR 0.022 0.001 TYR C1138 PHE 0.018 0.001 PHE B 92 TRP 0.015 0.002 TRP A 353 HIS 0.003 0.001 HIS C1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 (22695) covalent geometry : angle 0.49426 / 0.26 (30903) SS BOND : bond 0.00379 / 0.25 ( 39) SS BOND : angle 1.65203 / 0.96 ( 78) hydrogen bonds : bond 0.04603 / 2.99 ( 973) hydrogen bonds : angle 5.39038 / 3.83 ( 2802) link_BETA1-4 : bond 0.00316 / 0.19 ( 9) link_BETA1-4 : angle 1.08646 / 0.65 ( 27) link_NAG-ASN : bond 0.00440 / 0.20 ( 42) link_NAG-ASN : angle 2.51840 / 1.93 ( 126) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 231 time to evaluate : 0.861 Fit side-chains REVERT: A 40 ASP cc_start: 0.6936 (OUTLIER) cc_final: 0.6237 (p0) REVERT: A 50 SER cc_start: 0.8397 (t) cc_final: 0.8174 (t) REVERT: A 61 ASN cc_start: 0.5024 (m-40) cc_final: 0.4097 (p0) REVERT: A 319 ARG cc_start: 0.7208 (ttm110) cc_final: 0.6153 (tpt170) REVERT: A 357 ARG cc_start: 0.8179 (ptm160) cc_final: 0.7873 (ttp80) REVERT: A 360 ASN cc_start: 0.7361 (t0) cc_final: 0.6838 (p0) REVERT: A 513 LEU cc_start: 0.7779 (mt) cc_final: 0.7431 (mt) REVERT: A 576 VAL cc_start: 0.8731 (t) cc_final: 0.8435 (p) REVERT: A 645 THR cc_start: 0.7465 (p) cc_final: 0.6850 (t) REVERT: A 787 GLN cc_start: 0.7923 (mt0) cc_final: 0.7498 (mt0) REVERT: A 918 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.6877 (mp0) REVERT: A 1119 ASN cc_start: 0.7731 (m110) cc_final: 0.7143 (m-40) REVERT: A 1138 TYR cc_start: 0.7075 (t80) cc_final: 0.6340 (m-10) REVERT: B 40 ASP cc_start: 0.6462 (OUTLIER) cc_final: 0.5909 (p0) REVERT: B 353 TRP cc_start: 0.8637 (p-90) cc_final: 0.8325 (p-90) REVERT: B 360 ASN cc_start: 0.7525 (t0) cc_final: 0.6532 (t0) REVERT: B 513 LEU cc_start: 0.7790 (mt) cc_final: 0.7452 (mt) REVERT: B 584 ILE cc_start: 0.6929 (OUTLIER) cc_final: 0.6126 (mm) REVERT: B 645 THR cc_start: 0.7666 (OUTLIER) cc_final: 0.7289 (t) REVERT: B 886 TRP cc_start: 0.7682 (p90) cc_final: 0.7342 (p90) REVERT: B 983 ARG cc_start: 0.7951 (mtp180) cc_final: 0.7610 (mtp85) REVERT: B 995 ARG cc_start: 0.8021 (OUTLIER) cc_final: 0.7143 (mpp80) REVERT: B 1010 GLN cc_start: 0.8247 (OUTLIER) cc_final: 0.7725 (pt0) REVERT: B 1138 TYR cc_start: 0.7165 (t80) cc_final: 0.6498 (m-10) REVERT: C 40 ASP cc_start: 0.6438 (OUTLIER) cc_final: 0.6002 (p0) REVERT: C 303 LEU cc_start: 0.7224 (OUTLIER) cc_final: 0.6932 (mt) REVERT: C 360 ASN cc_start: 0.7676 (t0) cc_final: 0.6982 (p0) REVERT: C 403 ARG cc_start: 0.6540 (ttp-170) cc_final: 0.5396 (mpt180) REVERT: C 428 ASP cc_start: 0.7678 (p0) cc_final: 0.7351 (p0) REVERT: C 513 LEU cc_start: 0.7950 (mt) cc_final: 0.7607 (mt) REVERT: C 584 ILE cc_start: 0.7158 (OUTLIER) cc_final: 0.6260 (mm) REVERT: C 731 MET cc_start: 0.9029 (ptm) cc_final: 0.8689 (ptm) REVERT: C 784 GLN cc_start: 0.8117 (OUTLIER) cc_final: 0.7583 (mt0) REVERT: C 918 GLU cc_start: 0.8138 (OUTLIER) cc_final: 0.7764 (mp0) REVERT: C 1138 TYR cc_start: 0.7079 (t80) cc_final: 0.6519 (m-80) outliers start: 74 outliers final: 38 residues processed: 283 average time/residue: 0.4528 time to fit residues: 155.0926 Evaluate side-chains 270 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 220 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 383 CYS Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1125 ASN Chi-restraints excluded: chain B residue 40 ASP Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 985 CYS Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 995 ARG Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain C residue 40 ASP Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 383 CYS Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 596 SER Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 784 GLN Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 995 ARG Chi-restraints excluded: chain C residue 1077 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/iotbx/cli_parser.py", line 987, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( ^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( ^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( ^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1602, in energies_sites pair_proxies = self.pair_proxies( ^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1505, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1386, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 69.953 > 50: distance: 72 - 138: 25.818 distance: 73 - 129: 34.876 distance: 76 - 126: 35.080 distance: 99 - 102: 34.320 distance: 103 - 106: 40.682 distance: 104 - 105: 56.695 distance: 104 - 107: 39.666 distance: 107 - 108: 24.336 distance: 108 - 109: 43.061 distance: 108 - 111: 16.221 distance: 109 - 110: 7.175 distance: 109 - 114: 13.332 distance: 111 - 112: 41.283 distance: 114 - 115: 24.164 distance: 115 - 116: 22.599 distance: 115 - 118: 45.343 distance: 116 - 119: 28.769 distance: 119 - 120: 9.280 distance: 123 - 125: 13.308 distance: 127 - 128: 28.703 distance: 128 - 129: 41.759 distance: 128 - 133: 9.233 distance: 130 - 131: 4.425 distance: 130 - 132: 37.285 distance: 133 - 134: 39.314 distance: 134 - 135: 36.511 distance: 134 - 137: 28.185 distance: 135 - 136: 53.096 distance: 135 - 139: 21.832 distance: 137 - 138: 20.323 distance: 140 - 141: 16.596 distance: 141 - 142: 47.039 distance: 141 - 143: 14.975 distance: 143 - 144: 33.293 distance: 143 - 149: 12.894 distance: 144 - 145: 40.757 distance: 145 - 146: 40.477 distance: 147 - 148: 24.752 distance: 148 - 149: 22.934 distance: 152 - 159: 40.573 distance: 154 - 155: 13.657 distance: 155 - 156: 16.192 distance: 156 - 157: 39.954 distance: 157 - 158: 40.040 distance: 161 - 162: 11.139 distance: 161 - 168: 35.172 distance: 163 - 164: 39.715 distance: 164 - 165: 40.269 distance: 165 - 166: 45.834 distance: 166 - 167: 40.533