Starting phenix.real_space_refine on Sun Jul 5 08:06:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7yqt_34034/07_2026/7yqt_34034.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yqt_34034/07_2026/7yqt_34034.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7yqt_34034/07_2026/7yqt_34034.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yqt_34034/07_2026/7yqt_34034.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7yqt_34034/07_2026/7yqt_34034.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yqt_34034/07_2026/7yqt_34034.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7yqt_34034/07_2026/7yqt_34034.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7yqt_34034/07_2026/7yqt_34034.cif" } resolution = 3.45 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= -0.000 sd= 0.070 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 111 5.16 5 C 16861 2.51 5 N 4332 2.21 5 O 5189 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.03s 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: 26493 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 8535 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1097, 8530 Classifications: {'peptide': 1097} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 57, 'TRANS': 1037} Chain breaks: 2 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 75 Unresolved non-hydrogen dihedrals: 59 Planarities with less than four sites: {'ARG:plan': 4, 'TYR:plan': 1, 'TRP:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 42 Conformer: "B" Number of residues, atoms: 1097, 8530 Classifications: {'peptide': 1097} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 57, 'TRANS': 1037} Chain breaks: 2 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 75 Unresolved non-hydrogen dihedrals: 59 Planarities with less than four sites: {'ARG:plan': 4, 'TYR:plan': 1, 'TRP:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 42 bond proxies already assigned to first conformer: 8729 Chain: "B" Number of atoms: 8540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1097, 8540 Classifications: {'peptide': 1097} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 58, 'TRANS': 1038} Chain breaks: 2 Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 48 Planarities with less than four sites: {'ARG:plan': 4, 'TYR:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 36 Chain: "C" Number of atoms: 8536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1097, 8536 Classifications: {'peptide': 1097} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 58, 'TRANS': 1038} Chain breaks: 2 Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 53 Planarities with less than four sites: {'ARG:plan': 3, 'GLU:plan': 1, 'TYR:plan': 1, 'TRP:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 41 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: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 210 Unusual residues: {'NAG': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen chiralities: 15 Chain: "B" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 210 Unusual residues: {'NAG': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen chiralities: 15 Chain: "C" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 210 Unusual residues: {'NAG': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen chiralities: 15 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AARG A 78 " occ=0.51 ... (8 atoms not shown) pdb=" CB BARG A 78 " occ=0.49 Time building chain proxies: 7.24, per 1000 atoms: 0.27 Number of scatterers: 26493 At special positions: 0 Unit cell: (156.22, 161.57, 196.88, 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 111 16.00 O 5189 8.00 N 4332 7.00 C 16861 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.02 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=2.04 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 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 61 " " NAG A1302 " - " ASN A 74 " " NAG A1303 " - " ASN A 122 " " NAG A1304 " - " ASN A 149 " " NAG A1305 " - " ASN A 165 " " NAG A1306 " - " ASN A 234 " " NAG A1307 " - " ASN A 282 " " NAG A1308 " - " ASN A 331 " " NAG A1309 " - " ASN A 343 " " NAG A1310 " - " ASN A 603 " " NAG A1311 " - " ASN A 616 " " NAG A1312 " - " ASN A 657 " " NAG A1313 " - " ASN A 709 " " NAG A1314 " - " ASN A1098 " " NAG A1315 " - " ASN A1134 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 74 " " NAG B1303 " - " ASN B 122 " " NAG B1304 " - " ASN B 149 " " NAG B1305 " - " ASN B 165 " " NAG B1306 " - " ASN B 234 " " NAG B1307 " - " ASN B 282 " " NAG B1308 " - " ASN B 331 " " NAG B1309 " - " ASN B 343 " " NAG B1310 " - " ASN B 603 " " NAG B1311 " - " ASN B 616 " " NAG B1312 " - " ASN B 657 " " NAG B1313 " - " ASN B 709 " " NAG B1314 " - " ASN B1098 " " NAG B1315 " - " ASN B1134 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 74 " " NAG C1303 " - " ASN C 122 " " NAG C1304 " - " ASN C 149 " " NAG C1305 " - " ASN C 165 " " NAG C1306 " - " ASN C 234 " " NAG C1307 " - " ASN C 282 " " NAG C1308 " - " ASN C 331 " " NAG C1309 " - " ASN C 343 " " NAG C1310 " - " ASN C 603 " " NAG C1311 " - " ASN C 616 " " NAG C1312 " - " ASN C 657 " " NAG C1313 " - " ASN C 709 " " NAG C1314 " - " ASN C1098 " " NAG C1315 " - " ASN C1134 " " NAG D 1 " - " ASN A 717 " " NAG E 1 " - " ASN A 801 " " NAG F 1 " - " ASN A1074 " " NAG G 1 " - " ASN B 717 " " NAG H 1 " - " ASN B 801 " " NAG I 1 " - " ASN B1074 " " NAG J 1 " - " ASN C 717 " " NAG K 1 " - " ASN C 801 " " NAG L 1 " - " ASN C1074 " Time building additional restraints: 2.37 Conformation dependent library (CDL) restraints added in 1.4 seconds 6552 Ramachandran restraints generated. 3276 Oldfield, 0 Emsley, 3276 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6164 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 51 sheets defined 21.1% alpha, 17.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.03 Creating SS restraints... Processing helix chain 'A' and resid 109 through 111 No H-bonds generated for 'chain 'A' and resid 109 through 111' Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 338 through 343 removed outlier: 3.644A pdb=" N PHE A 342 " --> pdb=" O PHE A 338 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ASN A 343 " --> pdb=" O HIS A 339 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 338 through 343' Processing helix chain 'A' and resid 405 through 407 No H-bonds generated for 'chain 'A' and resid 405 through 407' Processing helix chain 'A' and resid 417 through 422 removed outlier: 3.760A pdb=" N TYR A 421 " --> pdb=" O ASN A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 742 Processing helix chain 'A' and resid 746 through 754 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 760 through 783 removed outlier: 3.862A pdb=" N LEU A 767 " --> pdb=" O LEU A 763 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLN A 779 " --> pdb=" O ASP A 775 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLU A 780 " --> pdb=" O LYS A 776 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N PHE A 782 " --> pdb=" O THR A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 868 through 884 removed outlier: 3.670A pdb=" N GLN A 872 " --> pdb=" O GLU A 868 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 941 removed outlier: 4.356A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N LYS A 921 " --> pdb=" O TYR A 917 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N LEU A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.983A pdb=" N ASN A 955 " --> pdb=" O VAL A 951 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA A 956 " --> pdb=" O VAL A 952 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 983 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.028A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N THR A1006 " --> pdb=" O GLN A1002 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N TYR A1007 " --> pdb=" O SER A1003 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N VAL A1008 " --> pdb=" O LEU A1004 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ILE A1013 " --> pdb=" O THR A1009 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 111 removed outlier: 3.903A pdb=" N ASP B 111 " --> pdb=" O THR B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 removed outlier: 3.540A pdb=" N LEU B 303 " --> pdb=" O THR B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 343 removed outlier: 3.905A pdb=" N PHE B 342 " --> pdb=" O PHE B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 372 removed outlier: 4.041A pdb=" N ASN B 370 " --> pdb=" O VAL B 367 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ALA B 372 " --> pdb=" O TYR B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.432A pdb=" N SER B 408 " --> pdb=" O ASN B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 422 removed outlier: 3.580A pdb=" N TYR B 421 " --> pdb=" O ASN B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 762 through 783 removed outlier: 3.808A pdb=" N ALA B 766 " --> pdb=" O GLN B 762 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N LEU B 767 " --> pdb=" O LEU B 763 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLN B 779 " --> pdb=" O ASP B 775 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 851 through 855 removed outlier: 3.638A pdb=" N LYS B 854 " --> pdb=" O CYS B 851 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N PHE B 855 " --> pdb=" O ALA B 852 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 851 through 855' Processing helix chain 'B' and resid 868 through 884 removed outlier: 3.685A pdb=" N GLN B 872 " --> pdb=" O GLU B 868 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 890 removed outlier: 3.790A pdb=" N ALA B 890 " --> pdb=" O THR B 887 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 913 through 941 removed outlier: 7.184A pdb=" N LYS B 921 " --> pdb=" O TYR B 917 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N LEU B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N THR B 941 " --> pdb=" O SER B 937 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.791A pdb=" N ASN B 955 " --> pdb=" O VAL B 951 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.472A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N THR B1006 " --> pdb=" O GLN B1002 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N TYR B1007 " --> pdb=" O SER B1003 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL B1008 " --> pdb=" O LEU B1004 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ILE B1013 " --> pdb=" O THR B1009 " (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 367 through 371 removed outlier: 3.822A pdb=" N ASN C 370 " --> pdb=" O VAL C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 388 removed outlier: 3.597A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 384 through 388' Processing helix chain 'C' and resid 405 through 410 removed outlier: 5.397A pdb=" N SER C 408 " --> pdb=" O ASN C 405 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ILE C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 422 Processing helix chain 'C' and resid 619 through 623 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 755 removed outlier: 3.690A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 761 through 783 removed outlier: 3.559A pdb=" N ARG C 765 " --> pdb=" O THR C 761 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ALA C 766 " --> pdb=" O GLN C 762 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N LEU C 767 " --> pdb=" O LEU C 763 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLN C 779 " --> pdb=" O ASP C 775 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N VAL C 781 " --> pdb=" O ASN C 777 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE C 782 " --> pdb=" O THR C 778 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.607A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 850 through 854 Processing helix chain 'C' and resid 869 through 884 Processing helix chain 'C' and resid 886 through 890 removed outlier: 3.708A pdb=" N ALA C 890 " --> pdb=" O THR C 887 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.729A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 941 removed outlier: 7.161A pdb=" N LYS C 921 " --> pdb=" O TYR C 917 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N LEU C 922 " --> pdb=" O GLU C 918 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.562A pdb=" N GLN C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ASN C 955 " --> pdb=" O VAL C 951 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA C 956 " --> pdb=" O VAL C 952 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.741A pdb=" N LEU C 984 " --> pdb=" O ILE C 980 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.854A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N THR C1006 " --> pdb=" O GLN C1002 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N TYR C1007 " --> pdb=" O SER C1003 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N VAL C1008 " --> pdb=" O LEU C1004 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ILE C1013 " --> pdb=" O THR C1009 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 26 through 30 removed outlier: 8.473A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 50 through 55 removed outlier: 3.977A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 168 through 169 removed outlier: 3.929A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 189 through 190 removed outlier: 3.510A pdb=" N LEU A 189 " --> pdb=" O THR A 208 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N THR A 208 " --> pdb=" O LEU A 189 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 7.060A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 326 removed outlier: 7.277A pdb=" N ILE A 326 " --> pdb=" O ASN A 542 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.857A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 575 through 577 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.132A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.527A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 702 through 704 Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 715 Processing sheet with id=AB4, first strand: chain 'A' and resid 718 through 722 Processing sheet with id=AB5, first strand: chain 'A' and resid 718 through 722 removed outlier: 5.799A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 734 through 735 Processing sheet with id=AB7, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AB8, first strand: chain 'A' and resid 1089 through 1090 Processing sheet with id=AB9, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AC1, first strand: chain 'B' and resid 26 through 30 removed outlier: 3.979A pdb=" N SER B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N TYR B 265 " --> pdb=" O PHE B 65 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N THR B 208 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N TYR B 204 " --> pdb=" O VAL B 193 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 50 through 55 removed outlier: 4.064A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 168 through 169 removed outlier: 3.603A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.990A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.262A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.116A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 453 through 454 removed outlier: 3.663A pdb=" N TYR B 453 " --> pdb=" O GLN B 493 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 538 through 543 Processing sheet with id=AC9, first strand: chain 'B' and resid 565 through 567 removed outlier: 4.091A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.152A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.806A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 702 through 704 Processing sheet with id=AD3, first strand: chain 'B' and resid 711 through 715 Processing sheet with id=AD4, first strand: chain 'B' and resid 718 through 722 Processing sheet with id=AD5, first strand: chain 'B' and resid 718 through 722 removed outlier: 5.911A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 733 through 735 removed outlier: 4.709A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N THR B 859 " --> pdb=" O SER B 735 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 1089 through 1090 Processing sheet with id=AD8, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AD9, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.395A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ALA C 93 " --> pdb=" O TYR C 266 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU C 191 " --> pdb=" O LYS C 206 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS C 206 " --> pdb=" O GLU C 191 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 50 through 55 removed outlier: 3.905A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 129 through 131 removed outlier: 4.335A pdb=" N PHE C 106 " --> pdb=" O LEU C 117 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 311 through 319 removed outlier: 3.540A pdb=" N THR C 599 " --> pdb=" O GLY C 311 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 324 through 325 removed outlier: 7.706A pdb=" N GLU C 324 " --> pdb=" O ASN C 540 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.095A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 391 through 392 Processing sheet with id=AE7, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE8, first strand: chain 'C' and resid 542 through 543 Processing sheet with id=AE9, first strand: chain 'C' and resid 566 through 567 removed outlier: 6.586A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.062A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.707A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.585A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 718 through 722 Processing sheet with id=AF4, first strand: chain 'C' and resid 718 through 722 removed outlier: 3.674A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 735 through 736 Processing sheet with id=AF6, first strand: chain 'C' and resid 1081 through 1082 removed outlier: 3.714A pdb=" N ILE C1081 " --> pdb=" O HIS C1088 " (cutoff:3.500A) 769 hydrogen bonds defined for protein. 2121 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: 5.44 Time building geometry restraints manager: 3.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8405 1.34 - 1.46: 6484 1.46 - 1.58: 12083 1.58 - 1.70: 0 1.70 - 1.82: 138 Bond restraints: 27110 Sorted by residual: bond pdb=" C1 NAG C1306 " pdb=" O5 NAG C1306 " ideal model delta sigma weight residual 1.406 1.450 -0.044 2.00e-02 2.50e+03 4.94e+00 bond pdb=" C1 NAG C1311 " pdb=" O5 NAG C1311 " ideal model delta sigma weight residual 1.406 1.449 -0.043 2.00e-02 2.50e+03 4.63e+00 bond pdb=" C1 NAG B1306 " pdb=" O5 NAG B1306 " ideal model delta sigma weight residual 1.406 1.446 -0.040 2.00e-02 2.50e+03 4.02e+00 bond pdb=" C1 NAG A1303 " pdb=" O5 NAG A1303 " ideal model delta sigma weight residual 1.406 1.445 -0.039 2.00e-02 2.50e+03 3.78e+00 bond pdb=" C1 NAG E 2 " pdb=" O5 NAG E 2 " ideal model delta sigma weight residual 1.406 1.443 -0.037 2.00e-02 2.50e+03 3.41e+00 ... (remaining 27105 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.24: 36256 2.24 - 4.47: 604 4.47 - 6.71: 54 6.71 - 8.94: 11 8.94 - 11.18: 1 Bond angle restraints: 36926 Sorted by residual: angle pdb=" C ASP C 568 " pdb=" N ILE C 569 " pdb=" CA ILE C 569 " ideal model delta sigma weight residual 121.65 117.83 3.82 9.40e-01 1.13e+00 1.65e+01 angle pdb=" N ILE A 666 " pdb=" CA ILE A 666 " pdb=" C ILE A 666 " ideal model delta sigma weight residual 111.62 108.42 3.20 7.90e-01 1.60e+00 1.64e+01 angle pdb=" N GLY C 496 " pdb=" CA GLY C 496 " pdb=" C GLY C 496 " ideal model delta sigma weight residual 111.36 116.08 -4.72 1.17e+00 7.31e-01 1.63e+01 angle pdb=" C TYR C 495 " pdb=" N GLY C 496 " pdb=" CA GLY C 496 " ideal model delta sigma weight residual 119.92 123.78 -3.86 9.60e-01 1.09e+00 1.62e+01 angle pdb=" CA PRO C 209 " pdb=" N PRO C 209 " pdb=" CD PRO C 209 " ideal model delta sigma weight residual 112.00 106.40 5.60 1.40e+00 5.10e-01 1.60e+01 ... (remaining 36921 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 14206 17.97 - 35.94: 1152 35.94 - 53.91: 192 53.91 - 71.88: 54 71.88 - 89.85: 30 Dihedral angle restraints: 15634 sinusoidal: 6039 harmonic: 9595 Sorted by residual: dihedral pdb=" CB CYS B 662 " pdb=" SG CYS B 662 " pdb=" SG CYS B 671 " pdb=" CB CYS B 671 " ideal model delta sinusoidal sigma weight residual 93.00 5.68 87.32 1 1.00e+01 1.00e-02 9.15e+01 dihedral pdb=" CB CYS A 336 " pdb=" SG CYS A 336 " pdb=" SG CYS A 361 " pdb=" CB CYS A 361 " ideal model delta sinusoidal sigma weight residual 93.00 22.02 70.98 1 1.00e+01 1.00e-02 6.47e+01 dihedral pdb=" CA CYS C 617 " pdb=" C CYS C 617 " pdb=" N THR C 618 " pdb=" CA THR C 618 " ideal model delta harmonic sigma weight residual 180.00 142.69 37.31 0 5.00e+00 4.00e-02 5.57e+01 ... (remaining 15631 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.135: 4305 0.135 - 0.270: 48 0.270 - 0.404: 6 0.404 - 0.539: 2 0.539 - 0.674: 2 Chirality restraints: 4363 Sorted by residual: chirality pdb=" C1 NAG K 1 " pdb=" ND2 ASN C 801 " pdb=" C2 NAG K 1 " pdb=" O5 NAG K 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.73 -0.67 2.00e-01 2.50e+01 1.14e+01 chirality pdb=" C1 NAG C1301 " pdb=" ND2 ASN C 61 " pdb=" C2 NAG C1301 " pdb=" O5 NAG C1301 " both_signs ideal model delta sigma weight residual False -2.40 -1.83 -0.57 2.00e-01 2.50e+01 7.99e+00 chirality pdb=" C1 NAG B1301 " pdb=" ND2 ASN B 61 " pdb=" C2 NAG B1301 " pdb=" O5 NAG B1301 " both_signs ideal model delta sigma weight residual False -2.40 -1.89 -0.51 2.00e-01 2.50e+01 6.53e+00 ... (remaining 4360 not shown) Planarity restraints: 4764 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 224 " 0.080 5.00e-02 4.00e+02 1.20e-01 2.29e+01 pdb=" N PRO A 225 " -0.207 5.00e-02 4.00e+02 pdb=" CA PRO A 225 " 0.063 5.00e-02 4.00e+02 pdb=" CD PRO A 225 " 0.063 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 208 " -0.063 5.00e-02 4.00e+02 9.31e-02 1.39e+01 pdb=" N PRO C 209 " 0.161 5.00e-02 4.00e+02 pdb=" CA PRO C 209 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO C 209 " -0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 61 " -0.028 2.00e-02 2.50e+03 2.63e-02 8.65e+00 pdb=" CG ASN C 61 " 0.034 2.00e-02 2.50e+03 pdb=" OD1 ASN C 61 " -0.005 2.00e-02 2.50e+03 pdb=" ND2 ASN C 61 " 0.027 2.00e-02 2.50e+03 pdb=" C1 NAG C1301 " -0.027 2.00e-02 2.50e+03 ... (remaining 4761 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 408 2.66 - 3.22: 24432 3.22 - 3.78: 36898 3.78 - 4.34: 50206 4.34 - 4.90: 83822 Nonbonded interactions: 195766 Sorted by model distance: nonbonded pdb=" O GLU A 661 " pdb=" OH TYR A 695 " model vdw 2.100 3.040 nonbonded pdb=" OE2 GLU B 516 " pdb=" OH TYR C 200 " model vdw 2.119 3.040 nonbonded pdb=" OG1 THR B 108 " pdb=" O7 NAG B1306 " model vdw 2.130 3.040 nonbonded pdb=" OG1 THR B 323 " pdb=" OE1 GLU B 324 " model vdw 2.157 3.040 nonbonded pdb=" O ALA A 879 " pdb=" OG1 THR A 883 " model vdw 2.159 3.040 ... (remaining 195761 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 25 through 77 or resid 79 through 95 or (resid 96 and (nam \ e N or name CA or name C or name O or name CB )) or resid 97 through 189 or (res \ id 190 and (name N or name CA or name C or name O or name CB )) or resid 191 thr \ ough 346 or (resid 347 through 348 and (name N or name CA or name C or name O or \ name CB )) or resid 349 through 1315)) selection = (chain 'B' and (resid 25 through 77 or resid 79 through 95 or (resid 96 and (nam \ e N or name CA or name C or name O or name CB )) or resid 97 through 194 or (res \ id 195 and (name N or name CA or name C or name O or name CB )) or resid 196 thr \ ough 327 or (resid 328 through 329 and (name N or name CA or name C or name O or \ name CB )) or resid 330 through 346 or (resid 347 through 348 and (name N or na \ me CA or name C or name O or name CB )) or resid 349 through 1315)) selection = (chain 'C' and (resid 25 through 77 or resid 79 through 189 or (resid 190 and (n \ ame N or name CA or name C or name O or name CB )) or resid 191 through 194 or ( \ resid 195 and (name N or name CA or name C or name O or name CB )) or resid 196 \ through 327 or (resid 328 through 329 and (name N or name CA or name C or name O \ or name CB )) or resid 330 through 1315)) } 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=0.49 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: 2.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.470 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 26.660 Find NCS groups from input model: 0.900 Set up NCS constraints: 0.060 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:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 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 : 0.004 0.086 27209 Z= 0.176 Angle : 0.720 19.743 37187 Z= 0.352 Chirality : 0.052 0.674 4363 Planarity : 0.005 0.120 4710 Dihedral : 13.783 89.850 9362 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.07 % Favored : 90.83 % Rotamer: Outliers : 0.07 % Allowed : 0.18 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.57 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.51 (0.14), residues: 3276 helix: 1.64 (0.22), residues: 595 sheet: -0.25 (0.21), residues: 577 loop : -2.18 (0.13), residues: 2104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 237 TYR 0.024 0.001 TYR C 204 PHE 0.024 0.001 PHE B 377 TRP 0.031 0.002 TRP B 633 HIS 0.011 0.001 HIS A 339 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.18 (27110) covalent geometry : angle 0.66837 / 0.34 (36926) SS BOND : bond 0.00297 / 0.17 ( 36) SS BOND : angle 1.64968 / 1.35 ( 72) hydrogen bonds : bond 0.16032 / 10.13 ( 757) hydrogen bonds : angle 7.24164 / 5.07 ( 2121) link_BETA1-4 : bond 0.00577 / 0.37 ( 9) link_BETA1-4 : angle 2.78587 / 1.75 ( 27) link_NAG-ASN : bond 0.00729 / 0.46 ( 54) link_NAG-ASN : angle 3.82322 / 2.36 ( 162) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6552 Ramachandran restraints generated. 3276 Oldfield, 0 Emsley, 3276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6552 Ramachandran restraints generated. 3276 Oldfield, 0 Emsley, 3276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 2873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 256 time to evaluate : 0.987 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 347 PHE cc_start: 0.6548 (m-10) cc_final: 0.6318 (m-10) REVERT: C 177 MET cc_start: 0.2166 (mmp) cc_final: 0.1952 (mmp) REVERT: C 994 ASP cc_start: 0.6956 (t0) cc_final: 0.6713 (t0) REVERT: C 1125 ASN cc_start: 0.7491 (t0) cc_final: 0.7243 (t0) outliers start: 2 outliers final: 0 residues processed: 258 average time/residue: 0.1651 time to fit residues: 69.0180 Evaluate side-chains 158 residues out of total 2873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 158 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 7.9990 chunk 183 optimal weight: 3.9990 chunk 298 optimal weight: 7.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 360 ASN A 644 GLN ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 926 GLN B1002 GLN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 487 ASN C 804 GLN C 926 GLN C1005 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.165069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 110)---------------| | r_work = 0.3400 r_free = 0.3400 target = 0.107615 restraints weight = 46285.664| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 3.83 r_work: 0.3154 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3155 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3155 r_free = 0.3155 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3155 r_free = 0.3155 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3155 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.1634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.086 27209 Z= 0.278 Angle : 0.772 18.995 37187 Z= 0.384 Chirality : 0.052 0.358 4363 Planarity : 0.005 0.072 4710 Dihedral : 4.805 37.201 3531 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.05 % Favored : 89.86 % Rotamer: Outliers : 1.05 % Allowed : 5.62 % Favored : 93.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.57 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.97 (0.14), residues: 3276 helix: 0.78 (0.21), residues: 606 sheet: -0.42 (0.20), residues: 624 loop : -2.42 (0.12), residues: 2046 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B1014 TYR 0.023 0.002 TYR C1067 PHE 0.034 0.002 PHE C 906 TRP 0.040 0.002 TRP B 64 HIS 0.005 0.001 HIS B 339 Details of bonding type rmsd/Z covalent geometry : bond 0.00684 / 0.28 (27110) covalent geometry : angle 0.73385 / 0.38 (36926) SS BOND : bond 0.00373 / 0.24 ( 36) SS BOND : angle 1.83644 / 1.26 ( 72) hydrogen bonds : bond 0.06689 / 4.46 ( 757) hydrogen bonds : angle 6.06411 / 4.24 ( 2121) link_BETA1-4 : bond 0.00936 / 0.55 ( 9) link_BETA1-4 : angle 3.02930 / 1.87 ( 27) link_NAG-ASN : bond 0.00564 / 0.31 ( 54) link_NAG-ASN : angle 3.29542 / 2.03 ( 162) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6552 Ramachandran restraints generated. 3276 Oldfield, 0 Emsley, 3276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6552 Ramachandran restraints generated. 3276 Oldfield, 0 Emsley, 3276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 2873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 158 time to evaluate : 0.916 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 552 LEU cc_start: 0.8161 (OUTLIER) cc_final: 0.7891 (tt) REVERT: A 755 GLN cc_start: 0.8140 (mt0) cc_final: 0.7796 (mm110) REVERT: A 979 ASP cc_start: 0.8344 (t70) cc_final: 0.8029 (t0) REVERT: B 347 PHE cc_start: 0.7737 (m-10) cc_final: 0.7315 (m-10) REVERT: B 1029 MET cc_start: 0.8846 (tpp) cc_final: 0.8390 (ttm) REVERT: C 170 TYR cc_start: 0.7851 (t80) cc_final: 0.7558 (t80) REVERT: C 237 ARG cc_start: 0.6717 (ttp-170) cc_final: 0.6330 (ttm170) outliers start: 30 outliers final: 23 residues processed: 175 average time/residue: 0.1430 time to fit residues: 42.9601 Evaluate side-chains 168 residues out of total 2873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 144 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 663 ASP Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 775 ASP Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1119 ASN Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 219 optimal weight: 0.0060 chunk 59 optimal weight: 0.2980 chunk 192 optimal weight: 0.0020 chunk 309 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 281 optimal weight: 2.9990 chunk 92 optimal weight: 0.9980 chunk 68 optimal weight: 0.6980 chunk 75 optimal weight: 0.6980 chunk 259 optimal weight: 0.8980 chunk 221 optimal weight: 0.9980 overall best weight: 0.3404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 148 ASN A 360 ASN ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1048 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.168499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.112216 restraints weight = 47075.181| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 3.40 r_work: 0.3221 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3233 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3233 r_free = 0.3233 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3233 r_free = 0.3233 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3233 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.1489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 27209 Z= 0.110 Angle : 0.613 18.553 37187 Z= 0.301 Chirality : 0.046 0.427 4363 Planarity : 0.004 0.062 4710 Dihedral : 4.305 32.212 3531 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.22 % Favored : 91.69 % Rotamer: Outliers : 0.91 % Allowed : 6.95 % Favored : 92.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.57 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.66 (0.14), residues: 3276 helix: 1.22 (0.22), residues: 618 sheet: -0.20 (0.21), residues: 595 loop : -2.27 (0.13), residues: 2063 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B1091 TYR 0.020 0.001 TYR B1067 PHE 0.020 0.001 PHE B 220 TRP 0.021 0.001 TRP B 64 HIS 0.003 0.001 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.11 (27110) covalent geometry : angle 0.57498 / 0.29 (36926) SS BOND : bond 0.00199 / 0.12 ( 36) SS BOND : angle 1.00945 / 0.68 ( 72) hydrogen bonds : bond 0.04194 / 2.76 ( 757) hydrogen bonds : angle 5.44967 / 3.82 ( 2121) link_BETA1-4 : bond 0.00715 / 0.45 ( 9) link_BETA1-4 : angle 2.66067 / 1.66 ( 27) link_NAG-ASN : bond 0.00582 / 0.32 ( 54) link_NAG-ASN : angle 3.02310 / 1.84 ( 162) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6552 Ramachandran restraints generated. 3276 Oldfield, 0 Emsley, 3276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6552 Ramachandran restraints generated. 3276 Oldfield, 0 Emsley, 3276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 2873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 164 time to evaluate : 0.805 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 755 GLN cc_start: 0.8187 (mt0) cc_final: 0.7732 (mm110) REVERT: A 979 ASP cc_start: 0.8280 (t70) cc_final: 0.7939 (t0) REVERT: B 347 PHE cc_start: 0.7733 (m-10) cc_final: 0.7370 (m-10) REVERT: B 633 TRP cc_start: 0.8152 (p-90) cc_final: 0.7779 (p-90) REVERT: B 1029 MET cc_start: 0.8858 (tpp) cc_final: 0.8417 (ttm) REVERT: C 177 MET cc_start: 0.3137 (mmp) cc_final: 0.2775 (mmp) REVERT: C 237 ARG cc_start: 0.6461 (ttp-170) cc_final: 0.6254 (ttm170) REVERT: C 558 LYS cc_start: 0.8311 (mptt) cc_final: 0.7815 (mppt) outliers start: 26 outliers final: 17 residues processed: 182 average time/residue: 0.1509 time to fit residues: 46.4891 Evaluate side-chains 168 residues out of total 2873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 151 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 541 PHE Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain C residue 1097 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 98 optimal weight: 1.9990 chunk 252 optimal weight: 1.9990 chunk 316 optimal weight: 0.0770 chunk 65 optimal weight: 2.9990 chunk 305 optimal weight: 0.9980 chunk 124 optimal weight: 20.0000 chunk 192 optimal weight: 0.7980 chunk 168 optimal weight: 5.9990 chunk 249 optimal weight: 0.4980 chunk 101 optimal weight: 0.8980 chunk 26 optimal weight: 7.9990 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 360 ASN ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.168355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.112330 restraints weight = 45971.201| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 3.12 r_work: 0.3235 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3249 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3249 r_free = 0.3249 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3249 r_free = 0.3249 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3249 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.1608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 27209 Z= 0.110 Angle : 0.594 18.019 37187 Z= 0.291 Chirality : 0.046 0.444 4363 Planarity : 0.004 0.053 4710 Dihedral : 4.150 30.208 3531 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.62 % Favored : 91.29 % Rotamer: Outliers : 1.09 % Allowed : 7.97 % Favored : 90.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.57 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.53 (0.14), residues: 3276 helix: 1.38 (0.22), residues: 610 sheet: -0.07 (0.22), residues: 557 loop : -2.17 (0.13), residues: 2109 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 646 TYR 0.017 0.001 TYR B1138 PHE 0.021 0.001 PHE B 220 TRP 0.018 0.001 TRP A 436 HIS 0.003 0.000 HIS A 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 (27110) covalent geometry : angle 0.55941 / 0.28 (36926) SS BOND : bond 0.00192 / 0.11 ( 36) SS BOND : angle 0.96211 / 0.64 ( 72) hydrogen bonds : bond 0.03994 / 2.64 ( 757) hydrogen bonds : angle 5.21217 / 3.66 ( 2121) link_BETA1-4 : bond 0.00730 / 0.42 ( 9) link_BETA1-4 : angle 2.41933 / 1.51 ( 27) link_NAG-ASN : bond 0.00514 / 0.26 ( 54) link_NAG-ASN : angle 2.88278 / 1.74 ( 162) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6552 Ramachandran restraints generated. 3276 Oldfield, 0 Emsley, 3276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6552 Ramachandran restraints generated. 3276 Oldfield, 0 Emsley, 3276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 2873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 153 time to evaluate : 0.797 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 220 PHE cc_start: 0.7973 (OUTLIER) cc_final: 0.7760 (t80) REVERT: B 347 PHE cc_start: 0.7862 (m-10) cc_final: 0.7617 (m-10) REVERT: B 1029 MET cc_start: 0.8790 (tpp) cc_final: 0.8354 (ttm) REVERT: C 170 TYR cc_start: 0.7723 (t80) cc_final: 0.7504 (t80) REVERT: C 177 MET cc_start: 0.3060 (mmp) cc_final: 0.2740 (mmp) REVERT: C 201 PHE cc_start: 0.6938 (OUTLIER) cc_final: 0.5790 (m-10) REVERT: C 387 LEU cc_start: 0.8609 (OUTLIER) cc_final: 0.8395 (tt) outliers start: 31 outliers final: 22 residues processed: 175 average time/residue: 0.1408 time to fit residues: 42.7169 Evaluate side-chains 173 residues out of total 2873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 148 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 541 PHE Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 220 PHE Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain C residue 201 PHE Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- 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: 53.2764 > 50: distance: 15 - 35: 4.419 distance: 22 - 26: 3.271 distance: 27 - 28: 8.788 distance: 27 - 30: 4.081 distance: 28 - 29: 10.462 distance: 28 - 35: 7.054 distance: 30 - 31: 10.975 distance: 31 - 32: 8.598 distance: 32 - 33: 4.363 distance: 33 - 34: 7.562 distance: 35 - 36: 8.813 distance: 36 - 37: 13.144 distance: 36 - 39: 12.492 distance: 37 - 38: 12.042 distance: 37 - 42: 13.099 distance: 39 - 40: 6.768 distance: 39 - 41: 4.487 distance: 42 - 43: 3.206 distance: 43 - 44: 7.164 distance: 43 - 46: 15.440 distance: 44 - 45: 15.355 distance: 44 - 49: 6.873 distance: 46 - 47: 4.120 distance: 46 - 48: 7.416 distance: 49 - 50: 5.526 distance: 50 - 51: 13.613 distance: 50 - 53: 13.408 distance: 51 - 52: 8.648 distance: 51 - 57: 18.775 distance: 53 - 54: 11.039 distance: 54 - 55: 16.187 distance: 54 - 56: 21.287 distance: 57 - 58: 18.830 distance: 58 - 59: 36.446 distance: 58 - 61: 22.530 distance: 59 - 60: 4.768 distance: 59 - 62: 17.691 distance: 62 - 63: 3.634 distance: 63 - 64: 4.844 distance: 63 - 66: 7.359 distance: 64 - 65: 10.323 distance: 64 - 70: 9.359 distance: 66 - 67: 13.713 distance: 70 - 71: 12.016 distance: 71 - 72: 8.732 distance: 71 - 74: 15.014 distance: 72 - 73: 3.753 distance: 72 - 75: 8.152 distance: 75 - 76: 23.570 distance: 76 - 77: 34.222 distance: 77 - 78: 5.886 distance: 77 - 79: 3.271 distance: 79 - 80: 12.125 distance: 80 - 81: 17.892 distance: 80 - 83: 13.602 distance: 81 - 82: 16.634 distance: 81 - 90: 18.251 distance: 83 - 84: 9.394 distance: 84 - 85: 11.847 distance: 84 - 86: 7.040 distance: 85 - 87: 9.602 distance: 86 - 88: 8.466 distance: 87 - 89: 9.136 distance: 88 - 89: 10.008 distance: 90 - 91: 7.690 distance: 91 - 92: 10.689 distance: 91 - 94: 4.769 distance: 92 - 93: 14.304 distance: 92 - 98: 8.383 distance: 94 - 95: 16.460 distance: 94 - 96: 22.303 distance: 95 - 97: 17.945