Starting phenix.real_space_refine on Mon Jul 6 08:33:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7e9o_31034/07_2026/7e9o_31034.cif Found real_map, /net/cci-nas-00/data/ceres_data/7e9o_31034/07_2026/7e9o_31034.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.41 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7e9o_31034/07_2026/7e9o_31034.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7e9o_31034/07_2026/7e9o_31034.map" model { file = "/net/cci-nas-00/data/ceres_data/7e9o_31034/07_2026/7e9o_31034.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7e9o_31034/07_2026/7e9o_31034.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7e9o_31034/07_2026/7e9o_31034.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7e9o_31034/07_2026/7e9o_31034.cif" } resolution = 3.41 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= 1.000 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 147 5.16 5 C 21504 2.51 5 N 5622 2.21 5 O 6603 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 197 residue(s): 0.04s 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: 33876 Number of models: 1 Model: "" Number of chains: 12 Chain: "B" Number of atoms: 7825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1002, 7825 Classifications: {'peptide': 1002} Link IDs: {'PTRANS': 53, 'TRANS': 948} Chain breaks: 7 Chain: "A" Number of atoms: 7825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1002, 7825 Classifications: {'peptide': 1002} Link IDs: {'PTRANS': 53, 'TRANS': 948} Chain breaks: 7 Chain: "C" Number of atoms: 7825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1002, 7825 Classifications: {'peptide': 1002} Link IDs: {'PTRANS': 53, 'TRANS': 948} Chain breaks: 7 Chain: "L" Number of atoms: 1673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1673 Classifications: {'peptide': 218} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 203} Chain: "H" Number of atoms: 1668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1668 Classifications: {'peptide': 226} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 213} Chain breaks: 2 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 16 Chain: "O" Number of atoms: 1673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1673 Classifications: {'peptide': 218} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 203} Chain: "P" Number of atoms: 1668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1668 Classifications: {'peptide': 226} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 213} Chain breaks: 2 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 16 Chain: "X" Number of atoms: 1673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1673 Classifications: {'peptide': 218} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 203} Chain: "Y" Number of atoms: 1668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1668 Classifications: {'peptide': 226} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 213} Chain breaks: 2 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 16 Chain: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Chain: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Chain: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 6.95, per 1000 atoms: 0.21 Number of scatterers: 33876 At special positions: 0 Unit cell: (203.67, 199.29, 226.665, 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 147 16.00 O 6603 8.00 N 5622 7.00 C 21504 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=49, symmetry=0 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 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 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 A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.04 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=2.02 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 C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 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 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 93 " distance=2.03 Simple disulfide: pdb=" SG CYS L 139 " - pdb=" SG CYS L 199 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 157 " - pdb=" SG CYS H 213 " distance=2.03 Simple disulfide: pdb=" SG CYS O 23 " - pdb=" SG CYS O 93 " distance=2.03 Simple disulfide: pdb=" SG CYS O 139 " - pdb=" SG CYS O 199 " distance=2.04 Simple disulfide: pdb=" SG CYS P 22 " - pdb=" SG CYS P 96 " distance=2.04 Simple disulfide: pdb=" SG CYS P 157 " - pdb=" SG CYS P 213 " distance=2.04 Simple disulfide: pdb=" SG CYS X 23 " - pdb=" SG CYS X 93 " distance=2.03 Simple disulfide: pdb=" SG CYS X 139 " - pdb=" SG CYS X 199 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 22 " - pdb=" SG CYS Y 96 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 157 " - pdb=" SG CYS Y 213 " 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 NAG-ASN " NAG A1301 " - " ASN A 282 " " NAG A1302 " - " ASN A 331 " " NAG A1303 " - " ASN A1098 " " NAG A1304 " - " ASN A 616 " " NAG A1305 " - " ASN A 709 " " NAG A1306 " - " ASN A 717 " " NAG A1307 " - " ASN A 801 " " NAG A1308 " - " ASN A1134 " " NAG A1309 " - " ASN A1074 " " NAG B1301 " - " ASN B 282 " " NAG B1302 " - " ASN B 616 " " NAG B1303 " - " ASN B 709 " " NAG B1304 " - " ASN B 717 " " NAG B1305 " - " ASN B 801 " " NAG B1306 " - " ASN B1074 " " NAG B1307 " - " ASN B1134 " " NAG B1308 " - " ASN B1098 " " NAG B1309 " - " ASN B 331 " " NAG C1301 " - " ASN C1134 " " NAG C1302 " - " ASN C 282 " " NAG C1303 " - " ASN C 331 " " NAG C1304 " - " ASN C 616 " " NAG C1305 " - " ASN C 709 " " NAG C1306 " - " ASN C 717 " " NAG C1307 " - " ASN C 801 " " NAG C1308 " - " ASN C1074 " " NAG C1309 " - " ASN C1098 " Time building additional restraints: 2.81 Conformation dependent library (CDL) restraints added in 1.3 seconds 8532 Ramachandran restraints generated. 4266 Oldfield, 0 Emsley, 4266 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8064 Finding SS restraints... Secondary structure from input PDB file: 77 helices and 75 sheets defined 19.3% alpha, 29.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.17 Creating SS restraints... Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 384 through 388 removed outlier: 4.316A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 409 removed outlier: 3.558A pdb=" N VAL B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 502 through 506 removed outlier: 3.708A pdb=" N GLN B 506 " --> pdb=" O VAL B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 742 Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.505A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASN B 751 " --> pdb=" O THR B 747 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 4.080A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU B 763 " --> pdb=" O PHE B 759 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 897 through 908 removed outlier: 3.569A pdb=" N GLN B 901 " --> pdb=" O PRO B 897 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 941 removed outlier: 7.302A pdb=" N LYS B 921 " --> pdb=" O TYR B 917 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N LEU B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N THR B 941 " --> pdb=" O SER B 937 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.444A 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 984 removed outlier: 4.011A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.932A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL B1033 " --> pdb=" O MET B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 4.329A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N SER B1147 " --> pdb=" O PRO B1143 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 removed outlier: 4.076A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 371 removed outlier: 3.541A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 390 Processing helix chain 'A' and resid 404 through 410 removed outlier: 3.789A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ILE A 410 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 502 through 506 removed outlier: 3.918A pdb=" N GLN A 506 " --> pdb=" O VAL A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 744 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 758 through 783 removed outlier: 3.663A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 890 removed outlier: 3.523A pdb=" N ALA A 890 " --> pdb=" O THR A 887 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 removed outlier: 3.708A pdb=" N GLN A 901 " --> pdb=" O PRO A 897 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 919 Processing helix chain 'A' and resid 919 through 941 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 966 removed outlier: 4.583A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 5.187A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 3.772A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 336 through 340 removed outlier: 3.942A pdb=" N GLY C 339 " --> pdb=" O CYS C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.524A pdb=" N ALA C 352 " --> pdb=" O SER C 349 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 349 through 353' Processing helix chain 'C' and resid 365 through 371 Processing helix chain 'C' and resid 405 through 408 removed outlier: 3.707A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 405 through 408' Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 737 through 743 removed outlier: 3.714A pdb=" N TYR C 741 " --> pdb=" O ASP C 737 " (cutoff:3.500A) Processing helix chain 'C' and resid 747 through 755 removed outlier: 3.943A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.625A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.914A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 890 removed outlier: 3.501A pdb=" N ALA C 890 " --> pdb=" O THR C 887 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 removed outlier: 3.602A pdb=" N GLN C 901 " --> pdb=" O PRO C 897 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 918 Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.574A pdb=" N GLN C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) removed outlier: 4.405A 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 984 removed outlier: 3.599A pdb=" N LEU C 984 " --> pdb=" O ILE C 980 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.473A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 4.155A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N SER C1147 " --> pdb=" O PRO C1143 " (cutoff:3.500A) Processing helix chain 'L' and resid 84 through 88 removed outlier: 4.048A pdb=" N VAL L 88 " --> pdb=" O ALA L 85 " (cutoff:3.500A) Processing helix chain 'L' and resid 127 through 132 removed outlier: 4.061A pdb=" N LYS L 131 " --> pdb=" O ASP L 127 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N SER L 132 " --> pdb=" O GLU L 128 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 127 through 132' Processing helix chain 'L' and resid 188 through 194 removed outlier: 3.915A pdb=" N HIS L 194 " --> pdb=" O ASP L 190 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'H' and resid 204 through 206 No H-bonds generated for 'chain 'H' and resid 204 through 206' Processing helix chain 'O' and resid 84 through 88 removed outlier: 4.192A pdb=" N VAL O 88 " --> pdb=" O ALA O 85 " (cutoff:3.500A) Processing helix chain 'O' and resid 126 through 131 Processing helix chain 'O' and resid 187 through 194 removed outlier: 3.582A pdb=" N LYS O 193 " --> pdb=" O ALA O 189 " (cutoff:3.500A) Processing helix chain 'P' and resid 87 through 91 Processing helix chain 'P' and resid 173 through 175 No H-bonds generated for 'chain 'P' and resid 173 through 175' Processing helix chain 'P' and resid 202 through 206 removed outlier: 3.625A pdb=" N LEU P 206 " --> pdb=" O SER P 203 " (cutoff:3.500A) Processing helix chain 'X' and resid 84 through 88 removed outlier: 3.624A pdb=" N VAL X 88 " --> pdb=" O ALA X 85 " (cutoff:3.500A) Processing helix chain 'X' and resid 129 through 133 Processing helix chain 'X' and resid 187 through 194 Processing helix chain 'Y' and resid 173 through 175 No H-bonds generated for 'chain 'Y' and resid 173 through 175' Processing sheet with id=AA1, first strand: chain 'B' and resid 28 through 30 removed outlier: 3.773A pdb=" N THR B 29 " --> pdb=" O VAL B 62 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N VAL B 62 " --> pdb=" O THR B 29 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.575A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.640A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.012A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 168 through 171 removed outlier: 4.134A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL B 130 " --> pdb=" O PHE B 168 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ASN B 121 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.419A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 325 through 328 Processing sheet with id=AA6, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.670A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AA8, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AA9, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.605A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.160A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.160A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 734 through 735 Processing sheet with id=AB4, first strand: chain 'B' and resid 788 through 789 removed outlier: 5.577A pdb=" N ILE B 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'B' and resid 1081 through 1082 Processing sheet with id=AB6, first strand: chain 'B' and resid 1089 through 1090 Processing sheet with id=AB7, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.192A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.979A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 84 through 85 removed outlier: 5.833A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ASN A 121 " --> pdb=" O ARG A 102 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 311 through 314 Processing sheet with id=AC2, first strand: chain 'A' and resid 318 through 319 Processing sheet with id=AC3, first strand: chain 'A' and resid 325 through 328 Processing sheet with id=AC4, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AC5, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AC6, first strand: chain 'A' and resid 565 through 566 removed outlier: 7.040A pdb=" N PHE A 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.171A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 711 through 712 Processing sheet with id=AC9, first strand: chain 'A' and resid 718 through 728 removed outlier: 6.982A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AD2, first strand: chain 'A' and resid 1081 through 1082 Processing sheet with id=AD3, first strand: chain 'A' and resid 1089 through 1090 Processing sheet with id=AD4, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AD5, first strand: chain 'C' and resid 28 through 31 removed outlier: 3.625A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 8.146A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N THR C 95 " --> pdb=" O ALA C 264 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.657A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.264A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 47 through 55 removed outlier: 4.142A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 84 through 85 removed outlier: 5.828A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE C 128 " --> pdb=" O TYR C 170 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.877A pdb=" N LEU C 241 " --> pdb=" O ARG C 102 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.359A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 325 through 328 Processing sheet with id=AE2, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AE3, first strand: chain 'C' and resid 361 through 362 removed outlier: 7.550A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE5, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.943A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.788A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 712 through 715 Processing sheet with id=AE7, first strand: chain 'C' and resid 718 through 728 removed outlier: 7.061A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AE9, first strand: chain 'C' and resid 1081 through 1082 Processing sheet with id=AF1, first strand: chain 'C' and resid 1088 through 1090 Processing sheet with id=AF2, first strand: chain 'C' and resid 1094 through 1098 removed outlier: 3.921A pdb=" N HIS C1101 " --> pdb=" O ASN C1098 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'L' and resid 5 through 7 Processing sheet with id=AF4, first strand: chain 'L' and resid 11 through 13 removed outlier: 3.585A pdb=" N LEU L 11 " --> pdb=" O LYS L 108 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ASP L 110 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N TRP L 40 " --> pdb=" O LEU L 52 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N LYS L 44 " --> pdb=" O SER L 48 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N SER L 48 " --> pdb=" O LYS L 44 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'L' and resid 119 through 123 removed outlier: 6.206A pdb=" N TYR L 178 " --> pdb=" O ASN L 143 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'L' and resid 158 through 159 Processing sheet with id=AF7, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AF8, first strand: chain 'H' and resid 57 through 60 removed outlier: 7.148A pdb=" N GLY H 50 " --> pdb=" O ILE H 58 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N TYR H 60 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N VAL H 48 " --> pdb=" O TYR H 60 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N GLY H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N MET H 34 " --> pdb=" O GLY H 50 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'H' and resid 137 through 141 Processing sheet with id=AG1, first strand: chain 'H' and resid 137 through 141 removed outlier: 4.038A pdb=" N SER H 194 " --> pdb=" O VAL H 186 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'H' and resid 168 through 171 removed outlier: 4.321A pdb=" N TYR H 211 " --> pdb=" O VAL H 228 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'O' and resid 5 through 7 Processing sheet with id=AG4, first strand: chain 'O' and resid 58 through 59 removed outlier: 6.331A pdb=" N TRP O 40 " --> pdb=" O LEU O 52 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N TYR O 54 " --> pdb=" O LEU O 38 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N LEU O 38 " --> pdb=" O TYR O 54 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'O' and resid 119 through 123 removed outlier: 5.817A pdb=" N TYR O 178 " --> pdb=" O ASN O 143 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'O' and resid 158 through 160 removed outlier: 4.352A pdb=" N TRP O 153 " --> pdb=" O GLN O 160 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'P' and resid 3 through 7 Processing sheet with id=AG8, first strand: chain 'P' and resid 46 through 51 removed outlier: 5.092A pdb=" N TRP P 47 " --> pdb=" O ARG P 38 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N ARG P 38 " --> pdb=" O TRP P 47 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LYS P 98 " --> pdb=" O VAL P 119 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N VAL P 119 " --> pdb=" O LYS P 98 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'P' and resid 137 through 141 Processing sheet with id=AH1, first strand: chain 'P' and resid 137 through 141 Processing sheet with id=AH2, first strand: chain 'P' and resid 168 through 171 Processing sheet with id=AH3, first strand: chain 'X' and resid 5 through 7 Processing sheet with id=AH4, first strand: chain 'X' and resid 10 through 13 removed outlier: 3.630A pdb=" N LEU X 11 " --> pdb=" O LYS X 108 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ASP X 110 " --> pdb=" O LEU X 11 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N TRP X 40 " --> pdb=" O LEU X 52 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'X' and resid 119 through 123 removed outlier: 4.129A pdb=" N ASN X 143 " --> pdb=" O TYR X 178 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N TYR X 178 " --> pdb=" O ASN X 143 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N SER X 179 " --> pdb=" O THR X 169 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'X' and resid 158 through 160 removed outlier: 4.386A pdb=" N TRP X 153 " --> pdb=" O GLN X 160 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'Y' and resid 3 through 7 Processing sheet with id=AH8, first strand: chain 'Y' and resid 11 through 12 Processing sheet with id=AH9, first strand: chain 'Y' and resid 45 through 51 removed outlier: 6.632A pdb=" N TRP Y 36 " --> pdb=" O VAL Y 48 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N GLY Y 50 " --> pdb=" O MET Y 34 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N MET Y 34 " --> pdb=" O GLY Y 50 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'Y' and resid 137 through 141 Processing sheet with id=AI2, first strand: chain 'Y' and resid 137 through 141 Processing sheet with id=AI3, first strand: chain 'Y' and resid 168 through 171 removed outlier: 4.326A pdb=" N TYR Y 211 " --> pdb=" O VAL Y 228 " (cutoff:3.500A) 1372 hydrogen bonds defined for protein. 3648 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: 9.06 Time building geometry restraints manager: 3.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 5564 1.31 - 1.44: 9451 1.44 - 1.57: 19437 1.57 - 1.70: 0 1.70 - 1.83: 189 Bond restraints: 34641 Sorted by residual: bond pdb=" C7 NAG C1303 " pdb=" N2 NAG C1303 " ideal model delta sigma weight residual 1.346 1.466 -0.120 2.00e-02 2.50e+03 3.63e+01 bond pdb=" C7 NAG A1301 " pdb=" N2 NAG A1301 " ideal model delta sigma weight residual 1.346 1.456 -0.110 2.00e-02 2.50e+03 3.01e+01 bond pdb=" C7 NAG A1303 " pdb=" N2 NAG A1303 " ideal model delta sigma weight residual 1.346 1.456 -0.110 2.00e-02 2.50e+03 3.00e+01 bond pdb=" C7 NAG B1304 " pdb=" N2 NAG B1304 " ideal model delta sigma weight residual 1.346 1.456 -0.110 2.00e-02 2.50e+03 3.00e+01 bond pdb=" C7 NAG A1306 " pdb=" N2 NAG A1306 " ideal model delta sigma weight residual 1.346 1.455 -0.109 2.00e-02 2.50e+03 2.98e+01 ... (remaining 34636 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.08: 45596 2.08 - 4.17: 1308 4.17 - 6.25: 217 6.25 - 8.33: 19 8.33 - 10.41: 8 Bond angle restraints: 47148 Sorted by residual: angle pdb=" N ILE A 909 " pdb=" CA ILE A 909 " pdb=" C ILE A 909 " ideal model delta sigma weight residual 111.88 102.35 9.53 1.06e+00 8.90e-01 8.08e+01 angle pdb=" N PRO C 942 " pdb=" CA PRO C 942 " pdb=" C PRO C 942 " ideal model delta sigma weight residual 113.40 123.72 -10.32 1.34e+00 5.57e-01 5.94e+01 angle pdb=" C PHE B 906 " pdb=" CA PHE B 906 " pdb=" CB PHE B 906 " ideal model delta sigma weight residual 110.90 100.49 10.41 1.58e+00 4.01e-01 4.34e+01 angle pdb=" CA PHE A 888 " pdb=" CB PHE A 888 " pdb=" CG PHE A 888 " ideal model delta sigma weight residual 113.80 120.17 -6.37 1.00e+00 1.00e+00 4.06e+01 angle pdb=" C PRO A 892 " pdb=" CA PRO A 892 " pdb=" CB PRO A 892 " ideal model delta sigma weight residual 111.46 103.53 7.93 1.29e+00 6.01e-01 3.78e+01 ... (remaining 47143 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.01: 18819 18.01 - 36.02: 1355 36.02 - 54.03: 217 54.03 - 72.04: 45 72.04 - 90.05: 24 Dihedral angle restraints: 20460 sinusoidal: 7908 harmonic: 12552 Sorted by residual: dihedral pdb=" CB CYS B1032 " pdb=" SG CYS B1032 " pdb=" SG CYS B1043 " pdb=" CB CYS B1043 " ideal model delta sinusoidal sigma weight residual 93.00 -176.95 -90.05 1 1.00e+01 1.00e-02 9.61e+01 dihedral pdb=" CB CYS C1032 " pdb=" SG CYS C1032 " pdb=" SG CYS C1043 " pdb=" CB CYS C1043 " ideal model delta sinusoidal sigma weight residual -86.00 -172.07 86.07 1 1.00e+01 1.00e-02 8.94e+01 dihedral pdb=" CB CYS C 662 " pdb=" SG CYS C 662 " pdb=" SG CYS C 671 " pdb=" CB CYS C 671 " ideal model delta sinusoidal sigma weight residual -86.00 -168.23 82.23 1 1.00e+01 1.00e-02 8.30e+01 ... (remaining 20457 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 4999 0.093 - 0.187: 404 0.187 - 0.280: 25 0.280 - 0.374: 2 0.374 - 0.467: 3 Chirality restraints: 5433 Sorted by residual: chirality pdb=" C1 NAG B1308 " pdb=" ND2 ASN B1098 " pdb=" C2 NAG B1308 " pdb=" O5 NAG B1308 " both_signs ideal model delta sigma weight residual False -2.40 -1.93 -0.47 2.00e-01 2.50e+01 5.46e+00 chirality pdb=" C1 NAG C1303 " pdb=" ND2 ASN C 331 " pdb=" C2 NAG C1303 " pdb=" O5 NAG C1303 " both_signs ideal model delta sigma weight residual False -2.40 -1.95 -0.45 2.00e-01 2.50e+01 4.99e+00 chirality pdb=" CA PHE B 898 " pdb=" N PHE B 898 " pdb=" C PHE B 898 " pdb=" CB PHE B 898 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.04e+00 ... (remaining 5430 not shown) Planarity restraints: 6099 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO B 897 " 0.021 2.00e-02 2.50e+03 4.09e-02 1.67e+01 pdb=" C PRO B 897 " -0.071 2.00e-02 2.50e+03 pdb=" O PRO B 897 " 0.026 2.00e-02 2.50e+03 pdb=" N PHE B 898 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET B 740 " 0.018 2.00e-02 2.50e+03 3.52e-02 1.24e+01 pdb=" C MET B 740 " -0.061 2.00e-02 2.50e+03 pdb=" O MET B 740 " 0.023 2.00e-02 2.50e+03 pdb=" N TYR B 741 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 887 " 0.016 2.00e-02 2.50e+03 3.25e-02 1.05e+01 pdb=" C THR B 887 " -0.056 2.00e-02 2.50e+03 pdb=" O THR B 887 " 0.021 2.00e-02 2.50e+03 pdb=" N PHE B 888 " 0.019 2.00e-02 2.50e+03 ... (remaining 6096 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2777 2.74 - 3.28: 33288 3.28 - 3.82: 52847 3.82 - 4.36: 61784 4.36 - 4.90: 108254 Nonbonded interactions: 258950 Sorted by model distance: nonbonded pdb=" NE2 GLN A 804 " pdb=" OE1 GLN A 935 " model vdw 2.202 3.120 nonbonded pdb=" O GLU C 661 " pdb=" OH TYR C 695 " model vdw 2.206 3.040 nonbonded pdb=" O GLU A 661 " pdb=" OH TYR A 695 " model vdw 2.208 3.040 nonbonded pdb=" OD1 ASN A 282 " pdb=" O3 NAG A1301 " model vdw 2.221 3.040 nonbonded pdb=" O PHE A 329 " pdb=" NE2 GLN A 580 " model vdw 2.222 3.120 ... (remaining 258945 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'H' selection = chain 'P' selection = chain 'Y' } ncs_group { reference = chain 'L' selection = chain 'O' selection = chain 'X' } 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: 2.960 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: 0.030 Extract box with map and model: 0.580 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 32.120 Find NCS groups from input model: 0.890 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 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 : 0.007 0.120 34717 Z= 0.355 Angle : 0.831 10.414 47327 Z= 0.475 Chirality : 0.052 0.467 5433 Planarity : 0.005 0.072 6072 Dihedral : 12.754 89.908 12249 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 0.24 % Allowed : 0.80 % Favored : 98.96 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 6.33 % 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: -1.55 (0.12), residues: 4266 helix: 0.47 (0.20), residues: 657 sheet: -0.40 (0.15), residues: 1194 loop : -1.85 (0.12), residues: 2415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG Y 67 TYR 0.021 0.001 TYR H 211 PHE 0.036 0.002 PHE A 888 TRP 0.020 0.002 TRP C 64 HIS 0.006 0.001 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00660 / 0.35 (34641) covalent geometry : angle 0.81951 / 0.47 (47148) SS BOND : bond 0.00385 / 0.25 ( 49) SS BOND : angle 1.90065 / 1.20 ( 98) hydrogen bonds : bond 0.13937 / 9.38 ( 1321) hydrogen bonds : angle 7.20307 / 5.00 ( 3648) link_NAG-ASN : bond 0.00478 / 0.31 ( 27) link_NAG-ASN : angle 2.80234 / 1.80 ( 81) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8532 Ramachandran restraints generated. 4266 Oldfield, 0 Emsley, 4266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8532 Ramachandran restraints generated. 4266 Oldfield, 0 Emsley, 4266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 3768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 342 time to evaluate : 1.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 244 LEU cc_start: 0.6116 (tp) cc_final: 0.5800 (pt) REVERT: B 740 MET cc_start: 0.8076 (mmt) cc_final: 0.7741 (mmm) REVERT: B 823 PHE cc_start: 0.7491 (m-80) cc_final: 0.7272 (m-80) REVERT: B 902 MET cc_start: 0.8350 (tpt) cc_final: 0.8075 (mmt) REVERT: B 950 ASP cc_start: 0.8412 (p0) cc_final: 0.8106 (p0) REVERT: A 129 LYS cc_start: 0.7191 (tmtt) cc_final: 0.6730 (tptp) REVERT: A 237 ARG cc_start: 0.7839 (ptm-80) cc_final: 0.7277 (mtm110) REVERT: A 399 SER cc_start: 0.6735 (m) cc_final: 0.6517 (m) REVERT: A 400 PHE cc_start: 0.7566 (p90) cc_final: 0.7226 (p90) REVERT: A 983 ARG cc_start: 0.7999 (ttp80) cc_final: 0.7603 (ptt90) REVERT: A 1001 LEU cc_start: 0.8444 (pp) cc_final: 0.8205 (tp) REVERT: A 1142 GLN cc_start: 0.7953 (mm-40) cc_final: 0.7503 (tt0) REVERT: C 215 ASP cc_start: 0.6659 (OUTLIER) cc_final: 0.6329 (t70) REVERT: C 287 ASP cc_start: 0.7961 (t0) cc_final: 0.7480 (m-30) REVERT: C 740 MET cc_start: 0.8530 (tpt) cc_final: 0.8171 (mtt) REVERT: H 30 ASP cc_start: 0.7664 (m-30) cc_final: 0.7162 (m-30) REVERT: H 60 TYR cc_start: 0.5903 (m-80) cc_final: 0.5634 (m-80) REVERT: O 94 MET cc_start: 0.4423 (tmm) cc_final: 0.4105 (tmm) REVERT: P 39 GLN cc_start: 0.6466 (tm-30) cc_final: 0.6253 (tt0) REVERT: P 46 GLU cc_start: 0.4539 (mm-30) cc_final: 0.4312 (pp20) REVERT: P 65 LYS cc_start: 0.3520 (tttt) cc_final: 0.2427 (mttt) REVERT: P 98 LYS cc_start: 0.3970 (ptmt) cc_final: 0.3348 (mmtp) REVERT: P 102 MET cc_start: 0.6825 (ppp) cc_final: 0.5352 (mpp) REVERT: P 132 SER cc_start: 0.5232 (OUTLIER) cc_final: 0.5002 (t) REVERT: X 31 HIS cc_start: 0.6544 (t70) cc_final: 0.6016 (t70) REVERT: X 101 PHE cc_start: 0.7332 (m-10) cc_final: 0.7073 (m-10) REVERT: Y 31 ASP cc_start: 0.8754 (m-30) cc_final: 0.8532 (t70) REVERT: Y 227 LYS cc_start: 0.3225 (tmtt) cc_final: 0.2772 (ttmt) outliers start: 9 outliers final: 1 residues processed: 349 average time/residue: 0.2165 time to fit residues: 125.0635 Evaluate side-chains 220 residues out of total 3768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 217 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain P residue 132 SER Chi-restraints excluded: chain Y residue 201 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 197 optimal weight: 3.9990 chunk 388 optimal weight: 50.0000 chunk 215 optimal weight: 0.0770 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 1.9990 chunk 401 optimal weight: 30.0000 chunk 424 optimal weight: 8.9990 chunk 155 optimal weight: 0.4980 overall best weight: 1.5144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 804 GLN B 935 GLN A 394 ASN A 450 ASN A 487 ASN A 658 ASN A 751 ASN A 804 GLN A 907 ASN C 762 GLN L 31 HIS ** O 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 172 ASN Y 35 HIS ** Y 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4440 r_free = 0.4440 target = 0.187527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.122239 restraints weight = 58414.762| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 4.45 r_work: 0.3203 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.1121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 34717 Z= 0.149 Angle : 0.643 9.747 47327 Z= 0.329 Chirality : 0.047 0.383 5433 Planarity : 0.005 0.052 6072 Dihedral : 5.032 33.365 4633 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 0.61 % Allowed : 6.23 % Favored : 93.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.33 % 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: -1.18 (0.13), residues: 4266 helix: 1.19 (0.20), residues: 655 sheet: -0.33 (0.15), residues: 1210 loop : -1.64 (0.12), residues: 2401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG P 72 TYR 0.026 0.001 TYR Y 162 PHE 0.032 0.002 PHE B 168 TRP 0.013 0.001 TRP C 64 HIS 0.005 0.001 HIS B1058 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.15 (34641) covalent geometry : angle 0.62934 / 0.33 (47148) SS BOND : bond 0.00447 / 0.30 ( 49) SS BOND : angle 1.78818 / 1.16 ( 98) hydrogen bonds : bond 0.05036 / 3.33 ( 1321) hydrogen bonds : angle 5.86101 / 4.05 ( 3648) link_NAG-ASN : bond 0.00407 / 0.27 ( 27) link_NAG-ASN : angle 2.69079 / 1.76 ( 81) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8532 Ramachandran restraints generated. 4266 Oldfield, 0 Emsley, 4266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8532 Ramachandran restraints generated. 4266 Oldfield, 0 Emsley, 4266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 3768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 240 time to evaluate : 1.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 244 LEU cc_start: 0.6209 (tp) cc_final: 0.5807 (pt) REVERT: B 823 PHE cc_start: 0.8168 (m-80) cc_final: 0.7857 (m-80) REVERT: B 902 MET cc_start: 0.8761 (tpt) cc_final: 0.8459 (mmt) REVERT: B 981 LEU cc_start: 0.8427 (OUTLIER) cc_final: 0.8141 (mm) REVERT: A 129 LYS cc_start: 0.7421 (tmtt) cc_final: 0.7025 (tmtt) REVERT: A 237 ARG cc_start: 0.7800 (ptm-80) cc_final: 0.7248 (mtm110) REVERT: A 399 SER cc_start: 0.6715 (m) cc_final: 0.6435 (m) REVERT: A 400 PHE cc_start: 0.7553 (p90) cc_final: 0.7178 (p90) REVERT: A 974 SER cc_start: 0.9093 (t) cc_final: 0.8843 (t) REVERT: A 1001 LEU cc_start: 0.8388 (pp) cc_final: 0.8087 (tp) REVERT: A 1142 GLN cc_start: 0.7951 (mm-40) cc_final: 0.7483 (tt0) REVERT: C 287 ASP cc_start: 0.8586 (t0) cc_final: 0.7563 (m-30) REVERT: C 598 ILE cc_start: 0.8712 (pt) cc_final: 0.8511 (pt) REVERT: C 740 MET cc_start: 0.9011 (tpt) cc_final: 0.8209 (mtt) REVERT: L 123 PHE cc_start: 0.4378 (m-80) cc_final: 0.4022 (m-80) REVERT: H 32 TYR cc_start: 0.6928 (m-10) cc_final: 0.6528 (m-80) REVERT: H 60 TYR cc_start: 0.5783 (m-80) cc_final: 0.5484 (m-80) REVERT: P 46 GLU cc_start: 0.4647 (mm-30) cc_final: 0.4373 (pp20) REVERT: P 65 LYS cc_start: 0.2610 (tttt) cc_final: 0.1820 (mttt) REVERT: P 98 LYS cc_start: 0.4270 (ptmt) cc_final: 0.3560 (mmtp) REVERT: P 102 MET cc_start: 0.6885 (ppp) cc_final: 0.5464 (mpp) REVERT: X 31 HIS cc_start: 0.6426 (t70) cc_final: 0.6004 (t-90) REVERT: X 101 PHE cc_start: 0.7168 (m-10) cc_final: 0.6899 (m-10) REVERT: Y 30 ASP cc_start: 0.7585 (m-30) cc_final: 0.7360 (m-30) REVERT: Y 31 ASP cc_start: 0.8919 (m-30) cc_final: 0.8561 (t70) REVERT: Y 83 MET cc_start: 0.3326 (mpp) cc_final: 0.3103 (mpp) outliers start: 23 outliers final: 14 residues processed: 257 average time/residue: 0.2153 time to fit residues: 91.4526 Evaluate side-chains 221 residues out of total 3768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 206 time to evaluate : 1.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 155 LEU Chi-restraints excluded: chain Y residue 102 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 17 optimal weight: 10.0000 chunk 380 optimal weight: 0.6980 chunk 415 optimal weight: 30.0000 chunk 326 optimal weight: 9.9990 chunk 100 optimal weight: 10.0000 chunk 7 optimal weight: 0.7980 chunk 253 optimal weight: 4.9990 chunk 133 optimal weight: 9.9990 chunk 229 optimal weight: 0.7980 chunk 120 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 422 ASN ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 804 GLN B 935 GLN A 394 ASN A 949 GLN H 77 ASN Y 209 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4427 r_free = 0.4427 target = 0.184435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.119850 restraints weight = 58819.052| |-----------------------------------------------------------------------------| r_work (start): 0.3590 rms_B_bonded: 4.39 r_work: 0.3214 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.3072 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.1511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 34717 Z= 0.128 Angle : 0.594 10.432 47327 Z= 0.303 Chirality : 0.046 0.300 5433 Planarity : 0.004 0.049 6072 Dihedral : 4.709 28.981 4629 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 1.09 % Allowed : 8.92 % Favored : 89.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.33 % 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: -0.98 (0.13), residues: 4266 helix: 1.37 (0.20), residues: 658 sheet: -0.21 (0.15), residues: 1213 loop : -1.51 (0.12), residues: 2395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 24 TYR 0.029 0.001 TYR O 54 PHE 0.030 0.001 PHE B 168 TRP 0.032 0.001 TRP L 40 HIS 0.006 0.001 HIS C1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 (34641) covalent geometry : angle 0.58134 / 0.30 (47148) SS BOND : bond 0.00405 / 0.28 ( 49) SS BOND : angle 1.62471 / 1.12 ( 98) hydrogen bonds : bond 0.04545 / 3.00 ( 1321) hydrogen bonds : angle 5.48493 / 3.78 ( 3648) link_NAG-ASN : bond 0.00426 / 0.28 ( 27) link_NAG-ASN : angle 2.46196 / 1.62 ( 81) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8532 Ramachandran restraints generated. 4266 Oldfield, 0 Emsley, 4266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8532 Ramachandran restraints generated. 4266 Oldfield, 0 Emsley, 4266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 3768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 246 time to evaluate : 1.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 200 TYR cc_start: 0.7155 (m-80) cc_final: 0.6892 (m-10) REVERT: B 244 LEU cc_start: 0.6171 (tp) cc_final: 0.5799 (pt) REVERT: B 823 PHE cc_start: 0.8104 (m-80) cc_final: 0.7807 (m-80) REVERT: B 902 MET cc_start: 0.8753 (tpt) cc_final: 0.8460 (tpp) REVERT: A 237 ARG cc_start: 0.7842 (ptm-80) cc_final: 0.7600 (mtp-110) REVERT: A 332 ILE cc_start: 0.7950 (OUTLIER) cc_final: 0.7720 (mp) REVERT: A 399 SER cc_start: 0.6605 (m) cc_final: 0.6327 (m) REVERT: A 400 PHE cc_start: 0.7498 (p90) cc_final: 0.7116 (p90) REVERT: A 957 GLN cc_start: 0.7959 (mm-40) cc_final: 0.7675 (mt0) REVERT: A 974 SER cc_start: 0.9036 (t) cc_final: 0.8691 (t) REVERT: A 983 ARG cc_start: 0.8172 (ttp-170) cc_final: 0.7566 (ptt-90) REVERT: A 1001 LEU cc_start: 0.8290 (pp) cc_final: 0.8078 (tp) REVERT: A 1142 GLN cc_start: 0.7942 (mm-40) cc_final: 0.7515 (tt0) REVERT: C 83 VAL cc_start: 0.8634 (m) cc_final: 0.8428 (p) REVERT: C 287 ASP cc_start: 0.8620 (t0) cc_final: 0.7653 (m-30) REVERT: C 598 ILE cc_start: 0.8737 (pt) cc_final: 0.8524 (pt) REVERT: C 740 MET cc_start: 0.9039 (tpt) cc_final: 0.8246 (mtt) REVERT: C 1031 GLU cc_start: 0.8872 (OUTLIER) cc_final: 0.8411 (mt-10) REVERT: C 1114 ILE cc_start: 0.8847 (tp) cc_final: 0.8594 (mt) REVERT: C 1145 LEU cc_start: 0.7263 (mm) cc_final: 0.7014 (mm) REVERT: L 121 PHE cc_start: 0.5047 (m-80) cc_final: 0.4692 (t80) REVERT: L 139 CYS cc_start: 0.4132 (t) cc_final: 0.3748 (t) REVERT: L 144 PHE cc_start: 0.4200 (p90) cc_final: 0.3707 (p90) REVERT: L 178 TYR cc_start: 0.6127 (m-10) cc_final: 0.5616 (m-80) REVERT: H 32 TYR cc_start: 0.6666 (m-10) cc_final: 0.6445 (m-80) REVERT: H 60 TYR cc_start: 0.5884 (m-80) cc_final: 0.5464 (m-80) REVERT: H 87 ARG cc_start: 0.7048 (tpp-160) cc_final: 0.6788 (mmt180) REVERT: H 114 GLU cc_start: 0.8199 (mt-10) cc_final: 0.7962 (mt-10) REVERT: P 46 GLU cc_start: 0.4717 (mm-30) cc_final: 0.4423 (pp20) REVERT: P 65 LYS cc_start: 0.2603 (tttt) cc_final: 0.1749 (mttt) REVERT: P 98 LYS cc_start: 0.4401 (ptmt) cc_final: 0.3687 (mmtp) REVERT: P 102 MET cc_start: 0.6830 (ppp) cc_final: 0.5326 (mpp) REVERT: X 31 HIS cc_start: 0.6406 (t70) cc_final: 0.6078 (t70) REVERT: X 101 PHE cc_start: 0.7118 (m-10) cc_final: 0.6876 (m-10) REVERT: Y 31 ASP cc_start: 0.8992 (m-30) cc_final: 0.8450 (p0) outliers start: 41 outliers final: 20 residues processed: 274 average time/residue: 0.2111 time to fit residues: 95.8881 Evaluate side-chains 240 residues out of total 3768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 218 time to evaluate : 1.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 442 ASP Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain O residue 54 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 161 optimal weight: 0.6980 chunk 253 optimal weight: 5.9990 chunk 114 optimal weight: 4.9990 chunk 291 optimal weight: 2.9990 chunk 148 optimal weight: 0.9980 chunk 226 optimal weight: 20.0000 chunk 402 optimal weight: 50.0000 chunk 36 optimal weight: 9.9990 chunk 55 optimal weight: 4.9990 chunk 195 optimal weight: 1.9990 chunk 117 optimal weight: 8.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 965 GLN L 31 HIS H 77 ASN Y 3 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.182251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.116844 restraints weight = 58245.407| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 4.47 r_work: 0.3156 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.1793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.104 34717 Z= 0.180 Angle : 0.634 11.532 47327 Z= 0.323 Chirality : 0.047 0.287 5433 Planarity : 0.004 0.052 6072 Dihedral : 4.795 26.662 4629 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 1.84 % Allowed : 10.06 % Favored : 88.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.33 % 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: -0.99 (0.13), residues: 4266 helix: 1.25 (0.20), residues: 652 sheet: -0.16 (0.15), residues: 1193 loop : -1.51 (0.12), residues: 2421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1107 TYR 0.023 0.001 TYR O 54 PHE 0.028 0.002 PHE B 168 TRP 0.019 0.002 TRP H 53 HIS 0.006 0.001 HIS C1058 Details of bonding type rmsd/Z covalent geometry : bond 0.00447 / 0.18 (34641) covalent geometry : angle 0.61926 / 0.32 (47148) SS BOND : bond 0.00458 / 0.29 ( 49) SS BOND : angle 1.94721 / 1.40 ( 98) hydrogen bonds : bond 0.05118 / 3.37 ( 1321) hydrogen bonds : angle 5.50500 / 3.79 ( 3648) link_NAG-ASN : bond 0.00386 / 0.25 ( 27) link_NAG-ASN : angle 2.59690 / 1.72 ( 81) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8532 Ramachandran restraints generated. 4266 Oldfield, 0 Emsley, 4266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8532 Ramachandran restraints generated. 4266 Oldfield, 0 Emsley, 4266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 3768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 231 time to evaluate : 1.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 244 LEU cc_start: 0.6232 (tp) cc_final: 0.5844 (pt) REVERT: B 811 LYS cc_start: 0.7889 (mttm) cc_final: 0.7424 (mttm) REVERT: B 902 MET cc_start: 0.8784 (tpt) cc_final: 0.8453 (tpp) REVERT: A 399 SER cc_start: 0.6634 (m) cc_final: 0.6350 (m) REVERT: A 400 PHE cc_start: 0.7536 (p90) cc_final: 0.7087 (p90) REVERT: A 957 GLN cc_start: 0.8058 (mm-40) cc_final: 0.7774 (mt0) REVERT: A 1001 LEU cc_start: 0.8471 (pp) cc_final: 0.8168 (tp) REVERT: A 1142 GLN cc_start: 0.7990 (mm-40) cc_final: 0.7582 (tt0) REVERT: C 83 VAL cc_start: 0.8631 (m) cc_final: 0.8392 (p) REVERT: C 287 ASP cc_start: 0.8591 (t0) cc_final: 0.7623 (m-30) REVERT: C 740 MET cc_start: 0.8981 (tpt) cc_final: 0.8226 (mtt) REVERT: C 945 LEU cc_start: 0.8328 (OUTLIER) cc_final: 0.8109 (pp) REVERT: C 1031 GLU cc_start: 0.9026 (OUTLIER) cc_final: 0.8355 (mp0) REVERT: C 1114 ILE cc_start: 0.8859 (tp) cc_final: 0.8615 (mt) REVERT: C 1145 LEU cc_start: 0.7198 (mm) cc_final: 0.6894 (mm) REVERT: L 121 PHE cc_start: 0.5050 (m-80) cc_final: 0.4721 (t80) REVERT: L 144 PHE cc_start: 0.4226 (p90) cc_final: 0.3763 (p90) REVERT: L 178 TYR cc_start: 0.5977 (m-10) cc_final: 0.5471 (m-80) REVERT: H 60 TYR cc_start: 0.6231 (m-80) cc_final: 0.5797 (m-80) REVERT: H 114 GLU cc_start: 0.8133 (mt-10) cc_final: 0.7933 (mt-10) REVERT: H 117 MET cc_start: 0.3777 (OUTLIER) cc_final: 0.2529 (mmm) REVERT: P 54 ASN cc_start: 0.4939 (p0) cc_final: 0.4704 (p0) REVERT: P 65 LYS cc_start: 0.2517 (tttt) cc_final: 0.1695 (mttt) REVERT: P 98 LYS cc_start: 0.4312 (ptmt) cc_final: 0.3627 (mmmt) REVERT: P 102 MET cc_start: 0.7023 (ppp) cc_final: 0.5613 (mpp) REVERT: P 112 ASP cc_start: 0.3909 (m-30) cc_final: 0.3625 (p0) REVERT: X 31 HIS cc_start: 0.6305 (t70) cc_final: 0.5998 (t70) REVERT: X 101 PHE cc_start: 0.7158 (m-10) cc_final: 0.6873 (m-10) REVERT: Y 31 ASP cc_start: 0.8989 (m-30) cc_final: 0.8458 (p0) outliers start: 69 outliers final: 39 residues processed: 288 average time/residue: 0.2081 time to fit residues: 100.5789 Evaluate side-chains 255 residues out of total 3768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 213 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 442 ASP Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 773 GLU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 945 LEU Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 117 MET Chi-restraints excluded: chain H residue 120 TRP Chi-restraints excluded: chain O residue 54 TYR Chi-restraints excluded: chain O residue 159 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 1 optimal weight: 0.9990 chunk 315 optimal weight: 40.0000 chunk 169 optimal weight: 0.6980 chunk 350 optimal weight: 10.0000 chunk 208 optimal weight: 6.9990 chunk 9 optimal weight: 4.9990 chunk 68 optimal weight: 0.9980 chunk 137 optimal weight: 6.9990 chunk 159 optimal weight: 0.9980 chunk 383 optimal weight: 10.0000 chunk 52 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 774 GLN A 321 GLN A 414 GLN L 31 HIS H 77 ASN ** P 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4438 r_free = 0.4438 target = 0.186994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.119785 restraints weight = 58498.489| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 3.96 r_work: 0.3225 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.1992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 34717 Z= 0.119 Angle : 0.577 12.643 47327 Z= 0.293 Chirality : 0.045 0.254 5433 Planarity : 0.004 0.049 6072 Dihedral : 4.474 31.707 4629 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 1.86 % Allowed : 10.92 % Favored : 87.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.83 (0.13), residues: 4266 helix: 1.51 (0.20), residues: 654 sheet: -0.19 (0.15), residues: 1232 loop : -1.37 (0.13), residues: 2380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 237 TYR 0.024 0.001 TYR O 54 PHE 0.027 0.001 PHE B 168 TRP 0.013 0.001 TRP H 53 HIS 0.005 0.001 HIS C1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 (34641) covalent geometry : angle 0.56454 / 0.29 (47148) SS BOND : bond 0.00370 / 0.23 ( 49) SS BOND : angle 1.73138 / 1.16 ( 98) hydrogen bonds : bond 0.04314 / 2.84 ( 1321) hydrogen bonds : angle 5.20983 / 3.58 ( 3648) link_NAG-ASN : bond 0.00417 / 0.27 ( 27) link_NAG-ASN : angle 2.35114 / 1.53 ( 81) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8532 Ramachandran restraints generated. 4266 Oldfield, 0 Emsley, 4266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8532 Ramachandran restraints generated. 4266 Oldfield, 0 Emsley, 4266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 3768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 234 time to evaluate : 1.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 244 LEU cc_start: 0.6169 (tp) cc_final: 0.5821 (pt) REVERT: B 811 LYS cc_start: 0.7857 (mttm) cc_final: 0.7400 (mttm) REVERT: B 902 MET cc_start: 0.8739 (tpt) cc_final: 0.8441 (tpp) REVERT: A 301 CYS cc_start: 0.8322 (OUTLIER) cc_final: 0.7992 (m) REVERT: A 400 PHE cc_start: 0.7532 (p90) cc_final: 0.7096 (p90) REVERT: A 957 GLN cc_start: 0.8004 (mm-40) cc_final: 0.7752 (mt0) REVERT: A 983 ARG cc_start: 0.8026 (ttp-170) cc_final: 0.7672 (ptt-90) REVERT: A 1142 GLN cc_start: 0.8098 (mm-40) cc_final: 0.7685 (tt0) REVERT: C 83 VAL cc_start: 0.8628 (m) cc_final: 0.8409 (p) REVERT: C 287 ASP cc_start: 0.8626 (t0) cc_final: 0.7681 (m-30) REVERT: C 598 ILE cc_start: 0.8749 (pt) cc_final: 0.8524 (pt) REVERT: C 740 MET cc_start: 0.8955 (tpt) cc_final: 0.8212 (mtt) REVERT: C 945 LEU cc_start: 0.8087 (OUTLIER) cc_final: 0.7682 (pt) REVERT: C 1031 GLU cc_start: 0.8896 (OUTLIER) cc_final: 0.8311 (mp0) REVERT: C 1061 VAL cc_start: 0.9063 (OUTLIER) cc_final: 0.8795 (m) REVERT: C 1114 ILE cc_start: 0.8819 (tp) cc_final: 0.8585 (mt) REVERT: C 1145 LEU cc_start: 0.7233 (mm) cc_final: 0.6913 (mm) REVERT: L 121 PHE cc_start: 0.5077 (m-80) cc_final: 0.4729 (t80) REVERT: L 144 PHE cc_start: 0.4192 (p90) cc_final: 0.3729 (p90) REVERT: L 178 TYR cc_start: 0.6063 (m-10) cc_final: 0.5532 (m-80) REVERT: H 32 TYR cc_start: 0.6817 (m-80) cc_final: 0.6269 (m-80) REVERT: H 60 TYR cc_start: 0.6290 (m-80) cc_final: 0.5781 (m-80) REVERT: H 114 GLU cc_start: 0.8135 (mt-10) cc_final: 0.7921 (mt-10) REVERT: H 117 MET cc_start: 0.3493 (OUTLIER) cc_final: 0.2199 (mmm) REVERT: P 65 LYS cc_start: 0.2155 (tttt) cc_final: 0.1342 (mttt) REVERT: P 98 LYS cc_start: 0.4306 (ptmt) cc_final: 0.3622 (mmmt) REVERT: P 102 MET cc_start: 0.7117 (ppp) cc_final: 0.5714 (mpp) REVERT: P 112 ASP cc_start: 0.3994 (m-30) cc_final: 0.3732 (p0) REVERT: X 31 HIS cc_start: 0.6331 (t70) cc_final: 0.6054 (t70) REVERT: X 101 PHE cc_start: 0.7167 (m-10) cc_final: 0.6961 (m-10) REVERT: Y 31 ASP cc_start: 0.8948 (m-30) cc_final: 0.8409 (p0) outliers start: 70 outliers final: 47 residues processed: 290 average time/residue: 0.2053 time to fit residues: 100.5130 Evaluate side-chains 265 residues out of total 3768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 213 time to evaluate : 1.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 762 GLN Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 442 ASP Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 773 GLU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 945 LEU Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1061 VAL Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 139 CYS Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 77 ASN Chi-restraints excluded: chain H residue 117 MET Chi-restraints excluded: chain H residue 120 TRP Chi-restraints excluded: chain O residue 54 TYR Chi-restraints excluded: chain O residue 88 VAL Chi-restraints excluded: chain O residue 92 TYR Chi-restraints excluded: chain O residue 159 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 76 optimal weight: 0.9990 chunk 275 optimal weight: 0.9990 chunk 56 optimal weight: 7.9990 chunk 137 optimal weight: 5.9990 chunk 20 optimal weight: 0.8980 chunk 108 optimal weight: 10.0000 chunk 281 optimal weight: 1.9990 chunk 192 optimal weight: 3.9990 chunk 9 optimal weight: 7.9990 chunk 220 optimal weight: 6.9990 chunk 70 optimal weight: 4.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 77 ASN ** P 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 209 GLN ** 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 = 0.4429 r_free = 0.4429 target = 0.186100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.120150 restraints weight = 57959.353| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 4.30 r_work: 0.3174 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.2105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 34717 Z= 0.147 Angle : 0.595 12.822 47327 Z= 0.301 Chirality : 0.046 0.255 5433 Planarity : 0.004 0.048 6072 Dihedral : 4.501 31.502 4629 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 2.21 % Allowed : 11.47 % Favored : 86.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.81 (0.13), residues: 4266 helix: 1.46 (0.20), residues: 655 sheet: -0.11 (0.15), residues: 1197 loop : -1.38 (0.12), residues: 2414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B1107 TYR 0.021 0.001 TYR O 54 PHE 0.025 0.001 PHE B 168 TRP 0.013 0.001 TRP H 120 HIS 0.004 0.001 HIS C1058 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.15 (34641) covalent geometry : angle 0.58197 / 0.30 (47148) SS BOND : bond 0.00424 / 0.26 ( 49) SS BOND : angle 1.77032 / 1.20 ( 98) hydrogen bonds : bond 0.04566 / 3.01 ( 1321) hydrogen bonds : angle 5.20682 / 3.58 ( 3648) link_NAG-ASN : bond 0.00375 / 0.24 ( 27) link_NAG-ASN : angle 2.39827 / 1.57 ( 81) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8532 Ramachandran restraints generated. 4266 Oldfield, 0 Emsley, 4266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8532 Ramachandran restraints generated. 4266 Oldfield, 0 Emsley, 4266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 3768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 222 time to evaluate : 1.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 244 LEU cc_start: 0.6148 (tp) cc_final: 0.5791 (pt) REVERT: B 811 LYS cc_start: 0.7814 (mttm) cc_final: 0.7603 (mttm) REVERT: B 902 MET cc_start: 0.8776 (tpt) cc_final: 0.8463 (tpp) REVERT: A 301 CYS cc_start: 0.8351 (OUTLIER) cc_final: 0.8027 (m) REVERT: A 400 PHE cc_start: 0.7407 (p90) cc_final: 0.6977 (p90) REVERT: A 598 ILE cc_start: 0.8184 (OUTLIER) cc_final: 0.7534 (mt) REVERT: A 957 GLN cc_start: 0.7963 (mm-40) cc_final: 0.7710 (mt0) REVERT: A 983 ARG cc_start: 0.7931 (ttp-170) cc_final: 0.7473 (ptt-90) REVERT: A 1142 GLN cc_start: 0.8069 (mm-40) cc_final: 0.7634 (tt0) REVERT: C 56 LEU cc_start: 0.8307 (OUTLIER) cc_final: 0.7824 (tp) REVERT: C 83 VAL cc_start: 0.8657 (m) cc_final: 0.8406 (p) REVERT: C 287 ASP cc_start: 0.8596 (t0) cc_final: 0.7652 (m-30) REVERT: C 740 MET cc_start: 0.8994 (tpt) cc_final: 0.8213 (mtt) REVERT: C 1031 GLU cc_start: 0.8973 (OUTLIER) cc_final: 0.8325 (mp0) REVERT: C 1061 VAL cc_start: 0.9102 (OUTLIER) cc_final: 0.8807 (m) REVERT: C 1114 ILE cc_start: 0.8812 (tp) cc_final: 0.8574 (mt) REVERT: C 1145 LEU cc_start: 0.7223 (mm) cc_final: 0.6883 (mm) REVERT: L 121 PHE cc_start: 0.5085 (m-80) cc_final: 0.4733 (t80) REVERT: L 144 PHE cc_start: 0.4126 (p90) cc_final: 0.3701 (p90) REVERT: L 178 TYR cc_start: 0.6033 (m-10) cc_final: 0.5448 (m-80) REVERT: H 60 TYR cc_start: 0.6076 (m-80) cc_final: 0.5577 (m-80) REVERT: H 80 TYR cc_start: 0.5653 (m-80) cc_final: 0.5336 (m-10) REVERT: H 87 ARG cc_start: 0.6832 (tpp-160) cc_final: 0.6571 (mmt180) REVERT: H 114 GLU cc_start: 0.8178 (mt-10) cc_final: 0.7970 (mt-10) REVERT: H 117 MET cc_start: 0.3008 (OUTLIER) cc_final: 0.1811 (mmm) REVERT: P 65 LYS cc_start: 0.2146 (tttt) cc_final: 0.1356 (mttt) REVERT: P 98 LYS cc_start: 0.4353 (ptmt) cc_final: 0.3636 (mmmt) REVERT: P 101 GLU cc_start: 0.5003 (mt-10) cc_final: 0.4744 (mt-10) REVERT: P 102 MET cc_start: 0.7017 (ppp) cc_final: 0.5640 (mpp) REVERT: P 112 ASP cc_start: 0.3943 (m-30) cc_final: 0.3640 (p0) REVERT: X 31 HIS cc_start: 0.6316 (t70) cc_final: 0.6059 (t70) REVERT: X 101 PHE cc_start: 0.7087 (m-10) cc_final: 0.6884 (m-10) REVERT: Y 31 ASP cc_start: 0.8927 (m-30) cc_final: 0.8410 (p0) outliers start: 83 outliers final: 56 residues processed: 296 average time/residue: 0.1945 time to fit residues: 96.7790 Evaluate side-chains 269 residues out of total 3768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 207 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 651 ILE Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 762 GLN Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1060 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 442 ASP Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1061 VAL Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 139 CYS Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 117 MET Chi-restraints excluded: chain H residue 120 TRP Chi-restraints excluded: chain O residue 54 TYR Chi-restraints excluded: chain O residue 88 VAL Chi-restraints excluded: chain O residue 92 TYR Chi-restraints excluded: chain O residue 159 LEU 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: 71.5058 > 50: distance: 16 - 146: 16.848 distance: 47 - 150: 33.317 distance: 50 - 147: 26.428 distance: 68 - 132: 30.903 distance: 71 - 129: 13.848 distance: 86 - 113: 26.405 distance: 89 - 110: 22.038 distance: 108 - 110: 21.549 distance: 110 - 111: 17.798 distance: 111 - 112: 48.046 distance: 111 - 114: 38.333 distance: 112 - 113: 12.374 distance: 112 - 117: 42.577 distance: 114 - 115: 41.217 distance: 114 - 116: 38.889 distance: 117 - 118: 11.220 distance: 117 - 241: 28.948 distance: 118 - 119: 25.974 distance: 118 - 121: 25.580 distance: 119 - 120: 18.730 distance: 119 - 129: 21.247 distance: 120 - 238: 5.286 distance: 121 - 122: 9.788 distance: 122 - 123: 9.538 distance: 122 - 124: 12.702 distance: 123 - 125: 15.020 distance: 124 - 126: 10.665 distance: 125 - 127: 10.067 distance: 126 - 127: 19.881 distance: 127 - 128: 19.944 distance: 129 - 130: 33.464 distance: 130 - 133: 13.175 distance: 131 - 132: 9.989 distance: 133 - 134: 13.000 distance: 134 - 135: 11.885 distance: 134 - 136: 15.255 distance: 135 - 137: 14.424 distance: 136 - 138: 13.088 distance: 137 - 139: 11.811 distance: 138 - 139: 19.789 distance: 139 - 140: 16.333 distance: 141 - 142: 3.683 distance: 142 - 143: 26.260 distance: 142 - 145: 14.378 distance: 143 - 144: 37.830 distance: 143 - 147: 20.105 distance: 145 - 146: 22.664 distance: 147 - 148: 39.438 distance: 148 - 149: 22.179 distance: 148 - 151: 41.430 distance: 149 - 150: 26.337 distance: 149 - 155: 31.807 distance: 151 - 152: 40.275 distance: 155 - 156: 43.748 distance: 156 - 157: 6.559 distance: 156 - 159: 19.447 distance: 157 - 158: 10.111 distance: 157 - 164: 9.225 distance: 159 - 160: 32.598 distance: 160 - 161: 15.063 distance: 161 - 162: 19.951 distance: 161 - 163: 16.052 distance: 164 - 165: 7.456 distance: 165 - 166: 26.267 distance: 165 - 168: 11.545 distance: 166 - 167: 51.951 distance: 166 - 169: 16.555 distance: 169 - 170: 14.995 distance: 170 - 171: 31.588 distance: 170 - 173: 47.979 distance: 171 - 172: 26.851 distance: 171 - 177: 12.133 distance: 173 - 174: 3.013 distance: 174 - 175: 16.495 distance: 177 - 178: 9.413 distance: 178 - 179: 21.490 distance: 178 - 181: 7.337 distance: 179 - 180: 33.329 distance: 179 - 186: 46.508 distance: 181 - 182: 37.682 distance: 182 - 183: 40.816 distance: 183 - 184: 39.941 distance: 183 - 185: 36.041 distance: 186 - 187: 8.089 distance: 187 - 188: 26.966 distance: 187 - 190: 50.411 distance: 188 - 189: 54.417 distance: 188 - 193: 30.979 distance: 190 - 191: 10.510 distance: 190 - 192: 30.523