Starting phenix.real_space_refine on Sun Jan 26 13:56:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v0o_42863/01_2025/8v0o_42863.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v0o_42863/01_2025/8v0o_42863.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8v0o_42863/01_2025/8v0o_42863.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v0o_42863/01_2025/8v0o_42863.map" model { file = "/net/cci-nas-00/data/ceres_data/8v0o_42863/01_2025/8v0o_42863.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v0o_42863/01_2025/8v0o_42863.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.046 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 114 5.16 5 C 15861 2.51 5 N 4074 2.21 5 O 4830 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 35 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 24879 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 8069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1035, 8069 Classifications: {'peptide': 1035} Link IDs: {'PTRANS': 51, 'TRANS': 983} Chain breaks: 7 Chain: "B" Number of atoms: 8069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1035, 8069 Classifications: {'peptide': 1035} Link IDs: {'PTRANS': 51, 'TRANS': 983} Chain breaks: 7 Chain: "C" Number of atoms: 8069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1035, 8069 Classifications: {'peptide': 1035} Link IDs: {'PTRANS': 51, 'TRANS': 983} Chain breaks: 7 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 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 dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Time building chain proxies: 14.16, per 1000 atoms: 0.57 Number of scatterers: 24879 At special positions: 0 Unit cell: (138.24, 131.76, 173.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 114 16.00 O 4830 8.00 N 4074 7.00 C 15861 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=40, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A 840 " - pdb=" SG CYS A 851 " distance=2.04 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.05 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=2.04 Simple disulfide: pdb=" SG CYS B 840 " - pdb=" SG CYS B 851 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 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=2.02 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C 840 " - pdb=" SG CYS C 851 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 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=1, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 282 " " NAG A1303 " - " ASN A 331 " " NAG A1304 " - " ASN A 343 " " NAG A1305 " - " ASN A 616 " " NAG A1306 " - " ASN A 709 " " NAG A1307 " - " ASN A1074 " " NAG A1308 " - " ASN A1134 " " NAG A1309 " - " ASN A 165 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 165 " " NAG B1303 " - " ASN B 282 " " NAG B1304 " - " ASN B 331 " " NAG B1305 " - " ASN B 343 " " NAG B1306 " - " ASN B 616 " " NAG B1307 " - " ASN B 709 " " NAG B1308 " - " ASN B1074 " " NAG B1309 " - " ASN B1134 " " NAG B1310 " - " ASN B 234 " " NAG C1301 " - " ASN A 234 " " NAG C1302 " - " ASN C 61 " " NAG C1303 " - " ASN C 282 " " NAG C1304 " - " ASN C 331 " " NAG C1305 " - " ASN C 343 " " NAG C1306 " - " ASN C 616 " " NAG C1307 " - " ASN C 709 " " NAG C1308 " - " ASN C1074 " " NAG C1309 " - " ASN C1134 " " NAG C1310 " - " ASN C 165 " " NAG C1311 " - " ASN C 234 " " NAG D 1 " - " ASN A 717 " " NAG E 1 " - " ASN A 801 " " NAG F 1 " - " ASN A1098 " " NAG G 1 " - " ASN B 717 " " NAG H 1 " - " ASN B 801 " " NAG I 1 " - " ASN B1098 " " NAG J 1 " - " ASN C 717 " " NAG K 1 " - " ASN C 801 " " NAG L 1 " - " ASN C1098 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.71 Conformation dependent library (CDL) restraints added in 3.3 seconds 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5814 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 47 sheets defined 25.1% alpha, 22.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.62 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.718A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.946A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 387 removed outlier: 3.793A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.404A pdb=" N SER A 408 " --> pdb=" O ASN A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 422 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.535A pdb=" N LYS A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE A 782 " --> pdb=" O THR A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.916A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 848 through 856 removed outlier: 3.945A pdb=" N ALA A 852 " --> pdb=" O ASP A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 897 through 907 removed outlier: 4.003A pdb=" N ALA A 903 " --> pdb=" O ALA A 899 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASN A 907 " --> pdb=" O ALA A 903 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.542A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.568A pdb=" N GLN A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASP A 950 " --> pdb=" O GLY A 946 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASN A 955 " --> pdb=" O VAL A 951 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU A 959 " --> pdb=" O ASN A 955 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.626A pdb=" N VAL A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL A1033 " --> pdb=" O MET A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 3.978A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.683A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 366 No H-bonds generated for 'chain 'B' and resid 364 through 366' Processing helix chain 'B' and resid 367 through 372 removed outlier: 3.755A pdb=" N PHE B 371 " --> pdb=" O VAL B 367 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA B 372 " --> pdb=" O ILE B 368 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 367 through 372' Processing helix chain 'B' and resid 383 through 387 removed outlier: 3.690A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.101A pdb=" N SER B 408 " --> pdb=" O ASN B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'B' and resid 737 through 743 removed outlier: 3.501A pdb=" N TYR B 741 " --> pdb=" O ASP B 737 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 757 removed outlier: 3.666A pdb=" N GLY B 757 " --> pdb=" O LEU B 753 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 4.134A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.852A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 848 through 855 removed outlier: 3.615A pdb=" N ALA B 852 " --> pdb=" O ASP B 848 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 890 removed outlier: 3.718A pdb=" N ALA B 890 " --> pdb=" O THR B 887 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 910 Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.630A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 947 through 965 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: 3.593A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 3.545A pdb=" N VAL B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL B1033 " --> pdb=" O MET B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 4.652A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 349 through 353 removed outlier: 4.091A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 366 No H-bonds generated for 'chain 'C' and resid 364 through 366' Processing helix chain 'C' and resid 367 through 372 removed outlier: 3.719A pdb=" N PHE C 371 " --> pdb=" O VAL C 367 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ALA C 372 " --> pdb=" O ILE C 368 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 367 through 372' Processing helix chain 'C' and resid 385 through 389 removed outlier: 4.060A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 422 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 757 removed outlier: 3.693A pdb=" N GLY C 757 " --> pdb=" O LEU C 753 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 4.012A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 825 Processing helix chain 'C' and resid 848 through 855 removed outlier: 3.619A pdb=" N ALA C 852 " --> pdb=" O ASP C 848 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 890 removed outlier: 3.578A pdb=" N ALA C 890 " --> pdb=" O THR C 887 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 910 Processing helix chain 'C' and resid 913 through 918 removed outlier: 3.775A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 942 through 946 removed outlier: 4.073A pdb=" N LEU C 945 " --> pdb=" O ALA C 942 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLY C 946 " --> pdb=" O SER C 943 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 942 through 946' Processing helix chain 'C' and resid 947 through 965 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 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.528A pdb=" N VAL C 991 " --> pdb=" O VAL C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 4.265A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 8.048A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ILE A 203 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 4.007A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.785A pdb=" N LEU A 84 " --> pdb=" O PHE A 238 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 101 through 103 Processing sheet with id=AA5, first strand: chain 'A' and resid 130 through 131 removed outlier: 6.824A pdb=" N VAL A 130 " --> pdb=" O THR A 167 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 316 removed outlier: 7.260A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 324 through 325 removed outlier: 6.907A pdb=" N GLU A 324 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 8.831A pdb=" N ASN A 542 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.611A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.991A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 453 Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.228A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.563A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.601A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 712 through 715 removed outlier: 3.746A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 718 through 728 removed outlier: 3.545A pdb=" N SER A 721 " --> pdb=" O THR A1066 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLY A1059 " --> pdb=" O ALA A1056 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.686A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 788 through 790 removed outlier: 5.951A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB9, first strand: chain 'B' and resid 26 through 31 removed outlier: 3.590A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU B 191 " --> pdb=" O LYS B 206 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LYS B 195 " --> pdb=" O LYS B 202 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 8.045A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LEU B 226 " --> pdb=" O ILE B 203 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 48 through 55 removed outlier: 4.072A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.550A pdb=" N GLY B 107 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 118 through 119 removed outlier: 4.286A pdb=" N VAL B 127 " --> pdb=" O LEU B 118 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 319 removed outlier: 7.397A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 325 through 328 removed outlier: 3.561A pdb=" N PHE B 541 " --> pdb=" O GLY B 548 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.533A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS B 378 " --> pdb=" O VAL B 433 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC8, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.742A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 654 through 660 removed outlier: 6.128A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.501A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 8.671A pdb=" N VAL B 656 " --> pdb=" O THR B 696 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 701 through 702 removed outlier: 6.684A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.597A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 718 through 722 Processing sheet with id=AD4, first strand: chain 'B' and resid 718 through 722 removed outlier: 5.886A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.618A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD7, first strand: chain 'C' and resid 27 through 30 removed outlier: 8.212A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS C 206 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE C 197 " --> pdb=" O TYR C 200 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLU C 224 " --> pdb=" O SER C 205 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.670A pdb=" N VAL C 47 " --> pdb=" O TYR C 279 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.917A pdb=" N GLY C 107 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE C 105 " --> pdb=" O GLN C 239 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 311 through 314 removed outlier: 3.549A pdb=" N GLY C 593 " --> pdb=" O PHE C 318 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 311 through 314 removed outlier: 4.058A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N CYS C 649 " --> pdb=" O TYR C 612 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.553A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (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 473 through 474 removed outlier: 3.668A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 538 through 543 removed outlier: 3.548A pdb=" N PHE C 541 " --> pdb=" O GLY C 548 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.166A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.419A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.734A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 718 through 728 removed outlier: 6.143A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.718A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 1120 through 1122 935 hydrogen bonds defined for protein. 2574 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: 11.42 Time building geometry restraints manager: 6.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 7337 1.34 - 1.46: 6726 1.46 - 1.59: 11223 1.59 - 1.72: 1 1.72 - 1.85: 141 Bond restraints: 25428 Sorted by residual: bond pdb=" CG PRO A 561 " pdb=" CD PRO A 561 " ideal model delta sigma weight residual 1.503 1.290 0.213 3.40e-02 8.65e+02 3.94e+01 bond pdb=" C1 NAG A1304 " pdb=" O5 NAG A1304 " ideal model delta sigma weight residual 1.406 1.457 -0.051 2.00e-02 2.50e+03 6.45e+00 bond pdb=" CB PRO A 561 " pdb=" CG PRO A 561 " ideal model delta sigma weight residual 1.492 1.616 -0.124 5.00e-02 4.00e+02 6.11e+00 bond pdb=" C1 NAG A1303 " pdb=" O5 NAG A1303 " ideal model delta sigma weight residual 1.406 1.453 -0.047 2.00e-02 2.50e+03 5.60e+00 bond pdb=" C1 NAG F 2 " pdb=" O5 NAG F 2 " ideal model delta sigma weight residual 1.406 1.453 -0.047 2.00e-02 2.50e+03 5.52e+00 ... (remaining 25423 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.80: 34156 2.80 - 5.60: 372 5.60 - 8.40: 44 8.40 - 11.20: 9 11.20 - 14.00: 3 Bond angle restraints: 34584 Sorted by residual: angle pdb=" N PRO A 561 " pdb=" CD PRO A 561 " pdb=" CG PRO A 561 " ideal model delta sigma weight residual 103.20 89.20 14.00 1.50e+00 4.44e-01 8.71e+01 angle pdb=" CA PRO A 561 " pdb=" N PRO A 561 " pdb=" CD PRO A 561 " ideal model delta sigma weight residual 112.00 99.84 12.16 1.40e+00 5.10e-01 7.54e+01 angle pdb=" C LYS A 113 " pdb=" N THR A 114 " pdb=" CA THR A 114 " ideal model delta sigma weight residual 121.54 132.07 -10.53 1.91e+00 2.74e-01 3.04e+01 angle pdb=" C GLY B 744 " pdb=" N ASP B 745 " pdb=" CA ASP B 745 " ideal model delta sigma weight residual 121.54 132.04 -10.50 1.91e+00 2.74e-01 3.02e+01 angle pdb=" CA TYR B 91 " pdb=" CB TYR B 91 " pdb=" CG TYR B 91 " ideal model delta sigma weight residual 113.90 122.96 -9.06 1.80e+00 3.09e-01 2.53e+01 ... (remaining 34579 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 14177 17.81 - 35.61: 1289 35.61 - 53.42: 229 53.42 - 71.22: 73 71.22 - 89.03: 18 Dihedral angle restraints: 15786 sinusoidal: 6753 harmonic: 9033 Sorted by residual: dihedral pdb=" CA CYS A 617 " pdb=" C CYS A 617 " pdb=" N THR A 618 " pdb=" CA THR A 618 " ideal model delta harmonic sigma weight residual 180.00 142.37 37.63 0 5.00e+00 4.00e-02 5.67e+01 dihedral pdb=" CA TYR B 91 " pdb=" C TYR B 91 " pdb=" N PHE B 92 " pdb=" CA PHE B 92 " ideal model delta harmonic sigma weight residual -180.00 -146.48 -33.52 0 5.00e+00 4.00e-02 4.49e+01 dihedral pdb=" CB CYS B 538 " pdb=" SG CYS B 538 " pdb=" SG CYS B 590 " pdb=" CB CYS B 590 " ideal model delta sinusoidal sigma weight residual -86.00 -28.81 -57.19 1 1.00e+01 1.00e-02 4.40e+01 ... (remaining 15783 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.204: 4063 0.204 - 0.408: 12 0.408 - 0.612: 1 0.612 - 0.817: 0 0.817 - 1.021: 1 Chirality restraints: 4077 Sorted by residual: chirality pdb=" C1 NAG C1311 " pdb=" ND2 ASN C 234 " pdb=" C2 NAG C1311 " pdb=" O5 NAG C1311 " both_signs ideal model delta sigma weight residual False -2.40 -1.38 -1.02 2.00e-01 2.50e+01 2.60e+01 chirality pdb=" C1 NAG A1303 " pdb=" ND2 ASN A 331 " pdb=" C2 NAG A1303 " pdb=" O5 NAG A1303 " both_signs ideal model delta sigma weight residual False -2.40 -1.98 -0.42 2.00e-01 2.50e+01 4.42e+00 chirality pdb=" C2 NAG C1301 " pdb=" C1 NAG C1301 " pdb=" C3 NAG C1301 " pdb=" N2 NAG C1301 " both_signs ideal model delta sigma weight residual False -2.49 -2.10 -0.40 2.00e-01 2.50e+01 3.92e+00 ... (remaining 4074 not shown) Planarity restraints: 4443 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 560 " 0.094 5.00e-02 4.00e+02 1.33e-01 2.81e+01 pdb=" N PRO A 561 " -0.229 5.00e-02 4.00e+02 pdb=" CA PRO A 561 " 0.066 5.00e-02 4.00e+02 pdb=" CD PRO A 561 " 0.068 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 234 " -0.047 2.00e-02 2.50e+03 4.46e-02 2.49e+01 pdb=" CG ASN C 234 " 0.054 2.00e-02 2.50e+03 pdb=" OD1 ASN C 234 " -0.011 2.00e-02 2.50e+03 pdb=" ND2 ASN C 234 " 0.051 2.00e-02 2.50e+03 pdb=" C1 NAG C1311 " -0.047 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 126 " 0.019 2.00e-02 2.50e+03 3.75e-02 1.41e+01 pdb=" C VAL A 126 " -0.065 2.00e-02 2.50e+03 pdb=" O VAL A 126 " 0.024 2.00e-02 2.50e+03 pdb=" N VAL A 127 " 0.022 2.00e-02 2.50e+03 ... (remaining 4440 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 5565 2.79 - 3.32: 19863 3.32 - 3.85: 39296 3.85 - 4.37: 44483 4.37 - 4.90: 81111 Nonbonded interactions: 190318 Sorted by model distance: nonbonded pdb=" OG1 THR B 415 " pdb=" OD1 ASP B 420 " model vdw 2.264 3.040 nonbonded pdb=" O ALA C 879 " pdb=" OG1 THR C 883 " model vdw 2.297 3.040 nonbonded pdb=" O GLY A 880 " pdb=" OG SER A 884 " model vdw 2.305 3.040 nonbonded pdb=" OE1 GLU C 819 " pdb=" OG SER C1055 " model vdw 2.306 3.040 nonbonded pdb=" OH TYR A 37 " pdb=" O LEU A 54 " model vdw 2.326 3.040 ... (remaining 190313 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 24 through 1147 or resid 1301 through 1309)) selection = (chain 'C' and (resid 24 through 1147 or resid 1301 through 1309)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 1.040 Check model and map are aligned: 0.190 Set scattering table: 0.220 Process input model: 56.250 Find NCS groups from input model: 1.470 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.213 25428 Z= 0.312 Angle : 0.767 14.002 34584 Z= 0.411 Chirality : 0.056 1.021 4077 Planarity : 0.006 0.133 4404 Dihedral : 14.089 89.030 9852 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.68 % Favored : 95.26 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.14), residues: 3057 helix: -0.84 (0.17), residues: 697 sheet: -0.12 (0.19), residues: 700 loop : -1.74 (0.14), residues: 1660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 64 HIS 0.005 0.001 HIS C 519 PHE 0.023 0.002 PHE C 906 TYR 0.030 0.001 TYR B 170 ARG 0.014 0.001 ARG A 319 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 235 time to evaluate : 2.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 646 ARG cc_start: 0.7957 (ttt90) cc_final: 0.7689 (ttt180) REVERT: A 1041 ASP cc_start: 0.8062 (m-30) cc_final: 0.7854 (m-30) REVERT: B 438 SER cc_start: 0.8719 (p) cc_final: 0.8503 (p) REVERT: B 449 TYR cc_start: 0.8078 (m-80) cc_final: 0.7724 (m-80) REVERT: B 568 ASP cc_start: 0.7705 (t0) cc_final: 0.7470 (t0) REVERT: B 1139 ASP cc_start: 0.8057 (t70) cc_final: 0.7786 (t0) REVERT: C 281 GLU cc_start: 0.7787 (pm20) cc_final: 0.7460 (pm20) outliers start: 0 outliers final: 0 residues processed: 235 average time/residue: 0.3814 time to fit residues: 143.2853 Evaluate side-chains 191 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 191 time to evaluate : 2.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 260 optimal weight: 0.7980 chunk 234 optimal weight: 0.9990 chunk 129 optimal weight: 5.9990 chunk 80 optimal weight: 0.9990 chunk 157 optimal weight: 0.9990 chunk 125 optimal weight: 4.9990 chunk 242 optimal weight: 9.9990 chunk 93 optimal weight: 2.9990 chunk 147 optimal weight: 0.4980 chunk 180 optimal weight: 2.9990 chunk 280 optimal weight: 3.9990 overall best weight: 0.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 GLN A 339 HIS A 417 ASN C 188 ASN C 218 GLN C1088 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.145112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.106631 restraints weight = 29897.596| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 2.55 r_work: 0.2875 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.0928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 25428 Z= 0.186 Angle : 0.548 10.205 34584 Z= 0.286 Chirality : 0.046 0.381 4077 Planarity : 0.004 0.052 4404 Dihedral : 7.461 59.786 4326 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.02 % Favored : 95.91 % Rotamer: Outliers : 0.45 % Allowed : 5.57 % Favored : 93.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.15), residues: 3057 helix: 0.91 (0.20), residues: 695 sheet: 0.06 (0.20), residues: 692 loop : -1.57 (0.14), residues: 1670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 436 HIS 0.005 0.001 HIS B 207 PHE 0.032 0.001 PHE C 168 TYR 0.026 0.001 TYR C 170 ARG 0.008 0.000 ARG C 567 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 209 time to evaluate : 2.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ARG cc_start: 0.7287 (mmt-90) cc_final: 0.7012 (tpp-160) REVERT: A 383 SER cc_start: 0.8692 (m) cc_final: 0.8473 (t) REVERT: A 646 ARG cc_start: 0.8154 (ttt90) cc_final: 0.7885 (ttt180) REVERT: A 1041 ASP cc_start: 0.8508 (m-30) cc_final: 0.8302 (m-30) REVERT: B 438 SER cc_start: 0.8836 (p) cc_final: 0.8603 (p) REVERT: B 449 TYR cc_start: 0.8257 (m-80) cc_final: 0.7884 (m-80) REVERT: B 568 ASP cc_start: 0.8012 (t0) cc_final: 0.7669 (t0) REVERT: B 935 GLN cc_start: 0.7213 (OUTLIER) cc_final: 0.6963 (tt0) REVERT: B 1139 ASP cc_start: 0.8174 (t70) cc_final: 0.7705 (t0) REVERT: C 781 VAL cc_start: 0.8377 (t) cc_final: 0.8067 (t) REVERT: C 1029 MET cc_start: 0.8822 (tpp) cc_final: 0.8510 (ttm) outliers start: 12 outliers final: 6 residues processed: 214 average time/residue: 0.3616 time to fit residues: 125.8656 Evaluate side-chains 199 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 192 time to evaluate : 2.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 441 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 266 optimal weight: 3.9990 chunk 244 optimal weight: 10.0000 chunk 173 optimal weight: 3.9990 chunk 138 optimal weight: 8.9990 chunk 254 optimal weight: 0.4980 chunk 57 optimal weight: 7.9990 chunk 68 optimal weight: 1.9990 chunk 126 optimal weight: 0.0470 chunk 107 optimal weight: 9.9990 chunk 86 optimal weight: 2.9990 chunk 219 optimal weight: 0.5980 overall best weight: 1.2282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 188 ASN C 405 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.143054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.104537 restraints weight = 29937.570| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 2.56 r_work: 0.2827 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.1279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 25428 Z= 0.227 Angle : 0.535 9.985 34584 Z= 0.277 Chirality : 0.046 0.352 4077 Planarity : 0.004 0.044 4404 Dihedral : 7.108 59.999 4326 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.19 % Favored : 95.75 % Rotamer: Outliers : 0.97 % Allowed : 7.94 % Favored : 91.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.15), residues: 3057 helix: 1.49 (0.20), residues: 683 sheet: 0.21 (0.20), residues: 681 loop : -1.49 (0.14), residues: 1693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 436 HIS 0.004 0.001 HIS B1048 PHE 0.022 0.001 PHE A 906 TYR 0.020 0.001 TYR B 91 ARG 0.008 0.000 ARG C 567 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 224 time to evaluate : 2.902 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 239 GLN cc_start: 0.8138 (mt0) cc_final: 0.7809 (mm-40) REVERT: A 383 SER cc_start: 0.8721 (m) cc_final: 0.8472 (t) REVERT: A 460 LYS cc_start: 0.8529 (mttp) cc_final: 0.8326 (mttp) REVERT: A 646 ARG cc_start: 0.8225 (ttt90) cc_final: 0.7976 (ttt180) REVERT: A 854 LYS cc_start: 0.8269 (OUTLIER) cc_final: 0.7906 (tmtt) REVERT: A 1092 GLU cc_start: 0.8407 (tp30) cc_final: 0.7858 (pt0) REVERT: B 207 HIS cc_start: 0.7667 (m-70) cc_final: 0.7396 (m90) REVERT: B 438 SER cc_start: 0.8889 (p) cc_final: 0.8657 (p) REVERT: B 449 TYR cc_start: 0.8255 (m-80) cc_final: 0.7993 (m-80) REVERT: B 467 ASP cc_start: 0.7858 (t70) cc_final: 0.7604 (t0) REVERT: B 568 ASP cc_start: 0.8123 (t0) cc_final: 0.7743 (t0) REVERT: B 586 ASP cc_start: 0.8451 (m-30) cc_final: 0.8213 (m-30) REVERT: B 904 TYR cc_start: 0.7817 (m-10) cc_final: 0.7562 (m-10) REVERT: B 935 GLN cc_start: 0.7445 (OUTLIER) cc_final: 0.7199 (tt0) REVERT: B 1139 ASP cc_start: 0.8289 (t70) cc_final: 0.7691 (t0) REVERT: C 52 GLN cc_start: 0.8596 (tm-30) cc_final: 0.8236 (tm-30) REVERT: C 568 ASP cc_start: 0.8502 (t0) cc_final: 0.8298 (t0) REVERT: C 755 GLN cc_start: 0.8032 (tm-30) cc_final: 0.7825 (tm-30) REVERT: C 781 VAL cc_start: 0.8595 (t) cc_final: 0.8253 (t) REVERT: C 1029 MET cc_start: 0.8874 (tpp) cc_final: 0.8540 (ttm) outliers start: 26 outliers final: 19 residues processed: 239 average time/residue: 0.3209 time to fit residues: 124.9911 Evaluate side-chains 225 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 204 time to evaluate : 2.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 339 HIS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 854 LYS Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 229 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 25 optimal weight: 3.9990 chunk 164 optimal weight: 0.6980 chunk 32 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 3 optimal weight: 0.9990 chunk 180 optimal weight: 1.9990 chunk 220 optimal weight: 8.9990 chunk 266 optimal weight: 3.9990 chunk 254 optimal weight: 5.9990 chunk 212 optimal weight: 8.9990 chunk 75 optimal weight: 1.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: