Starting phenix.real_space_refine on Sun Jan 26 12:42:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9f9y_50263/01_2025/9f9y_50263.cif Found real_map, /net/cci-nas-00/data/ceres_data/9f9y_50263/01_2025/9f9y_50263.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9f9y_50263/01_2025/9f9y_50263.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9f9y_50263/01_2025/9f9y_50263.map" model { file = "/net/cci-nas-00/data/ceres_data/9f9y_50263/01_2025/9f9y_50263.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9f9y_50263/01_2025/9f9y_50263.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.019 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 108 5.16 5 C 15834 2.51 5 N 4050 2.21 5 O 4818 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 24810 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 8004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1026, 8004 Classifications: {'peptide': 1026} Link IDs: {'PTRANS': 52, 'TRANS': 973} Chain breaks: 6 Chain: "B" Number of atoms: 8004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1026, 8004 Classifications: {'peptide': 1026} Link IDs: {'PTRANS': 52, 'TRANS': 973} Chain breaks: 6 Chain: "C" Number of atoms: 8004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1026, 8004 Classifications: {'peptide': 1026} Link IDs: {'PTRANS': 52, 'TRANS': 973} Chain breaks: 6 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: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "B" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "C" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Time building chain proxies: 14.83, per 1000 atoms: 0.60 Number of scatterers: 24810 At special positions: 0 Unit cell: (128.533, 129.993, 171.62, 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 108 16.00 O 4818 8.00 N 4050 7.00 C 15834 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 117 " - pdb=" SG CYS A 141 " distance=2.03 Simple disulfide: pdb=" SG CYS A 266 " - pdb=" SG CYS A 276 " distance=2.03 Simple disulfide: pdb=" SG CYS A 311 " - pdb=" SG CYS A 336 " distance=2.03 Simple disulfide: pdb=" SG CYS A 354 " - pdb=" SG CYS A 407 " distance=2.03 Simple disulfide: pdb=" SG CYS A 366 " - pdb=" SG CYS A 500 " distance=2.03 Simple disulfide: pdb=" SG CYS A 455 " - pdb=" SG CYS A 463 " distance=2.03 Simple disulfide: pdb=" SG CYS A 513 " - pdb=" SG CYS A 565 " distance=2.03 Simple disulfide: pdb=" SG CYS A 592 " - pdb=" SG CYS A 624 " distance=2.03 Simple disulfide: pdb=" SG CYS A 637 " - pdb=" SG CYS A 646 " distance=2.03 Simple disulfide: pdb=" SG CYS A 713 " - pdb=" SG CYS A 735 " distance=2.03 Simple disulfide: pdb=" SG CYS A 718 " - pdb=" SG CYS A 724 " distance=2.03 Simple disulfide: pdb=" SG CYS A1007 " - pdb=" SG CYS A1018 " distance=2.03 Simple disulfide: pdb=" SG CYS A1057 " - pdb=" SG CYS A1101 " distance=2.03 Simple disulfide: pdb=" SG CYS B 117 " - pdb=" SG CYS B 141 " distance=2.03 Simple disulfide: pdb=" SG CYS B 266 " - pdb=" SG CYS B 276 " distance=2.03 Simple disulfide: pdb=" SG CYS B 311 " - pdb=" SG CYS B 336 " distance=2.03 Simple disulfide: pdb=" SG CYS B 354 " - pdb=" SG CYS B 407 " distance=2.03 Simple disulfide: pdb=" SG CYS B 366 " - pdb=" SG CYS B 500 " distance=2.03 Simple disulfide: pdb=" SG CYS B 455 " - pdb=" SG CYS B 463 " distance=2.03 Simple disulfide: pdb=" SG CYS B 513 " - pdb=" SG CYS B 565 " distance=2.03 Simple disulfide: pdb=" SG CYS B 592 " - pdb=" SG CYS B 624 " distance=2.03 Simple disulfide: pdb=" SG CYS B 637 " - pdb=" SG CYS B 646 " distance=2.03 Simple disulfide: pdb=" SG CYS B 713 " - pdb=" SG CYS B 735 " distance=2.03 Simple disulfide: pdb=" SG CYS B 718 " - pdb=" SG CYS B 724 " distance=2.03 Simple disulfide: pdb=" SG CYS B1007 " - pdb=" SG CYS B1018 " distance=2.03 Simple disulfide: pdb=" SG CYS B1057 " - pdb=" SG CYS B1101 " distance=2.03 Simple disulfide: pdb=" SG CYS C 117 " - pdb=" SG CYS C 141 " distance=2.03 Simple disulfide: pdb=" SG CYS C 266 " - pdb=" SG CYS C 276 " distance=2.03 Simple disulfide: pdb=" SG CYS C 311 " - pdb=" SG CYS C 336 " distance=2.03 Simple disulfide: pdb=" SG CYS C 354 " - pdb=" SG CYS C 407 " distance=2.03 Simple disulfide: pdb=" SG CYS C 366 " - pdb=" SG CYS C 500 " distance=2.03 Simple disulfide: pdb=" SG CYS C 455 " - pdb=" SG CYS C 463 " distance=2.03 Simple disulfide: pdb=" SG CYS C 513 " - pdb=" SG CYS C 565 " distance=2.03 Simple disulfide: pdb=" SG CYS C 592 " - pdb=" SG CYS C 624 " distance=2.03 Simple disulfide: pdb=" SG CYS C 637 " - pdb=" SG CYS C 646 " distance=2.03 Simple disulfide: pdb=" SG CYS C 713 " - pdb=" SG CYS C 735 " distance=2.03 Simple disulfide: pdb=" SG CYS C 718 " - pdb=" SG CYS C 724 " distance=2.03 Simple disulfide: pdb=" SG CYS C1007 " - pdb=" SG CYS C1018 " distance=2.03 Simple disulfide: pdb=" SG CYS C1057 " - pdb=" SG CYS C1101 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " NAG-ASN " NAG A1301 " - " ASN A 49 " " NAG A1302 " - " ASN A 108 " " NAG A1303 " - " ASN A 140 " " NAG A1304 " - " ASN A 163 " " NAG A1305 " - " ASN A 209 " " NAG A1306 " - " ASN A 257 " " NAG A1307 " - " ASN A 306 " " NAG A1308 " - " ASN A 318 " " NAG A1309 " - " ASN A 591 " " NAG A1310 " - " ASN A 632 " " NAG A1311 " - " ASN A 684 " " NAG A1312 " - " ASN A1049 " " NAG A1313 " - " ASN A1109 " " NAG B1301 " - " ASN B 49 " " NAG B1302 " - " ASN B 108 " " NAG B1303 " - " ASN B 140 " " NAG B1304 " - " ASN B 163 " " NAG B1305 " - " ASN B 209 " " NAG B1306 " - " ASN B 257 " " NAG B1307 " - " ASN B 306 " " NAG B1308 " - " ASN B 318 " " NAG B1309 " - " ASN B 591 " " NAG B1310 " - " ASN B 632 " " NAG B1311 " - " ASN B 684 " " NAG B1312 " - " ASN B1049 " " NAG B1313 " - " ASN B1109 " " NAG C1301 " - " ASN C 49 " " NAG C1302 " - " ASN C 108 " " NAG C1303 " - " ASN C 140 " " NAG C1304 " - " ASN C 163 " " NAG C1305 " - " ASN C 209 " " NAG C1306 " - " ASN C 257 " " NAG C1307 " - " ASN C 306 " " NAG C1308 " - " ASN C 318 " " NAG C1309 " - " ASN C 591 " " NAG C1310 " - " ASN C 632 " " NAG C1311 " - " ASN C 684 " " NAG C1312 " - " ASN C1049 " " NAG C1313 " - " ASN C1109 " " NAG D 1 " - " ASN A 692 " " NAG E 1 " - " ASN A 776 " " NAG F 1 " - " ASN A1073 " " NAG G 1 " - " ASN B 692 " " NAG H 1 " - " ASN B 776 " " NAG I 1 " - " ASN B1073 " " NAG J 1 " - " ASN C 692 " " NAG K 1 " - " ASN C 776 " " NAG L 1 " - " ASN C1073 " Time building additional restraints: 6.54 Conformation dependent library (CDL) restraints added in 3.5 seconds 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5748 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 48 sheets defined 29.1% alpha, 25.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.24 Creating SS restraints... Processing helix chain 'A' and resid 269 through 279 Processing helix chain 'A' and resid 312 through 318 removed outlier: 3.532A pdb=" N VAL A 316 " --> pdb=" O PRO A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 328 Processing helix chain 'A' and resid 339 through 346 removed outlier: 3.637A pdb=" N VAL A 342 " --> pdb=" O ASP A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 364 removed outlier: 3.529A pdb=" N LEU A 362 " --> pdb=" O PRO A 359 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N ASN A 363 " --> pdb=" O THR A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 385 removed outlier: 4.233A pdb=" N SER A 383 " --> pdb=" O ASN A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 397 Processing helix chain 'A' and resid 413 through 418 Processing helix chain 'A' and resid 420 through 424 Processing helix chain 'A' and resid 477 through 480 Processing helix chain 'A' and resid 605 through 611 Processing helix chain 'A' and resid 612 through 615 removed outlier: 6.611A pdb=" N SER A 615 " --> pdb=" O SER A 612 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 612 through 615' Processing helix chain 'A' and resid 712 through 719 Processing helix chain 'A' and resid 721 through 729 Processing helix chain 'A' and resid 730 through 732 No H-bonds generated for 'chain 'A' and resid 730 through 732' Processing helix chain 'A' and resid 733 through 758 removed outlier: 3.584A pdb=" N ASP A 750 " --> pdb=" O ALA A 746 " (cutoff:3.500A) Processing helix chain 'A' and resid 791 through 801 Processing helix chain 'A' and resid 825 through 830 Processing helix chain 'A' and resid 841 through 860 Processing helix chain 'A' and resid 861 through 865 Processing helix chain 'A' and resid 872 through 884 Processing helix chain 'A' and resid 887 through 894 removed outlier: 4.079A pdb=" N LEU A 891 " --> pdb=" O THR A 887 " (cutoff:3.500A) Processing helix chain 'A' and resid 894 through 916 removed outlier: 3.934A pdb=" N GLN A 910 " --> pdb=" O ILE A 906 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N GLY A 911 " --> pdb=" O GLY A 907 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N THR A 916 " --> pdb=" O SER A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 920 through 940 removed outlier: 3.608A pdb=" N GLN A 924 " --> pdb=" O LEU A 920 " (cutoff:3.500A) Processing helix chain 'A' and resid 941 through 943 No H-bonds generated for 'chain 'A' and resid 941 through 943' Processing helix chain 'A' and resid 951 through 959 Processing helix chain 'A' and resid 960 through 1008 removed outlier: 4.711A pdb=" N VAL A 966 " --> pdb=" O PRO A 962 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N GLN A 967 " --> pdb=" O GLU A 963 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLY A 974 " --> pdb=" O ARG A 970 " (cutoff:3.500A) Processing helix chain 'A' and resid 1115 through 1122 removed outlier: 4.118A pdb=" N GLU A1119 " --> pdb=" O PRO A1115 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 279 Processing helix chain 'B' and resid 312 through 318 removed outlier: 3.536A pdb=" N VAL B 316 " --> pdb=" O PRO B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 328 Processing helix chain 'B' and resid 339 through 346 removed outlier: 3.633A pdb=" N VAL B 342 " --> pdb=" O ASP B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 364 removed outlier: 3.533A pdb=" N LEU B 362 " --> pdb=" O PRO B 359 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N ASN B 363 " --> pdb=" O THR B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 385 removed outlier: 4.233A pdb=" N SER B 383 " --> pdb=" O ASN B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 397 Processing helix chain 'B' and resid 413 through 418 Processing helix chain 'B' and resid 420 through 424 Processing helix chain 'B' and resid 477 through 480 Processing helix chain 'B' and resid 605 through 611 removed outlier: 3.666A pdb=" N VAL B 610 " --> pdb=" O PRO B 606 " (cutoff:3.500A) Processing helix chain 'B' and resid 612 through 615 removed outlier: 6.454A pdb=" N SER B 615 " --> pdb=" O SER B 612 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 612 through 615' Processing helix chain 'B' and resid 712 through 719 Processing helix chain 'B' and resid 721 through 729 Processing helix chain 'B' and resid 730 through 732 No H-bonds generated for 'chain 'B' and resid 730 through 732' Processing helix chain 'B' and resid 733 through 758 removed outlier: 3.589A pdb=" N ASP B 750 " --> pdb=" O ALA B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 791 through 801 Processing helix chain 'B' and resid 825 through 830 Processing helix chain 'B' and resid 841 through 860 Processing helix chain 'B' and resid 861 through 865 Processing helix chain 'B' and resid 872 through 884 Processing helix chain 'B' and resid 887 through 894 removed outlier: 4.085A pdb=" N LEU B 891 " --> pdb=" O THR B 887 " (cutoff:3.500A) Processing helix chain 'B' and resid 894 through 916 removed outlier: 3.933A pdb=" N GLN B 910 " --> pdb=" O ILE B 906 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N GLY B 911 " --> pdb=" O GLY B 907 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N THR B 916 " --> pdb=" O SER B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 920 through 940 removed outlier: 3.602A pdb=" N GLN B 924 " --> pdb=" O LEU B 920 " (cutoff:3.500A) Processing helix chain 'B' and resid 941 through 943 No H-bonds generated for 'chain 'B' and resid 941 through 943' Processing helix chain 'B' and resid 951 through 959 Processing helix chain 'B' and resid 960 through 1008 removed outlier: 4.730A pdb=" N VAL B 966 " --> pdb=" O PRO B 962 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLN B 967 " --> pdb=" O GLU B 963 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLY B 974 " --> pdb=" O ARG B 970 " (cutoff:3.500A) Processing helix chain 'B' and resid 1115 through 1122 removed outlier: 4.119A pdb=" N GLU B1119 " --> pdb=" O PRO B1115 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 279 Processing helix chain 'C' and resid 312 through 318 removed outlier: 3.537A pdb=" N VAL C 316 " --> pdb=" O PRO C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 328 Processing helix chain 'C' and resid 339 through 346 removed outlier: 3.638A pdb=" N VAL C 342 " --> pdb=" O ASP C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 364 removed outlier: 3.528A pdb=" N LEU C 362 " --> pdb=" O PRO C 359 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N ASN C 363 " --> pdb=" O THR C 360 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 385 removed outlier: 4.233A pdb=" N SER C 383 " --> pdb=" O ASN C 380 " (cutoff:3.500A) Processing helix chain 'C' and resid 391 through 397 Processing helix chain 'C' and resid 413 through 418 Processing helix chain 'C' and resid 420 through 424 Processing helix chain 'C' and resid 477 through 480 Processing helix chain 'C' and resid 605 through 611 removed outlier: 3.659A pdb=" N VAL C 610 " --> pdb=" O PRO C 606 " (cutoff:3.500A) Processing helix chain 'C' and resid 612 through 615 removed outlier: 6.454A pdb=" N SER C 615 " --> pdb=" O SER C 612 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 612 through 615' Processing helix chain 'C' and resid 712 through 719 Processing helix chain 'C' and resid 721 through 729 Processing helix chain 'C' and resid 730 through 732 No H-bonds generated for 'chain 'C' and resid 730 through 732' Processing helix chain 'C' and resid 733 through 758 removed outlier: 3.589A pdb=" N ASP C 750 " --> pdb=" O ALA C 746 " (cutoff:3.500A) Processing helix chain 'C' and resid 791 through 801 Processing helix chain 'C' and resid 825 through 830 Processing helix chain 'C' and resid 841 through 860 Processing helix chain 'C' and resid 861 through 865 Processing helix chain 'C' and resid 872 through 884 Processing helix chain 'C' and resid 887 through 894 removed outlier: 4.092A pdb=" N LEU C 891 " --> pdb=" O THR C 887 " (cutoff:3.500A) Processing helix chain 'C' and resid 894 through 916 removed outlier: 3.933A pdb=" N GLN C 910 " --> pdb=" O ILE C 906 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N GLY C 911 " --> pdb=" O GLY C 907 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N THR C 916 " --> pdb=" O SER C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 920 through 940 removed outlier: 3.603A pdb=" N GLN C 924 " --> pdb=" O LEU C 920 " (cutoff:3.500A) Processing helix chain 'C' and resid 941 through 943 No H-bonds generated for 'chain 'C' and resid 941 through 943' Processing helix chain 'C' and resid 951 through 959 Processing helix chain 'C' and resid 960 through 1008 removed outlier: 4.707A pdb=" N VAL C 966 " --> pdb=" O PRO C 962 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N GLN C 967 " --> pdb=" O GLU C 963 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLY C 974 " --> pdb=" O ARG C 970 " (cutoff:3.500A) Processing helix chain 'C' and resid 1115 through 1122 removed outlier: 4.117A pdb=" N GLU C1119 " --> pdb=" O PRO C1115 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 15 through 18 removed outlier: 8.020A pdb=" N ASN A 49 " --> pdb=" O TYR A 244 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N TYR A 244 " --> pdb=" O ASN A 49 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N SER A 180 " --> pdb=" O PRO A 200 " (cutoff:3.500A) removed outlier: 9.123A pdb=" N HIS A 182 " --> pdb=" O LEU A 198 " (cutoff:3.500A) removed outlier: 9.336A pdb=" N LEU A 198 " --> pdb=" O HIS A 182 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N VAL A 24 " --> pdb=" O LEU A 198 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 35 through 43 removed outlier: 4.031A pdb=" N ASP A 262 " --> pdb=" O LYS A 253 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 70 through 71 Processing sheet with id=AA4, first strand: chain 'A' and resid 118 through 121 removed outlier: 3.550A pdb=" N SER A 137 " --> pdb=" O GLN A 120 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 286 through 294 removed outlier: 4.299A pdb=" N VAL A 570 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N ASN A 292 " --> pdb=" O GLY A 568 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N GLY A 568 " --> pdb=" O ASN A 292 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N GLY A 569 " --> pdb=" O GLN A 588 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 300 through 303 removed outlier: 5.458A pdb=" N ASP A 549 " --> pdb=" O ILE A 562 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N GLY A 541 " --> pdb=" O ASP A 549 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 329 through 333 removed outlier: 3.727A pdb=" N ASN A 369 " --> pdb=" O GLU A 491 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA A 351 " --> pdb=" O ALA A 410 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 336 through 337 removed outlier: 6.686A pdb=" N CYS A 336 " --> pdb=" O CYS A 500 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 427 through 429 Processing sheet with id=AB1, first strand: chain 'A' and resid 448 through 449 Processing sheet with id=AB2, first strand: chain 'A' and resid 628 through 630 removed outlier: 6.024A pdb=" N GLU A 629 " --> pdb=" O ALA A 669 " (cutoff:3.500A) removed outlier: 8.536A pdb=" N THR A 671 " --> pdb=" O GLU A 629 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N ALA A 647 " --> pdb=" O PRO A 640 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 677 through 679 Processing sheet with id=AB4, first strand: chain 'A' and resid 686 through 690 removed outlier: 3.795A pdb=" N ALA A1053 " --> pdb=" O PHE A1070 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N PHE A1070 " --> pdb=" O ALA A1053 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 693 through 703 removed outlier: 6.974A pdb=" N GLY A1034 " --> pdb=" O SER A1030 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N SER A1030 " --> pdb=" O GLY A1034 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N VAL A1036 " --> pdb=" O PRO A1028 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N LEU A1038 " --> pdb=" O SER A1026 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N SER A1026 " --> pdb=" O LEU A1038 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N VAL A1040 " --> pdb=" O LEU A1024 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 708 through 711 removed outlier: 4.464A pdb=" N LYS A 708 " --> pdb=" O LEU A 836 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 763 through 765 removed outlier: 5.848A pdb=" N ILE A 763 " --> pdb=" O ASN B 678 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 1095 through 1097 Processing sheet with id=AB9, first strand: chain 'B' and resid 15 through 18 removed outlier: 8.031A pdb=" N ASN B 49 " --> pdb=" O TYR B 244 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N TYR B 244 " --> pdb=" O ASN B 49 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N SER B 180 " --> pdb=" O PRO B 200 " (cutoff:3.500A) removed outlier: 9.126A pdb=" N HIS B 182 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 9.334A pdb=" N LEU B 198 " --> pdb=" O HIS B 182 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N VAL B 24 " --> pdb=" O LEU B 198 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 35 through 43 removed outlier: 4.026A pdb=" N ASP B 262 " --> pdb=" O LYS B 253 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 70 through 71 Processing sheet with id=AC3, first strand: chain 'B' and resid 118 through 121 removed outlier: 3.545A pdb=" N SER B 137 " --> pdb=" O GLN B 120 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 286 through 294 removed outlier: 4.307A pdb=" N VAL B 570 " --> pdb=" O THR B 290 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N ASN B 292 " --> pdb=" O GLY B 568 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N GLY B 568 " --> pdb=" O ASN B 292 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N GLY B 569 " --> pdb=" O GLN B 588 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 300 through 303 removed outlier: 5.449A pdb=" N ASP B 549 " --> pdb=" O ILE B 562 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N GLY B 541 " --> pdb=" O ASP B 549 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 329 through 333 removed outlier: 3.725A pdb=" N ASN B 369 " --> pdb=" O GLU B 491 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA B 351 " --> pdb=" O ALA B 410 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 336 through 337 removed outlier: 6.689A pdb=" N CYS B 336 " --> pdb=" O CYS B 500 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 427 through 429 Processing sheet with id=AC9, first strand: chain 'B' and resid 448 through 449 Processing sheet with id=AD1, first strand: chain 'B' and resid 628 through 630 removed outlier: 6.028A pdb=" N GLU B 629 " --> pdb=" O ALA B 669 " (cutoff:3.500A) removed outlier: 8.534A pdb=" N THR B 671 " --> pdb=" O GLU B 629 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ILE B 645 " --> pdb=" O ILE B 641 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 686 through 690 removed outlier: 3.834A pdb=" N ALA B1053 " --> pdb=" O PHE B1070 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N PHE B1070 " --> pdb=" O ALA B1053 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 693 through 703 removed outlier: 6.985A pdb=" N GLY B1034 " --> pdb=" O SER B1030 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N SER B1030 " --> pdb=" O GLY B1034 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N VAL B1036 " --> pdb=" O PRO B1028 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N LEU B1038 " --> pdb=" O SER B1026 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N SER B1026 " --> pdb=" O LEU B1038 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N VAL B1040 " --> pdb=" O LEU B1024 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 708 through 711 removed outlier: 4.478A pdb=" N LYS B 708 " --> pdb=" O LEU B 836 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 763 through 765 removed outlier: 5.824A pdb=" N ILE B 763 " --> pdb=" O ASN C 678 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'B' and resid 1095 through 1097 Processing sheet with id=AD7, first strand: chain 'C' and resid 15 through 18 removed outlier: 8.031A pdb=" N ASN C 49 " --> pdb=" O TYR C 244 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N TYR C 244 " --> pdb=" O ASN C 49 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N SER C 180 " --> pdb=" O PRO C 200 " (cutoff:3.500A) removed outlier: 9.137A pdb=" N HIS C 182 " --> pdb=" O LEU C 198 " (cutoff:3.500A) removed outlier: 9.341A pdb=" N LEU C 198 " --> pdb=" O HIS C 182 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N VAL C 24 " --> pdb=" O LEU C 198 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 35 through 43 removed outlier: 4.029A pdb=" N ASP C 262 " --> pdb=" O LYS C 253 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 70 through 71 Processing sheet with id=AE1, first strand: chain 'C' and resid 118 through 121 removed outlier: 3.551A pdb=" N SER C 137 " --> pdb=" O GLN C 120 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 286 through 294 removed outlier: 4.306A pdb=" N VAL C 570 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N ASN C 292 " --> pdb=" O GLY C 568 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N GLY C 568 " --> pdb=" O ASN C 292 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N GLY C 569 " --> pdb=" O GLN C 588 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 300 through 303 removed outlier: 5.453A pdb=" N ASP C 549 " --> pdb=" O ILE C 562 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N GLY C 541 " --> pdb=" O ASP C 549 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 329 through 333 removed outlier: 3.725A pdb=" N ASN C 369 " --> pdb=" O GLU C 491 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA C 351 " --> pdb=" O ALA C 410 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 336 through 337 removed outlier: 6.683A pdb=" N CYS C 336 " --> pdb=" O CYS C 500 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 427 through 429 Processing sheet with id=AE7, first strand: chain 'C' and resid 448 through 449 Processing sheet with id=AE8, first strand: chain 'C' and resid 628 through 630 removed outlier: 6.016A pdb=" N GLU C 629 " --> pdb=" O ALA C 669 " (cutoff:3.500A) removed outlier: 8.528A pdb=" N THR C 671 " --> pdb=" O GLU C 629 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ILE C 645 " --> pdb=" O ILE C 641 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 686 through 690 removed outlier: 3.843A pdb=" N ALA C1053 " --> pdb=" O PHE C1070 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N PHE C1070 " --> pdb=" O ALA C1053 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 693 through 703 removed outlier: 6.992A pdb=" N GLY C1034 " --> pdb=" O SER C1030 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N SER C1030 " --> pdb=" O GLY C1034 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N VAL C1036 " --> pdb=" O PRO C1028 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N LEU C1038 " --> pdb=" O SER C1026 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N SER C1026 " --> pdb=" O LEU C1038 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N VAL C1040 " --> pdb=" O LEU C1024 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 708 through 711 removed outlier: 4.477A pdb=" N LYS C 708 " --> pdb=" O LEU C 836 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 1095 through 1097 1065 hydrogen bonds defined for protein. 2847 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: 13.21 Time building geometry restraints manager: 7.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 7826 1.34 - 1.46: 6034 1.46 - 1.58: 11379 1.58 - 1.69: 0 1.69 - 1.81: 135 Bond restraints: 25374 Sorted by residual: bond pdb=" C1 NAG H 2 " pdb=" O5 NAG H 2 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.17e+00 bond pdb=" C1 NAG B1302 " pdb=" O5 NAG B1302 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.16e+00 bond pdb=" C1 NAG K 2 " pdb=" O5 NAG K 2 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.15e+00 bond pdb=" C1 NAG E 2 " pdb=" O5 NAG E 2 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.10e+00 bond pdb=" C1 NAG B1312 " pdb=" O5 NAG B1312 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.09e+00 ... (remaining 25369 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.32: 33426 1.32 - 2.63: 868 2.63 - 3.95: 201 3.95 - 5.26: 20 5.26 - 6.58: 6 Bond angle restraints: 34521 Sorted by residual: angle pdb=" N ALA C 598 " pdb=" CA ALA C 598 " pdb=" C ALA C 598 " ideal model delta sigma weight residual 111.11 114.11 -3.00 1.20e+00 6.94e-01 6.27e+00 angle pdb=" N ALA B 598 " pdb=" CA ALA B 598 " pdb=" C ALA B 598 " ideal model delta sigma weight residual 111.11 114.04 -2.93 1.20e+00 6.94e-01 5.96e+00 angle pdb=" C SER A 596 " pdb=" N VAL A 597 " pdb=" CA VAL A 597 " ideal model delta sigma weight residual 120.46 123.48 -3.02 1.37e+00 5.33e-01 4.86e+00 angle pdb=" N PRO A 961 " pdb=" CA PRO A 961 " pdb=" C PRO A 961 " ideal model delta sigma weight residual 110.70 113.33 -2.63 1.22e+00 6.72e-01 4.66e+00 angle pdb=" N PRO C 961 " pdb=" CA PRO C 961 " pdb=" C PRO C 961 " ideal model delta sigma weight residual 110.70 113.32 -2.62 1.22e+00 6.72e-01 4.61e+00 ... (remaining 34516 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.58: 15060 17.58 - 35.16: 610 35.16 - 52.73: 93 52.73 - 70.31: 45 70.31 - 87.89: 17 Dihedral angle restraints: 15825 sinusoidal: 6882 harmonic: 8943 Sorted by residual: dihedral pdb=" CA THR B 574 " pdb=" C THR B 574 " pdb=" N PRO B 575 " pdb=" CA PRO B 575 " ideal model delta harmonic sigma weight residual 180.00 160.25 19.75 0 5.00e+00 4.00e-02 1.56e+01 dihedral pdb=" CA THR A 574 " pdb=" C THR A 574 " pdb=" N PRO A 575 " pdb=" CA PRO A 575 " ideal model delta harmonic sigma weight residual 180.00 160.35 19.65 0 5.00e+00 4.00e-02 1.54e+01 dihedral pdb=" CA THR C 574 " pdb=" C THR C 574 " pdb=" N PRO C 575 " pdb=" CA PRO C 575 " ideal model delta harmonic sigma weight residual 180.00 160.36 19.64 0 5.00e+00 4.00e-02 1.54e+01 ... (remaining 15822 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 2350 0.029 - 0.058: 1057 0.058 - 0.087: 319 0.087 - 0.116: 290 0.116 - 0.144: 64 Chirality restraints: 4080 Sorted by residual: chirality pdb=" C1 NAG A1304 " pdb=" ND2 ASN A 163 " pdb=" C2 NAG A1304 " pdb=" O5 NAG A1304 " both_signs ideal model delta sigma weight residual False -2.40 -2.26 -0.14 2.00e-01 2.50e+01 5.22e-01 chirality pdb=" C1 NAG B1304 " pdb=" ND2 ASN B 163 " pdb=" C2 NAG B1304 " pdb=" O5 NAG B1304 " both_signs ideal model delta sigma weight residual False -2.40 -2.26 -0.14 2.00e-01 2.50e+01 5.05e-01 chirality pdb=" C1 NAG C1304 " pdb=" ND2 ASN C 163 " pdb=" C2 NAG C1304 " pdb=" O5 NAG C1304 " both_signs ideal model delta sigma weight residual False -2.40 -2.26 -0.14 2.00e-01 2.50e+01 4.92e-01 ... (remaining 4077 not shown) Planarity restraints: 4428 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR C 605 " -0.045 5.00e-02 4.00e+02 6.79e-02 7.38e+00 pdb=" N PRO C 606 " 0.117 5.00e-02 4.00e+02 pdb=" CA PRO C 606 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO C 606 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 605 " 0.044 5.00e-02 4.00e+02 6.73e-02 7.25e+00 pdb=" N PRO B 606 " -0.116 5.00e-02 4.00e+02 pdb=" CA PRO B 606 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 606 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 605 " -0.026 5.00e-02 4.00e+02 3.98e-02 2.53e+00 pdb=" N PRO A 606 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO A 606 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 606 " -0.022 5.00e-02 4.00e+02 ... (remaining 4425 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 5759 2.79 - 3.32: 22578 3.32 - 3.84: 40041 3.84 - 4.37: 48421 4.37 - 4.90: 83598 Nonbonded interactions: 200397 Sorted by model distance: nonbonded pdb=" O GLN C 120 " pdb=" OG SER C 136 " model vdw 2.261 3.040 nonbonded pdb=" O GLN A 120 " pdb=" OG SER A 136 " model vdw 2.262 3.040 nonbonded pdb=" O GLN B 120 " pdb=" OG SER B 136 " model vdw 2.262 3.040 nonbonded pdb=" O TRP A 608 " pdb=" OG SER A 612 " model vdw 2.293 3.040 nonbonded pdb=" O PRO A1028 " pdb=" NE2 GLN A1029 " model vdw 2.306 3.120 ... (remaining 200392 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: 0.16 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 1.030 Check model and map are aligned: 0.190 Set scattering table: 0.220 Process input model: 60.870 Find NCS groups from input model: 1.150 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:13.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8806 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 25374 Z= 0.265 Angle : 0.519 6.576 34521 Z= 0.256 Chirality : 0.044 0.144 4080 Planarity : 0.003 0.068 4380 Dihedral : 10.390 87.887 9960 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 0.52 % Allowed : 4.04 % Favored : 95.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.15), residues: 3036 helix: 1.93 (0.20), residues: 732 sheet: 0.58 (0.18), residues: 735 loop : -0.63 (0.15), residues: 1569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 861 HIS 0.003 0.000 HIS C1039 PHE 0.009 0.001 PHE C1096 TYR 0.017 0.001 TYR B1042 ARG 0.003 0.000 ARG C 332 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 262 time to evaluate : 2.703 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: A 101 GLN cc_start: 0.8095 (mm-40) cc_final: 0.7780 (mm-40) REVERT: A 143 PHE cc_start: 0.8597 (t80) cc_final: 0.8361 (t80) REVERT: A 284 GLU cc_start: 0.8511 (mm-30) cc_final: 0.8230 (mm-30) REVERT: A 326 TYR cc_start: 0.9066 (p90) cc_final: 0.8656 (p90) REVERT: A 349 PHE cc_start: 0.8195 (OUTLIER) cc_final: 0.6645 (p90) REVERT: A 416 LEU cc_start: 0.9207 (mt) cc_final: 0.8673 (tt) REVERT: A 600 HIS cc_start: 0.6857 (OUTLIER) cc_final: 0.6629 (t-90) REVERT: A 715 MET cc_start: 0.9080 (tpp) cc_final: 0.8763 (tpt) REVERT: A 798 PHE cc_start: 0.8398 (t80) cc_final: 0.8071 (t80) REVERT: A 831 ASN cc_start: 0.8414 (m-40) cc_final: 0.8120 (m-40) REVERT: A 969 ASP cc_start: 0.8593 (t70) cc_final: 0.8293 (t0) REVERT: A 1120 LEU cc_start: 0.7590 (pp) cc_final: 0.7277 (pp) REVERT: B 101 GLN cc_start: 0.7991 (mm-40) cc_final: 0.7765 (mm-40) REVERT: B 143 PHE cc_start: 0.8617 (t80) cc_final: 0.8254 (t80) REVERT: B 284 GLU cc_start: 0.8438 (mm-30) cc_final: 0.8185 (mm-30) REVERT: B 326 TYR cc_start: 0.9066 (p90) cc_final: 0.8830 (p90) REVERT: B 349 PHE cc_start: 0.8220 (OUTLIER) cc_final: 0.7437 (p90) REVERT: B 416 LEU cc_start: 0.9186 (mt) cc_final: 0.8603 (tt) REVERT: B 706 MET cc_start: 0.9645 (ptt) cc_final: 0.9416 (ptt) REVERT: B 831 ASN cc_start: 0.8439 (m-40) cc_final: 0.8145 (m-40) REVERT: B 969 ASP cc_start: 0.8691 (t70) cc_final: 0.8330 (t0) REVERT: B 1120 LEU cc_start: 0.7726 (pp) cc_final: 0.7397 (pp) REVERT: C 326 TYR cc_start: 0.9062 (p90) cc_final: 0.8733 (p90) REVERT: C 349 PHE cc_start: 0.8215 (OUTLIER) cc_final: 0.6763 (p90) REVERT: C 358 SER cc_start: 0.8430 (m) cc_final: 0.8031 (p) REVERT: C 730 GLN cc_start: 0.9020 (tt0) cc_final: 0.8809 (tt0) REVERT: C 798 PHE cc_start: 0.8478 (t80) cc_final: 0.8188 (t80) REVERT: C 831 ASN cc_start: 0.8460 (m-40) cc_final: 0.8145 (m-40) REVERT: C 969 ASP cc_start: 0.8641 (t70) cc_final: 0.8316 (t0) REVERT: C 1120 LEU cc_start: 0.7690 (pp) cc_final: 0.7367 (pp) outliers start: 14 outliers final: 6 residues processed: 271 average time/residue: 1.1932 time to fit residues: 382.5338 Evaluate side-chains 179 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 169 time to evaluate : 2.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 ASN Chi-restraints excluded: chain A residue 349 PHE Chi-restraints excluded: chain A residue 600 HIS Chi-restraints excluded: chain B residue 107 ASN Chi-restraints excluded: chain B residue 349 PHE Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain C residue 107 ASN Chi-restraints excluded: chain C residue 349 PHE Chi-restraints excluded: chain C residue 574 THR Chi-restraints excluded: chain C residue 597 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 258 optimal weight: 0.0030 chunk 231 optimal weight: 10.0000 chunk 128 optimal weight: 20.0000 chunk 79 optimal weight: 5.9990 chunk 156 optimal weight: 7.9990 chunk 123 optimal weight: 7.9990 chunk 239 optimal weight: 0.9990 chunk 92 optimal weight: 6.9990 chunk 145 optimal weight: 7.9990 chunk 178 optimal weight: 4.9990 chunk 277 optimal weight: 10.0000 overall best weight: 3.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 ASN A 120 GLN A 139 ASN A 193 GLN A 494 HIS ** A 600 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 665 GLN A 932 GLN A 985 GLN B 18 ASN B 120 GLN B 139 ASN B 494 HIS B 600 HIS B 665 GLN B 730 GLN B 932 GLN B 985 GLN C 18 ASN C 120 GLN C 139 ASN C 494 HIS C 600 HIS C 665 GLN C 730 GLN C 932 GLN C 985 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.113917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.068998 restraints weight = 46775.037| |-----------------------------------------------------------------------------| r_work (start): 0.2911 rms_B_bonded: 2.85 r_work: 0.2774 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2634 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8838 moved from start: 0.0957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 25374 Z= 0.371 Angle : 0.560 11.040 34521 Z= 0.285 Chirality : 0.045 0.180 4080 Planarity : 0.004 0.072 4380 Dihedral : 6.723 59.580 4505 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.39 % Allowed : 7.27 % Favored : 91.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.30 (0.15), residues: 3036 helix: 1.69 (0.20), residues: 735 sheet: 0.62 (0.18), residues: 720 loop : -0.73 (0.15), residues: 1581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 52 HIS 0.005 0.001 HIS B 600 PHE 0.020 0.001 PHE C 143 TYR 0.019 0.001 TYR B1042 ARG 0.006 0.000 ARG A 970 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 182 time to evaluate : 2.683 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: A 101 GLN cc_start: 0.8079 (mm-40) cc_final: 0.7586 (mm-40) REVERT: A 119 PHE cc_start: 0.8738 (m-80) cc_final: 0.8534 (m-80) REVERT: A 143 PHE cc_start: 0.8584 (t80) cc_final: 0.8354 (t80) REVERT: A 284 GLU cc_start: 0.8872 (mm-30) cc_final: 0.8604 (mm-30) REVERT: A 326 TYR cc_start: 0.9121 (p90) cc_final: 0.8766 (p90) REVERT: A 345 ASN cc_start: 0.8603 (OUTLIER) cc_final: 0.8249 (p0) REVERT: A 349 PHE cc_start: 0.8181 (OUTLIER) cc_final: 0.6687 (p90) REVERT: A 416 LEU cc_start: 0.9203 (mt) cc_final: 0.8677 (tt) REVERT: A 427 MET cc_start: 0.7498 (mpp) cc_final: 0.7128 (mpp) REVERT: A 715 MET cc_start: 0.9155 (tpp) cc_final: 0.8945 (tpt) REVERT: A 798 PHE cc_start: 0.8581 (t80) cc_final: 0.8342 (t80) REVERT: A 831 ASN cc_start: 0.8435 (m-40) cc_final: 0.8191 (m-40) REVERT: A 969 ASP cc_start: 0.8804 (t70) cc_final: 0.8540 (t0) REVERT: B 101 GLN cc_start: 0.7973 (mm-40) cc_final: 0.7518 (mm-40) REVERT: B 143 PHE cc_start: 0.8607 (t80) cc_final: 0.8096 (t80) REVERT: B 284 GLU cc_start: 0.8826 (mm-30) cc_final: 0.8612 (mm-30) REVERT: B 326 TYR cc_start: 0.9135 (p90) cc_final: 0.8885 (p90) REVERT: B 345 ASN cc_start: 0.8569 (m110) cc_final: 0.8198 (p0) REVERT: B 346 PHE cc_start: 0.7496 (t80) cc_final: 0.7212 (t80) REVERT: B 349 PHE cc_start: 0.8099 (OUTLIER) cc_final: 0.7393 (p90) REVERT: B 377 ILE cc_start: 0.8659 (tp) cc_final: 0.8449 (tp) REVERT: B 416 LEU cc_start: 0.9139 (mt) cc_final: 0.8566 (tt) REVERT: B 427 MET cc_start: 0.7473 (mpp) cc_final: 0.7169 (mpp) REVERT: B 831 ASN cc_start: 0.8433 (m-40) cc_final: 0.8114 (m-40) REVERT: B 969 ASP cc_start: 0.8828 (t70) cc_final: 0.8524 (t0) REVERT: C 326 TYR cc_start: 0.9074 (p90) cc_final: 0.8772 (p90) REVERT: C 345 ASN cc_start: 0.8527 (m110) cc_final: 0.8155 (p0) REVERT: C 346 PHE cc_start: 0.7574 (t80) cc_final: 0.7239 (t80) REVERT: C 349 PHE cc_start: 0.8126 (OUTLIER) cc_final: 0.6846 (p90) REVERT: C 377 ILE cc_start: 0.8609 (tp) cc_final: 0.8383 (tp) REVERT: C 416 LEU cc_start: 0.9070 (mt) cc_final: 0.8457 (tt) REVERT: C 427 MET cc_start: 0.7514 (mpp) cc_final: 0.7177 (mpp) REVERT: C 621 ARG cc_start: 0.9033 (ttm-80) cc_final: 0.8578 (ttp-110) REVERT: C 798 PHE cc_start: 0.8613 (t80) cc_final: 0.8138 (m-80) REVERT: C 831 ASN cc_start: 0.8502 (m-40) cc_final: 0.8212 (m-40) REVERT: C 969 ASP cc_start: 0.8817 (t70) cc_final: 0.8533 (t0) outliers start: 37 outliers final: 16 residues processed: 205 average time/residue: 1.1726 time to fit residues: 286.3191 Evaluate side-chains 184 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 164 time to evaluate : 2.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 107 ASN Chi-restraints excluded: chain A residue 345 ASN Chi-restraints excluded: chain A residue 349 PHE Chi-restraints excluded: chain A residue 915 SER Chi-restraints excluded: chain B residue 107 ASN Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 349 PHE Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 915 SER Chi-restraints excluded: chain B residue 1111 THR Chi-restraints excluded: chain C residue 107 ASN Chi-restraints excluded: chain C residue 148 GLN Chi-restraints excluded: chain C residue 172 ILE Chi-restraints excluded: chain C residue 309 ASN Chi-restraints excluded: chain C residue 349 PHE Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 915 SER Chi-restraints excluded: chain C residue 1111 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 126 optimal weight: 0.9990 chunk 233 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 chunk 302 optimal weight: 3.9990 chunk 227 optimal weight: 6.9990 chunk 154 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 chunk 214 optimal weight: 7.9990 chunk 206 optimal weight: 1.9990 chunk 271 optimal weight: 2.9990 chunk 298 optimal weight: 0.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 ASN A 345 ASN A 600 HIS A 730 GLN A 985 GLN B 18 ASN B 600 HIS B 985 GLN C 600 HIS C 985 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.115560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.071113 restraints weight = 46327.388| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 2.85 r_work: 0.2818 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2677 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8802 moved from start: 0.1105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 25374 Z= 0.165 Angle : 0.503 9.937 34521 Z= 0.253 Chirality : 0.043 0.173 4080 Planarity : 0.004 0.071 4380 Dihedral : 5.829 59.638 4502 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.91 % Allowed : 7.42 % Favored : 90.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.15), residues: 3036 helix: 2.00 (0.20), residues: 711 sheet: 0.68 (0.19), residues: 654 loop : -0.60 (0.15), residues: 1671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 608 HIS 0.004 0.000 HIS A 600 PHE 0.025 0.001 PHE C 143 TYR 0.016 0.001 TYR A1042 ARG 0.004 0.000 ARG A 970 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 195 time to evaluate : 3.015 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: A 41 ASP cc_start: 0.8857 (t0) cc_final: 0.8636 (t70) REVERT: A 101 GLN cc_start: 0.8141 (mm-40) cc_final: 0.7655 (mm-40) REVERT: A 143 PHE cc_start: 0.8570 (t80) cc_final: 0.8320 (t80) REVERT: A 284 GLU cc_start: 0.8860 (mm-30) cc_final: 0.8597 (mm-30) REVERT: A 309 ASN cc_start: 0.6963 (OUTLIER) cc_final: 0.6650 (p0) REVERT: A 326 TYR cc_start: 0.9127 (p90) cc_final: 0.8735 (p90) REVERT: A 349 PHE cc_start: 0.8164 (OUTLIER) cc_final: 0.6638 (p90) REVERT: A 416 LEU cc_start: 0.9195 (mt) cc_final: 0.8678 (tt) REVERT: A 427 MET cc_start: 0.7637 (mpp) cc_final: 0.7245 (mpp) REVERT: A 561 ASP cc_start: 0.7982 (t0) cc_final: 0.7640 (t0) REVERT: A 798 PHE cc_start: 0.8542 (t80) cc_final: 0.8317 (t80) REVERT: A 831 ASN cc_start: 0.8367 (m-40) cc_final: 0.8102 (m-40) REVERT: A 969 ASP cc_start: 0.8729 (t70) cc_final: 0.8453 (t0) REVERT: B 33 SER cc_start: 0.9355 (p) cc_final: 0.9131 (m) REVERT: B 41 ASP cc_start: 0.8851 (t0) cc_final: 0.8605 (t70) REVERT: B 101 GLN cc_start: 0.8024 (mm-40) cc_final: 0.7609 (mm-40) REVERT: B 143 PHE cc_start: 0.8601 (t80) cc_final: 0.8067 (t80) REVERT: B 284 GLU cc_start: 0.8795 (mm-30) cc_final: 0.8589 (mm-30) REVERT: B 326 TYR cc_start: 0.9162 (p90) cc_final: 0.8877 (p90) REVERT: B 345 ASN cc_start: 0.8552 (m110) cc_final: 0.8180 (p0) REVERT: B 346 PHE cc_start: 0.7607 (t80) cc_final: 0.7365 (t80) REVERT: B 349 PHE cc_start: 0.8036 (OUTLIER) cc_final: 0.7328 (p90) REVERT: B 365 LEU cc_start: 0.8820 (mt) cc_final: 0.8582 (mp) REVERT: B 416 LEU cc_start: 0.9125 (mt) cc_final: 0.8554 (tt) REVERT: B 427 MET cc_start: 0.7602 (mpp) cc_final: 0.7289 (mpp) REVERT: B 561 ASP cc_start: 0.8037 (t0) cc_final: 0.7752 (t0) REVERT: B 798 PHE cc_start: 0.8211 (OUTLIER) cc_final: 0.7999 (m-80) REVERT: B 831 ASN cc_start: 0.8421 (m-40) cc_final: 0.8112 (m-40) REVERT: B 969 ASP cc_start: 0.8737 (t70) cc_final: 0.8450 (t0) REVERT: B 1117 GLN cc_start: 0.8727 (tp40) cc_final: 0.8501 (tm-30) REVERT: C 41 ASP cc_start: 0.8838 (t0) cc_final: 0.8605 (t70) REVERT: C 326 TYR cc_start: 0.9075 (p90) cc_final: 0.8737 (p90) REVERT: C 349 PHE cc_start: 0.8114 (OUTLIER) cc_final: 0.6821 (p90) REVERT: C 353 LYS cc_start: 0.8016 (ttmm) cc_final: 0.7771 (ttmm) REVERT: C 416 LEU cc_start: 0.9080 (mt) cc_final: 0.8482 (tt) REVERT: C 427 MET cc_start: 0.7592 (mpp) cc_final: 0.7234 (mpp) REVERT: C 621 ARG cc_start: 0.8997 (ttm-80) cc_final: 0.8570 (ttp-110) REVERT: C 798 PHE cc_start: 0.8561 (t80) cc_final: 0.8129 (m-80) REVERT: C 831 ASN cc_start: 0.8490 (m-40) cc_final: 0.8166 (m-40) REVERT: C 969 ASP cc_start: 0.8710 (t70) cc_final: 0.8403 (t0) outliers start: 51 outliers final: 17 residues processed: 216 average time/residue: 1.0789 time to fit residues: 282.1700 Evaluate side-chains 190 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 168 time to evaluate : 2.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 ASN Chi-restraints excluded: chain A residue 309 ASN Chi-restraints excluded: chain A residue 349 PHE Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 600 HIS Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 915 SER Chi-restraints excluded: chain B residue 107 ASN Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 349 PHE Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 798 PHE Chi-restraints excluded: chain B residue 915 SER Chi-restraints excluded: chain C residue 107 ASN Chi-restraints excluded: chain C residue 148 GLN Chi-restraints excluded: chain C residue 172 ILE Chi-restraints excluded: chain C residue 349 PHE Chi-restraints excluded: chain C residue 478 VAL Chi-restraints excluded: chain C residue 915 SER Chi-restraints excluded: chain C residue 1116 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 69.6847 > 50: distance: 71 - 160: 17.146 distance: 74 - 157: 28.053 distance: 126 - 131: 32.487 distance: 131 - 132: 41.519 distance: 132 - 133: 12.587 distance: 132 - 135: 6.036 distance: 133 - 142: 57.105 distance: 135 - 136: 5.831 distance: 137 - 139: 31.381 distance: 138 - 140: 28.380 distance: 139 - 141: 9.032 distance: 140 - 141: 11.773 distance: 142 - 143: 16.541 distance: 142 - 148: 24.702 distance: 143 - 144: 8.661 distance: 143 - 146: 22.101 distance: 144 - 145: 8.653 distance: 144 - 149: 26.780 distance: 146 - 147: 5.812 distance: 147 - 148: 41.503 distance: 149 - 150: 41.392 distance: 150 - 151: 8.692 distance: 150 - 153: 32.488 distance: 151 - 152: 5.391 distance: 151 - 157: 9.584 distance: 153 - 154: 5.832 distance: 154 - 155: 36.041 distance: 154 - 156: 36.372 distance: 157 - 158: 21.820 distance: 158 - 159: 25.082 distance: 158 - 161: 19.911 distance: 159 - 160: 11.248 distance: 159 - 166: 21.361 distance: 161 - 162: 27.984 distance: 162 - 163: 9.083 distance: 163 - 165: 13.034 distance: 166 - 167: 32.695 distance: 167 - 168: 7.416 distance: 167 - 170: 8.096 distance: 168 - 169: 25.093 distance: 168 - 172: 12.021 distance: 170 - 171: 38.508 distance: 172 - 173: 19.081 distance: 173 - 174: 39.162 distance: 173 - 176: 38.045 distance: 174 - 175: 8.953 distance: 176 - 177: 3.349 distance: 177 - 178: 15.631 distance: 177 - 179: 11.562 distance: 178 - 180: 17.200 distance: 179 - 181: 23.960 distance: 180 - 182: 9.238 distance: 181 - 182: 6.718 distance: 182 - 183: 7.906 distance: 184 - 185: 18.263 distance: 185 - 186: 26.020 distance: 186 - 187: 8.808 distance: 186 - 188: 39.881 distance: 188 - 189: 26.399 distance: 189 - 190: 24.201 distance: 189 - 192: 37.986 distance: 190 - 199: 39.395 distance: 192 - 193: 12.168 distance: 193 - 194: 18.710 distance: 193 - 195: 9.427 distance: 194 - 196: 12.327 distance: 195 - 197: 14.644 distance: 196 - 198: 5.620 distance: 197 - 198: 9.864 distance: 199 - 200: 11.218 distance: 200 - 201: 11.106 distance: 200 - 203: 5.352 distance: 201 - 202: 5.384 distance: 201 - 210: 12.191 distance: 203 - 204: 13.346 distance: 205 - 206: 5.823 distance: 206 - 207: 22.702 distance: 207 - 208: 14.021 distance: 207 - 209: 42.329 distance: 210 - 211: 20.249 distance: 210 - 216: 33.673 distance: 211 - 212: 21.274 distance: 211 - 214: 10.204 distance: 212 - 213: 29.125 distance: 212 - 217: 7.100 distance: 214 - 215: 5.988 distance: 215 - 216: 4.171