Starting phenix.real_space_refine on Sun Jan 26 14:08:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8h14_34424/01_2025/8h14_34424.cif Found real_map, /net/cci-nas-00/data/ceres_data/8h14_34424/01_2025/8h14_34424.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8h14_34424/01_2025/8h14_34424.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8h14_34424/01_2025/8h14_34424.map" model { file = "/net/cci-nas-00/data/ceres_data/8h14_34424/01_2025/8h14_34424.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8h14_34424/01_2025/8h14_34424.cif" } resolution = 3.39 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= 0.014 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 141 5.16 5 C 15801 2.51 5 N 4029 2.21 5 O 4779 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 111 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: 24750 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 8034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1029, 8034 Classifications: {'peptide': 1029} Link IDs: {'PTRANS': 49, 'TRANS': 979} Chain breaks: 6 Chain: "B" Number of atoms: 8034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1029, 8034 Classifications: {'peptide': 1029} Link IDs: {'PTRANS': 49, 'TRANS': 979} Chain breaks: 6 Chain: "C" Number of atoms: 8034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1029, 8034 Classifications: {'peptide': 1029} Link IDs: {'PTRANS': 49, 'TRANS': 979} Chain breaks: 6 Chain: "A" Number of atoms: 216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 216 Unusual residues: {'EIC': 1, 'NAG': 14} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 14 Chain: "B" Number of atoms: 216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 216 Unusual residues: {'EIC': 1, 'NAG': 14} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 14 Chain: "C" Number of atoms: 216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 216 Unusual residues: {'EIC': 1, 'NAG': 14} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 14 Time building chain proxies: 13.51, per 1000 atoms: 0.55 Number of scatterers: 24750 At special positions: 0 Unit cell: (121.5, 126.9, 174.15, 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 141 16.00 O 4779 8.00 N 4029 7.00 C 15801 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS A 128 " - pdb=" SG CYS A 159 " distance=2.03 Simple disulfide: pdb=" SG CYS A 278 " - pdb=" SG CYS A 288 " distance=2.03 Simple disulfide: pdb=" SG CYS A 323 " - pdb=" SG CYS A 348 " distance=2.05 Simple disulfide: pdb=" SG CYS A 366 " - pdb=" SG CYS A 419 " distance=2.07 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 511 " distance=2.03 Simple disulfide: pdb=" SG CYS A 414 " - pdb=" SG CYS C 969 " distance=2.04 Simple disulfide: pdb=" SG CYS A 467 " - pdb=" SG CYS A 474 " distance=2.04 Simple disulfide: pdb=" SG CYS A 524 " - pdb=" SG CYS A 576 " distance=2.03 Simple disulfide: pdb=" SG CYS A 603 " - pdb=" SG CYS A 635 " distance=2.03 Simple disulfide: pdb=" SG CYS A 648 " - pdb=" SG CYS A 657 " distance=2.03 Simple disulfide: pdb=" SG CYS A 720 " - pdb=" SG CYS A 742 " distance=2.03 Simple disulfide: pdb=" SG CYS A 725 " - pdb=" SG CYS A 731 " distance=2.02 Simple disulfide: pdb=" SG CYS A 822 " - pdb=" SG CYS A 833 " distance=2.04 Simple disulfide: pdb=" SG CYS A 969 " - pdb=" SG CYS B 414 " distance=2.07 Simple disulfide: pdb=" SG CYS A1014 " - pdb=" SG CYS A1025 " distance=2.03 Simple disulfide: pdb=" SG CYS A1064 " - pdb=" SG CYS A1108 " distance=2.03 Simple disulfide: pdb=" SG CYS B 128 " - pdb=" SG CYS B 159 " distance=2.03 Simple disulfide: pdb=" SG CYS B 278 " - pdb=" SG CYS B 288 " distance=2.03 Simple disulfide: pdb=" SG CYS B 323 " - pdb=" SG CYS B 348 " distance=2.04 Simple disulfide: pdb=" SG CYS B 366 " - pdb=" SG CYS B 419 " distance=2.07 Simple disulfide: pdb=" SG CYS B 378 " - pdb=" SG CYS B 511 " distance=2.03 Simple disulfide: pdb=" SG CYS B 467 " - pdb=" SG CYS B 474 " distance=2.04 Simple disulfide: pdb=" SG CYS B 524 " - pdb=" SG CYS B 576 " distance=2.03 Simple disulfide: pdb=" SG CYS B 603 " - pdb=" SG CYS B 635 " distance=2.03 Simple disulfide: pdb=" SG CYS B 648 " - pdb=" SG CYS B 657 " distance=2.03 Simple disulfide: pdb=" SG CYS B 720 " - pdb=" SG CYS B 742 " distance=2.03 Simple disulfide: pdb=" SG CYS B 725 " - pdb=" SG CYS B 731 " distance=2.02 Simple disulfide: pdb=" SG CYS B 822 " - pdb=" SG CYS B 833 " distance=2.04 Simple disulfide: pdb=" SG CYS B 969 " - pdb=" SG CYS C 414 " distance=1.99 Simple disulfide: pdb=" SG CYS B1014 " - pdb=" SG CYS B1025 " distance=2.03 Simple disulfide: pdb=" SG CYS B1064 " - pdb=" SG CYS B1108 " distance=2.03 Simple disulfide: pdb=" SG CYS C 128 " - pdb=" SG CYS C 159 " distance=2.03 Simple disulfide: pdb=" SG CYS C 278 " - pdb=" SG CYS C 288 " distance=2.03 Simple disulfide: pdb=" SG CYS C 323 " - pdb=" SG CYS C 348 " distance=2.04 Simple disulfide: pdb=" SG CYS C 366 " - pdb=" SG CYS C 419 " distance=2.07 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 511 " distance=2.03 Simple disulfide: pdb=" SG CYS C 467 " - pdb=" SG CYS C 474 " distance=2.03 Simple disulfide: pdb=" SG CYS C 524 " - pdb=" SG CYS C 576 " distance=2.03 Simple disulfide: pdb=" SG CYS C 603 " - pdb=" SG CYS C 635 " distance=2.03 Simple disulfide: pdb=" SG CYS C 648 " - pdb=" SG CYS C 657 " distance=2.03 Simple disulfide: pdb=" SG CYS C 720 " - pdb=" SG CYS C 742 " distance=2.03 Simple disulfide: pdb=" SG CYS C 725 " - pdb=" SG CYS C 731 " distance=2.02 Simple disulfide: pdb=" SG CYS C 822 " - pdb=" SG CYS C 833 " distance=2.04 Simple disulfide: pdb=" SG CYS C1014 " - pdb=" SG CYS C1025 " distance=2.03 Simple disulfide: pdb=" SG CYS C1064 " - pdb=" SG CYS C1108 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A1301 " - " ASN A 65 " " NAG A1302 " - " ASN A1080 " " NAG A1303 " - " ASN A 109 " " NAG A1304 " - " ASN A 119 " " NAG A1305 " - " ASN A 158 " " NAG A1306 " - " ASN A 227 " " NAG A1307 " - " ASN A 269 " " NAG A1308 " - " ASN A 318 " " NAG A1309 " - " ASN A 330 " " NAG A1310 " - " ASN A 357 " " NAG A1311 " - " ASN A 602 " " NAG A1312 " - " ASN A 699 " " NAG A1313 " - " ASN A 783 " " NAG A1314 " - " ASN A1116 " " NAG B1301 " - " ASN B 65 " " NAG B1302 " - " ASN B1080 " " NAG B1303 " - " ASN B 109 " " NAG B1304 " - " ASN B 119 " " NAG B1305 " - " ASN B 158 " " NAG B1306 " - " ASN B 227 " " NAG B1307 " - " ASN B 269 " " NAG B1308 " - " ASN B 318 " " NAG B1309 " - " ASN B 330 " " NAG B1310 " - " ASN B 357 " " NAG B1311 " - " ASN B 602 " " NAG B1312 " - " ASN B 699 " " NAG B1313 " - " ASN B 783 " " NAG B1314 " - " ASN B1116 " " NAG C1302 " - " ASN C 65 " " NAG C1303 " - " ASN C1080 " " NAG C1304 " - " ASN C 109 " " NAG C1305 " - " ASN C 119 " " NAG C1306 " - " ASN C 158 " " NAG C1307 " - " ASN C 227 " " NAG C1308 " - " ASN C 269 " " NAG C1309 " - " ASN C 318 " " NAG C1310 " - " ASN C 330 " " NAG C1311 " - " ASN C 357 " " NAG C1312 " - " ASN C 602 " " NAG C1313 " - " ASN C 699 " " NAG C1314 " - " ASN C 783 " " NAG C1315 " - " ASN C1116 " Time building additional restraints: 6.40 Conformation dependent library (CDL) restraints added in 3.2 seconds 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5778 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 48 sheets defined 26.2% alpha, 24.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.84 Creating SS restraints... Processing helix chain 'A' and resid 281 through 291 Processing helix chain 'A' and resid 324 through 330 removed outlier: 3.560A pdb=" N VAL A 328 " --> pdb=" O PRO A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 357 removed outlier: 3.571A pdb=" N VAL A 354 " --> pdb=" O ASP A 351 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU A 355 " --> pdb=" O TYR A 352 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N TYR A 356 " --> pdb=" O SER A 353 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ASN A 357 " --> pdb=" O VAL A 354 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 351 through 357' Processing helix chain 'A' and resid 370 through 374 Processing helix chain 'A' and resid 392 through 397 removed outlier: 4.456A pdb=" N ARG A 395 " --> pdb=" O ASP A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 409 Processing helix chain 'A' and resid 425 through 430 removed outlier: 3.617A pdb=" N ALA A 430 " --> pdb=" O ARG A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 491 Processing helix chain 'A' and resid 719 through 725 Processing helix chain 'A' and resid 728 through 736 Processing helix chain 'A' and resid 738 through 765 removed outlier: 3.553A pdb=" N CYS A 742 " --> pdb=" O TYR A 738 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLN A 744 " --> pdb=" O SER A 740 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU A 745 " --> pdb=" O PHE A 741 " (cutoff:3.500A) Processing helix chain 'A' and resid 785 through 788 removed outlier: 3.680A pdb=" N LEU A 788 " --> pdb=" O SER A 785 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 785 through 788' Processing helix chain 'A' and resid 798 through 808 removed outlier: 3.859A pdb=" N VAL A 808 " --> pdb=" O LEU A 804 " (cutoff:3.500A) Processing helix chain 'A' and resid 818 through 823 Processing helix chain 'A' and resid 830 through 838 Processing helix chain 'A' and resid 848 through 866 Processing helix chain 'A' and resid 879 through 891 removed outlier: 3.703A pdb=" N ILE A 891 " --> pdb=" O ARG A 887 " (cutoff:3.500A) Processing helix chain 'A' and resid 895 through 901 Processing helix chain 'A' and resid 901 through 922 removed outlier: 3.876A pdb=" N THR A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 927 through 947 removed outlier: 3.703A pdb=" N GLN A 931 " --> pdb=" O LEU A 927 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ASP A 932 " --> pdb=" O GLY A 928 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N VAL A 933 " --> pdb=" O LYS A 929 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N VAL A 934 " --> pdb=" O LEU A 930 " (cutoff:3.500A) Processing helix chain 'A' and resid 948 through 950 No H-bonds generated for 'chain 'A' and resid 948 through 950' Processing helix chain 'A' and resid 958 through 966 removed outlier: 3.503A pdb=" N ILE A 962 " --> pdb=" O VAL A 958 " (cutoff:3.500A) Processing helix chain 'A' and resid 967 through 1015 removed outlier: 3.742A pdb=" N ALA A 971 " --> pdb=" O ASP A 967 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N VAL A 973 " --> pdb=" O CYS A 969 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLN A 974 " --> pdb=" O GLU A 970 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ARG A 977 " --> pdb=" O VAL A 973 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU A 978 " --> pdb=" O GLN A 974 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 291 Processing helix chain 'B' and resid 324 through 330 removed outlier: 3.561A pdb=" N VAL B 328 " --> pdb=" O PRO B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 357 removed outlier: 3.571A pdb=" N VAL B 354 " --> pdb=" O ASP B 351 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU B 355 " --> pdb=" O TYR B 352 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N TYR B 356 " --> pdb=" O SER B 353 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ASN B 357 " --> pdb=" O VAL B 354 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 351 through 357' Processing helix chain 'B' and resid 370 through 374 Processing helix chain 'B' and resid 392 through 397 removed outlier: 4.456A pdb=" N ARG B 395 " --> pdb=" O ASP B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 409 Processing helix chain 'B' and resid 425 through 430 removed outlier: 3.617A pdb=" N ALA B 430 " --> pdb=" O ARG B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 491 Processing helix chain 'B' and resid 719 through 725 Processing helix chain 'B' and resid 728 through 736 Processing helix chain 'B' and resid 738 through 765 removed outlier: 3.553A pdb=" N CYS B 742 " --> pdb=" O TYR B 738 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLN B 744 " --> pdb=" O SER B 740 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU B 745 " --> pdb=" O PHE B 741 " (cutoff:3.500A) Processing helix chain 'B' and resid 785 through 788 removed outlier: 3.680A pdb=" N LEU B 788 " --> pdb=" O SER B 785 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 785 through 788' Processing helix chain 'B' and resid 798 through 808 removed outlier: 3.859A pdb=" N VAL B 808 " --> pdb=" O LEU B 804 " (cutoff:3.500A) Processing helix chain 'B' and resid 818 through 823 Processing helix chain 'B' and resid 830 through 838 Processing helix chain 'B' and resid 848 through 866 Processing helix chain 'B' and resid 879 through 891 removed outlier: 3.703A pdb=" N ILE B 891 " --> pdb=" O ARG B 887 " (cutoff:3.500A) Processing helix chain 'B' and resid 895 through 901 Processing helix chain 'B' and resid 901 through 922 removed outlier: 3.876A pdb=" N THR B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) Processing helix chain 'B' and resid 927 through 947 removed outlier: 3.702A pdb=" N GLN B 931 " --> pdb=" O LEU B 927 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ASP B 932 " --> pdb=" O GLY B 928 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N VAL B 933 " --> pdb=" O LYS B 929 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N VAL B 934 " --> pdb=" O LEU B 930 " (cutoff:3.500A) Processing helix chain 'B' and resid 948 through 950 No H-bonds generated for 'chain 'B' and resid 948 through 950' Processing helix chain 'B' and resid 958 through 966 removed outlier: 3.503A pdb=" N ILE B 962 " --> pdb=" O VAL B 958 " (cutoff:3.500A) Processing helix chain 'B' and resid 967 through 1015 removed outlier: 3.741A pdb=" N ALA B 971 " --> pdb=" O ASP B 967 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N VAL B 973 " --> pdb=" O CYS B 969 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLN B 974 " --> pdb=" O GLU B 970 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ARG B 977 " --> pdb=" O VAL B 973 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU B 978 " --> pdb=" O GLN B 974 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 291 Processing helix chain 'C' and resid 324 through 330 removed outlier: 3.561A pdb=" N VAL C 328 " --> pdb=" O PRO C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 357 removed outlier: 3.571A pdb=" N VAL C 354 " --> pdb=" O ASP C 351 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU C 355 " --> pdb=" O TYR C 352 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N TYR C 356 " --> pdb=" O SER C 353 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ASN C 357 " --> pdb=" O VAL C 354 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 351 through 357' Processing helix chain 'C' and resid 370 through 374 Processing helix chain 'C' and resid 392 through 397 removed outlier: 4.457A pdb=" N ARG C 395 " --> pdb=" O ASP C 392 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 409 Processing helix chain 'C' and resid 425 through 430 removed outlier: 3.617A pdb=" N ALA C 430 " --> pdb=" O ARG C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 491 Processing helix chain 'C' and resid 719 through 725 Processing helix chain 'C' and resid 728 through 736 Processing helix chain 'C' and resid 738 through 765 removed outlier: 3.553A pdb=" N CYS C 742 " --> pdb=" O TYR C 738 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLN C 744 " --> pdb=" O SER C 740 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU C 745 " --> pdb=" O PHE C 741 " (cutoff:3.500A) Processing helix chain 'C' and resid 785 through 788 removed outlier: 3.678A pdb=" N LEU C 788 " --> pdb=" O SER C 785 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 785 through 788' Processing helix chain 'C' and resid 798 through 808 removed outlier: 3.860A pdb=" N VAL C 808 " --> pdb=" O LEU C 804 " (cutoff:3.500A) Processing helix chain 'C' and resid 818 through 823 Processing helix chain 'C' and resid 830 through 838 Processing helix chain 'C' and resid 848 through 866 Processing helix chain 'C' and resid 879 through 891 removed outlier: 3.702A pdb=" N ILE C 891 " --> pdb=" O ARG C 887 " (cutoff:3.500A) Processing helix chain 'C' and resid 895 through 901 Processing helix chain 'C' and resid 901 through 922 removed outlier: 3.876A pdb=" N THR C 922 " --> pdb=" O GLU C 918 " (cutoff:3.500A) Processing helix chain 'C' and resid 927 through 947 removed outlier: 3.703A pdb=" N GLN C 931 " --> pdb=" O LEU C 927 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ASP C 932 " --> pdb=" O GLY C 928 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N VAL C 933 " --> pdb=" O LYS C 929 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N VAL C 934 " --> pdb=" O LEU C 930 " (cutoff:3.500A) Processing helix chain 'C' and resid 948 through 950 No H-bonds generated for 'chain 'C' and resid 948 through 950' Processing helix chain 'C' and resid 958 through 966 removed outlier: 3.504A pdb=" N ILE C 962 " --> pdb=" O VAL C 958 " (cutoff:3.500A) Processing helix chain 'C' and resid 967 through 1015 removed outlier: 3.741A pdb=" N ALA C 971 " --> pdb=" O ASP C 967 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N VAL C 973 " --> pdb=" O CYS C 969 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLN C 974 " --> pdb=" O GLU C 970 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ARG C 977 " --> pdb=" O VAL C 973 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU C 978 " --> pdb=" O GLN C 974 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 34 removed outlier: 7.491A pdb=" N ASN A 65 " --> pdb=" O TYR A 256 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N TYR A 256 " --> pdb=" O ASN A 65 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N LYS A 198 " --> pdb=" O PRO A 218 " (cutoff:3.500A) removed outlier: 8.845A pdb=" N TYR A 200 " --> pdb=" O LEU A 216 " (cutoff:3.500A) removed outlier: 8.307A pdb=" N LEU A 216 " --> pdb=" O TYR A 200 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N VAL A 40 " --> pdb=" O LEU A 216 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 46 through 47 removed outlier: 6.647A pdb=" N GLY C 552 " --> pdb=" O ASP C 560 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N ASP C 560 " --> pdb=" O ILE C 573 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N GLY C 311 " --> pdb=" O ASN C 526 " (cutoff:3.500A) removed outlier: 8.231A pdb=" N ASN C 528 " --> pdb=" O GLY C 311 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N VAL C 313 " --> pdb=" O ASN C 528 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 52 through 59 removed outlier: 4.127A pdb=" N ASP A 274 " --> pdb=" O LYS A 265 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 81 through 82 removed outlier: 7.151A pdb=" N ASN A 230 " --> pdb=" O PHE A 103 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N PHE A 103 " --> pdb=" O ASN A 230 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ARG A 232 " --> pdb=" O TRP A 101 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N TRP A 101 " --> pdb=" O ARG A 232 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ILE A 234 " --> pdb=" O ARG A 99 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N ARG A 99 " --> pdb=" O ASN A 118 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 130 through 132 removed outlier: 6.854A pdb=" N GLU A 131 " --> pdb=" O ASP A 154 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASP A 154 " --> pdb=" O GLU A 131 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 298 through 301 removed outlier: 3.586A pdb=" N PHE A 629 " --> pdb=" O LEU A 636 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 315 removed outlier: 6.294A pdb=" N GLY A 311 " --> pdb=" O ASN A 526 " (cutoff:3.500A) removed outlier: 8.232A pdb=" N ASN A 528 " --> pdb=" O GLY A 311 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N VAL A 313 " --> pdb=" O ASN A 528 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N ASP A 560 " --> pdb=" O ILE A 573 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N GLY A 552 " --> pdb=" O ASP A 560 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N PHE A 551 " --> pdb=" O PHE B 47 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 341 through 345 removed outlier: 4.238A pdb=" N VAL A 382 " --> pdb=" O ILE A 345 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 348 through 349 removed outlier: 6.710A pdb=" N CYS A 348 " --> pdb=" O CYS A 511 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 439 through 441 Processing sheet with id=AB2, first strand: chain 'A' and resid 640 through 641 removed outlier: 5.970A pdb=" N GLU A 640 " --> pdb=" O ALA A 676 " (cutoff:3.500A) removed outlier: 8.522A pdb=" N THR A 678 " --> pdb=" O GLU A 640 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ILE A 656 " --> pdb=" O ILE A 652 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 683 through 685 removed outlier: 6.561A pdb=" N ALA A 683 " --> pdb=" O MET B 770 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 693 through 710 removed outlier: 6.753A pdb=" N THR A 693 " --> pdb=" O THR A1058 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N THR A1058 " --> pdb=" O THR A 693 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ALA A 695 " --> pdb=" O ASN A1056 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ASN A1056 " --> pdb=" O ALA A 695 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N GLU A1054 " --> pdb=" O PRO A 697 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N TYR A1049 " --> pdb=" O HIS A1030 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N HIS A1030 " --> pdb=" O TYR A1049 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 715 through 718 removed outlier: 4.583A pdb=" N LYS A 715 " --> pdb=" O LEU A 843 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 769 through 771 Processing sheet with id=AB7, first strand: chain 'A' and resid 778 through 779 Processing sheet with id=AB8, first strand: chain 'A' and resid 1102 through 1104 Processing sheet with id=AB9, first strand: chain 'A' and resid 1076 through 1079 Processing sheet with id=AC1, first strand: chain 'B' and resid 32 through 34 removed outlier: 7.491A pdb=" N ASN B 65 " --> pdb=" O TYR B 256 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N TYR B 256 " --> pdb=" O ASN B 65 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N LYS B 198 " --> pdb=" O PRO B 218 " (cutoff:3.500A) removed outlier: 8.846A pdb=" N TYR B 200 " --> pdb=" O LEU B 216 " (cutoff:3.500A) removed outlier: 8.308A pdb=" N LEU B 216 " --> pdb=" O TYR B 200 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N VAL B 40 " --> pdb=" O LEU B 216 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 52 through 59 removed outlier: 4.126A pdb=" N ASP B 274 " --> pdb=" O LYS B 265 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 81 through 82 removed outlier: 7.151A pdb=" N ASN B 230 " --> pdb=" O PHE B 103 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N PHE B 103 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ARG B 232 " --> pdb=" O TRP B 101 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N TRP B 101 " --> pdb=" O ARG B 232 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ILE B 234 " --> pdb=" O ARG B 99 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N ARG B 99 " --> pdb=" O ASN B 118 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 130 through 132 removed outlier: 6.805A pdb=" N GLU B 131 " --> pdb=" O ASP B 154 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 298 through 301 removed outlier: 3.586A pdb=" N PHE B 629 " --> pdb=" O LEU B 636 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 311 through 315 removed outlier: 6.294A pdb=" N GLY B 311 " --> pdb=" O ASN B 526 " (cutoff:3.500A) removed outlier: 8.232A pdb=" N ASN B 528 " --> pdb=" O GLY B 311 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N VAL B 313 " --> pdb=" O ASN B 528 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N ASP B 560 " --> pdb=" O ILE B 573 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N GLY B 552 " --> pdb=" O ASP B 560 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 341 through 345 removed outlier: 4.239A pdb=" N VAL B 382 " --> pdb=" O ILE B 345 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 348 through 349 removed outlier: 6.709A pdb=" N CYS B 348 " --> pdb=" O CYS B 511 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 439 through 441 Processing sheet with id=AD1, first strand: chain 'B' and resid 640 through 641 removed outlier: 5.969A pdb=" N GLU B 640 " --> pdb=" O ALA B 676 " (cutoff:3.500A) removed outlier: 8.522A pdb=" N THR B 678 " --> pdb=" O GLU B 640 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ILE B 656 " --> pdb=" O ILE B 652 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 683 through 685 removed outlier: 6.667A pdb=" N ALA B 683 " --> pdb=" O MET C 770 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'B' and resid 693 through 710 removed outlier: 6.753A pdb=" N THR B 693 " --> pdb=" O THR B1058 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N THR B1058 " --> pdb=" O THR B 693 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ALA B 695 " --> pdb=" O ASN B1056 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ASN B1056 " --> pdb=" O ALA B 695 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N GLU B1054 " --> pdb=" O PRO B 697 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N TYR B1049 " --> pdb=" O HIS B1030 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N HIS B1030 " --> pdb=" O TYR B1049 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 715 through 718 removed outlier: 4.582A pdb=" N LYS B 715 " --> pdb=" O LEU B 843 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 778 through 779 Processing sheet with id=AD6, first strand: chain 'B' and resid 1102 through 1104 Processing sheet with id=AD7, first strand: chain 'B' and resid 1076 through 1079 Processing sheet with id=AD8, first strand: chain 'C' and resid 32 through 34 removed outlier: 7.491A pdb=" N ASN C 65 " --> pdb=" O TYR C 256 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N TYR C 256 " --> pdb=" O ASN C 65 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N LYS C 198 " --> pdb=" O PRO C 218 " (cutoff:3.500A) removed outlier: 8.846A pdb=" N TYR C 200 " --> pdb=" O LEU C 216 " (cutoff:3.500A) removed outlier: 8.308A pdb=" N LEU C 216 " --> pdb=" O TYR C 200 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N VAL C 40 " --> pdb=" O LEU C 216 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 52 through 59 removed outlier: 4.126A pdb=" N ASP C 274 " --> pdb=" O LYS C 265 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 81 through 82 removed outlier: 7.150A pdb=" N ASN C 230 " --> pdb=" O PHE C 103 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N PHE C 103 " --> pdb=" O ASN C 230 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ARG C 232 " --> pdb=" O TRP C 101 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N TRP C 101 " --> pdb=" O ARG C 232 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ILE C 234 " --> pdb=" O ARG C 99 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N ARG C 99 " --> pdb=" O ASN C 118 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 130 through 132 removed outlier: 6.804A pdb=" N GLU C 131 " --> pdb=" O ASP C 154 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 298 through 301 removed outlier: 3.585A pdb=" N PHE C 629 " --> pdb=" O LEU C 636 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 341 through 345 removed outlier: 4.239A pdb=" N VAL C 382 " --> pdb=" O ILE C 345 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 348 through 349 removed outlier: 6.709A pdb=" N CYS C 348 " --> pdb=" O CYS C 511 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 439 through 441 Processing sheet with id=AE7, first strand: chain 'C' and resid 640 through 641 removed outlier: 5.969A pdb=" N GLU C 640 " --> pdb=" O ALA C 676 " (cutoff:3.500A) removed outlier: 8.522A pdb=" N THR C 678 " --> pdb=" O GLU C 640 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ILE C 656 " --> pdb=" O ILE C 652 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 693 through 710 removed outlier: 6.753A pdb=" N THR C 693 " --> pdb=" O THR C1058 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N THR C1058 " --> pdb=" O THR C 693 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ALA C 695 " --> pdb=" O ASN C1056 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ASN C1056 " --> pdb=" O ALA C 695 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N GLU C1054 " --> pdb=" O PRO C 697 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N TYR C1049 " --> pdb=" O HIS C1030 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N HIS C1030 " --> pdb=" O TYR C1049 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 715 through 718 removed outlier: 4.582A pdb=" N LYS C 715 " --> pdb=" O LEU C 843 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 778 through 779 Processing sheet with id=AF2, first strand: chain 'C' and resid 1102 through 1104 Processing sheet with id=AF3, first strand: chain 'C' and resid 1076 through 1079 984 hydrogen bonds defined for protein. 2691 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: 10.47 Time building geometry restraints manager: 7.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.37: 7932 1.37 - 1.52: 12342 1.52 - 1.68: 4845 1.68 - 1.83: 180 1.83 - 1.99: 6 Bond restraints: 25305 Sorted by residual: bond pdb=" CB CYS C 419 " pdb=" SG CYS C 419 " ideal model delta sigma weight residual 1.808 1.988 -0.180 3.30e-02 9.18e+02 2.98e+01 bond pdb=" CB CYS B 419 " pdb=" SG CYS B 419 " ideal model delta sigma weight residual 1.808 1.988 -0.180 3.30e-02 9.18e+02 2.98e+01 bond pdb=" CB CYS A 419 " pdb=" SG CYS A 419 " ideal model delta sigma weight residual 1.808 1.988 -0.180 3.30e-02 9.18e+02 2.98e+01 bond pdb=" CB CYS A 366 " pdb=" SG CYS A 366 " ideal model delta sigma weight residual 1.808 1.651 0.157 3.30e-02 9.18e+02 2.26e+01 bond pdb=" CB CYS C 366 " pdb=" SG CYS C 366 " ideal model delta sigma weight residual 1.808 1.651 0.157 3.30e-02 9.18e+02 2.25e+01 ... (remaining 25300 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.94: 34295 5.94 - 11.89: 73 11.89 - 17.83: 9 17.83 - 23.78: 0 23.78 - 29.72: 3 Bond angle restraints: 34380 Sorted by residual: angle pdb=" CA CYS C 366 " pdb=" CB CYS C 366 " pdb=" SG CYS C 366 " ideal model delta sigma weight residual 114.40 144.12 -29.72 2.30e+00 1.89e-01 1.67e+02 angle pdb=" CA CYS A 366 " pdb=" CB CYS A 366 " pdb=" SG CYS A 366 " ideal model delta sigma weight residual 114.40 144.11 -29.71 2.30e+00 1.89e-01 1.67e+02 angle pdb=" CA CYS B 366 " pdb=" CB CYS B 366 " pdb=" SG CYS B 366 " ideal model delta sigma weight residual 114.40 144.10 -29.70 2.30e+00 1.89e-01 1.67e+02 angle pdb=" C PHE B 130 " pdb=" CA PHE B 130 " pdb=" CB PHE B 130 " ideal model delta sigma weight residual 109.79 96.52 13.27 2.05e+00 2.38e-01 4.19e+01 angle pdb=" C PHE C 130 " pdb=" CA PHE C 130 " pdb=" CB PHE C 130 " ideal model delta sigma weight residual 109.79 96.52 13.27 2.05e+00 2.38e-01 4.19e+01 ... (remaining 34375 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.77: 14129 17.77 - 35.55: 1137 35.55 - 53.32: 289 53.32 - 71.10: 51 71.10 - 88.87: 24 Dihedral angle restraints: 15630 sinusoidal: 6642 harmonic: 8988 Sorted by residual: dihedral pdb=" CB CYS A 648 " pdb=" SG CYS A 648 " pdb=" SG CYS A 657 " pdb=" CB CYS A 657 " ideal model delta sinusoidal sigma weight residual -86.00 2.49 -88.49 1 1.00e+01 1.00e-02 9.35e+01 dihedral pdb=" CB CYS C 648 " pdb=" SG CYS C 648 " pdb=" SG CYS C 657 " pdb=" CB CYS C 657 " ideal model delta sinusoidal sigma weight residual -86.00 2.47 -88.47 1 1.00e+01 1.00e-02 9.34e+01 dihedral pdb=" CB CYS B 648 " pdb=" SG CYS B 648 " pdb=" SG CYS B 657 " pdb=" CB CYS B 657 " ideal model delta sinusoidal sigma weight residual -86.00 2.46 -88.46 1 1.00e+01 1.00e-02 9.34e+01 ... (remaining 15627 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.136: 3896 0.136 - 0.272: 85 0.272 - 0.407: 0 0.407 - 0.543: 3 0.543 - 0.679: 6 Chirality restraints: 3990 Sorted by residual: chirality pdb=" C1 NAG B1302 " pdb=" ND2 ASN B1080 " pdb=" C2 NAG B1302 " pdb=" O5 NAG B1302 " both_signs ideal model delta sigma weight residual False -2.40 -1.72 -0.68 2.00e-01 2.50e+01 1.15e+01 chirality pdb=" C1 NAG A1302 " pdb=" ND2 ASN A1080 " pdb=" C2 NAG A1302 " pdb=" O5 NAG A1302 " both_signs ideal model delta sigma weight residual False -2.40 -1.72 -0.68 2.00e-01 2.50e+01 1.15e+01 chirality pdb=" C1 NAG C1303 " pdb=" ND2 ASN C1080 " pdb=" C2 NAG C1303 " pdb=" O5 NAG C1303 " both_signs ideal model delta sigma weight residual False -2.40 -1.73 -0.67 2.00e-01 2.50e+01 1.14e+01 ... (remaining 3987 not shown) Planarity restraints: 4434 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 699 " -0.048 2.00e-02 2.50e+03 4.65e-02 2.71e+01 pdb=" CG ASN A 699 " 0.056 2.00e-02 2.50e+03 pdb=" OD1 ASN A 699 " -0.014 2.00e-02 2.50e+03 pdb=" ND2 ASN A 699 " 0.054 2.00e-02 2.50e+03 pdb=" C1 NAG A1312 " -0.048 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 699 " -0.048 2.00e-02 2.50e+03 4.65e-02 2.70e+01 pdb=" CG ASN C 699 " 0.056 2.00e-02 2.50e+03 pdb=" OD1 ASN C 699 " -0.014 2.00e-02 2.50e+03 pdb=" ND2 ASN C 699 " 0.053 2.00e-02 2.50e+03 pdb=" C1 NAG C1313 " -0.048 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 699 " -0.048 2.00e-02 2.50e+03 4.62e-02 2.67e+01 pdb=" CG ASN B 699 " 0.056 2.00e-02 2.50e+03 pdb=" OD1 ASN B 699 " -0.013 2.00e-02 2.50e+03 pdb=" ND2 ASN B 699 " 0.053 2.00e-02 2.50e+03 pdb=" C1 NAG B1312 " -0.048 2.00e-02 2.50e+03 ... (remaining 4431 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 1052 2.72 - 3.27: 21737 3.27 - 3.81: 36483 3.81 - 4.36: 46347 4.36 - 4.90: 82633 Nonbonded interactions: 188252 Sorted by model distance: nonbonded pdb=" O THR C 925 " pdb=" OG1 THR C 925 " model vdw 2.177 3.040 nonbonded pdb=" O THR A 925 " pdb=" OG1 THR A 925 " model vdw 2.178 3.040 nonbonded pdb=" O THR B 925 " pdb=" OG1 THR B 925 " model vdw 2.179 3.040 nonbonded pdb=" O ASN C 960 " pdb=" OG SER C 964 " model vdw 2.243 3.040 nonbonded pdb=" O ASN A 960 " pdb=" OG SER A 964 " model vdw 2.244 3.040 ... (remaining 188247 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.07 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 31 through 1123 or resid 1302 through 1314)) selection = (chain 'B' and (resid 31 through 1123 or resid 1302 through 1314)) selection = (chain 'C' and (resid 31 through 1123 or resid 1302 through 1314)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 1.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.830 Check model and map are aligned: 0.160 Set scattering table: 0.200 Process input model: 54.260 Find NCS groups from input model: 1.190 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 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 0.180 25305 Z= 0.331 Angle : 0.954 29.719 34380 Z= 0.518 Chirality : 0.063 0.679 3990 Planarity : 0.006 0.057 4392 Dihedral : 13.867 88.870 9717 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 2.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.35 % Allowed : 1.46 % Favored : 97.19 % Cbeta Deviations : 0.21 % 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: -0.84 (0.14), residues: 3045 helix: 0.48 (0.19), residues: 666 sheet: 0.80 (0.20), residues: 687 loop : -1.66 (0.12), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 619 HIS 0.006 0.001 HIS B 181 PHE 0.035 0.002 PHE A 130 TYR 0.024 0.002 TYR A 886 ARG 0.014 0.001 ARG C1089 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 254 time to evaluate : 2.733 Fit side-chains REVERT: A 153 PHE cc_start: 0.7424 (OUTLIER) cc_final: 0.6608 (p90) REVERT: A 758 ARG cc_start: 0.7802 (ttp-110) cc_final: 0.7602 (ttp-110) REVERT: A 851 MET cc_start: 0.8382 (mtt) cc_final: 0.8007 (mtt) REVERT: A 884 MET cc_start: 0.8906 (OUTLIER) cc_final: 0.8471 (mmp) REVERT: B 128 CYS cc_start: 0.6404 (t) cc_final: 0.6186 (t) REVERT: B 572 ASP cc_start: 0.7158 (m-30) cc_final: 0.6858 (m-30) REVERT: B 736 LEU cc_start: 0.8627 (tp) cc_final: 0.8358 (tp) REVERT: B 758 ARG cc_start: 0.7651 (ttp-110) cc_final: 0.7444 (ttp-110) REVERT: B 973 VAL cc_start: 0.7320 (OUTLIER) cc_final: 0.6985 (p) REVERT: C 153 PHE cc_start: 0.6938 (OUTLIER) cc_final: 0.6518 (p90) REVERT: C 479 ASN cc_start: 0.8338 (t0) cc_final: 0.8019 (t0) REVERT: C 572 ASP cc_start: 0.7389 (m-30) cc_final: 0.6945 (m-30) REVERT: C 709 MET cc_start: 0.8705 (mtt) cc_final: 0.8209 (mtm) REVERT: C 740 SER cc_start: 0.7698 (OUTLIER) cc_final: 0.7462 (p) REVERT: C 1105 SER cc_start: 0.8827 (OUTLIER) cc_final: 0.8587 (m) outliers start: 36 outliers final: 13 residues processed: 278 average time/residue: 0.3924 time to fit residues: 170.9109 Evaluate side-chains 196 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 177 time to evaluate : 2.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 153 PHE Chi-restraints excluded: chain A residue 729 THR Chi-restraints excluded: chain A residue 884 MET Chi-restraints excluded: chain A residue 925 THR Chi-restraints excluded: chain A residue 973 VAL Chi-restraints excluded: chain B residue 729 THR Chi-restraints excluded: chain B residue 740 SER Chi-restraints excluded: chain B residue 884 MET Chi-restraints excluded: chain B residue 925 THR Chi-restraints excluded: chain B residue 973 VAL Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 153 PHE Chi-restraints excluded: chain C residue 729 THR Chi-restraints excluded: chain C residue 740 SER Chi-restraints excluded: chain C residue 884 MET Chi-restraints excluded: chain C residue 925 THR Chi-restraints excluded: chain C residue 973 VAL Chi-restraints excluded: chain C residue 1105 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 258 optimal weight: 10.0000 chunk 231 optimal weight: 0.9980 chunk 128 optimal weight: 0.0970 chunk 79 optimal weight: 0.0050 chunk 156 optimal weight: 6.9990 chunk 123 optimal weight: 0.8980 chunk 239 optimal weight: 0.8980 chunk 92 optimal weight: 5.9990 chunk 145 optimal weight: 0.0570 chunk 178 optimal weight: 3.9990 chunk 277 optimal weight: 3.9990 overall best weight: 0.3910 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 HIS A 883 GLN A 939 GLN B 181 HIS B 904 GLN B 931 GLN C 181 HIS C 883 GLN C 904 GLN C 939 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.131019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.105133 restraints weight = 30617.414| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 1.74 r_work: 0.2879 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2738 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.1070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 25305 Z= 0.153 Angle : 0.524 7.971 34380 Z= 0.280 Chirality : 0.047 0.477 3990 Planarity : 0.004 0.045 4392 Dihedral : 7.309 62.271 4275 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 0.82 % Allowed : 5.62 % Favored : 93.56 % 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: -0.26 (0.14), residues: 3045 helix: 1.45 (0.21), residues: 672 sheet: 1.13 (0.19), residues: 690 loop : -1.51 (0.13), residues: 1683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 423 HIS 0.002 0.000 HIS C 181 PHE 0.022 0.001 PHE B 130 TYR 0.016 0.001 TYR C1049 ARG 0.002 0.000 ARG B 38 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 190 time to evaluate : 3.321 Fit side-chains REVERT: A 96 ASN cc_start: 0.7599 (t0) cc_final: 0.6990 (t0) REVERT: A 572 ASP cc_start: 0.8144 (m-30) cc_final: 0.7904 (m-30) REVERT: A 758 ARG cc_start: 0.8347 (ttp-110) cc_final: 0.7990 (ttp-110) REVERT: A 851 MET cc_start: 0.8774 (mtt) cc_final: 0.8484 (mtt) REVERT: A 984 GLN cc_start: 0.8518 (tp40) cc_final: 0.8122 (tt0) REVERT: B 128 CYS cc_start: 0.7892 (t) cc_final: 0.7681 (t) REVERT: B 758 ARG cc_start: 0.8234 (ttp-110) cc_final: 0.7840 (ttp-110) REVERT: C 479 ASN cc_start: 0.8879 (t0) cc_final: 0.8668 (t0) REVERT: C 1059 THR cc_start: 0.9193 (t) cc_final: 0.8988 (t) REVERT: C 1105 SER cc_start: 0.9129 (t) cc_final: 0.8733 (m) outliers start: 22 outliers final: 10 residues processed: 207 average time/residue: 0.3745 time to fit residues: 125.2441 Evaluate side-chains 182 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 172 time to evaluate : 2.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 729 THR Chi-restraints excluded: chain A residue 973 VAL Chi-restraints excluded: chain B residue 502 GLU Chi-restraints excluded: chain B residue 729 THR Chi-restraints excluded: chain B residue 973 VAL Chi-restraints excluded: chain C residue 319 ILE Chi-restraints excluded: chain C residue 646 TYR Chi-restraints excluded: chain C residue 729 THR Chi-restraints excluded: chain C residue 958 VAL Chi-restraints excluded: chain C residue 973 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 124 optimal weight: 5.9990 chunk 19 optimal weight: 5.9990 chunk 205 optimal weight: 0.7980 chunk 257 optimal weight: 8.9990 chunk 212 optimal weight: 6.9990 chunk 112 optimal weight: 0.9990 chunk 105 optimal weight: 2.9990 chunk 246 optimal weight: 2.9990 chunk 230 optimal weight: 0.7980 chunk 51 optimal weight: 4.9990 chunk 137 optimal weight: 0.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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: