Starting phenix.real_space_refine on Thu Mar 5 19:42:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8h14_34424/03_2026/8h14_34424.cif Found real_map, /net/cci-nas-00/data/ceres_data/8h14_34424/03_2026/8h14_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 { model { file = "/net/cci-nas-00/data/ceres_data/8h14_34424/03_2026/8h14_34424.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8h14_34424/03_2026/8h14_34424.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8h14_34424/03_2026/8h14_34424.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8h14_34424/03_2026/8h14_34424.map" } resolution = 3.39 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.014 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 6.01, per 1000 atoms: 0.24 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: 2.06 Conformation dependent library (CDL) restraints added in 1.0 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: 1.07 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: 5.68 Time building geometry restraints manager: 2.70 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: 0.05 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: 1.430 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: 0.260 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 23.950 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.540 ------------------------------------------------------------------------------- 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 25392 Z= 0.246 Angle : 1.017 29.719 34596 Z= 0.535 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.84 (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 ARG 0.014 0.001 ARG C1089 TYR 0.024 0.002 TYR A 886 PHE 0.035 0.002 PHE A 130 TRP 0.010 0.002 TRP A 619 HIS 0.006 0.001 HIS B 181 Details of bonding type rmsd covalent geometry : bond 0.00537 (25305) covalent geometry : angle 0.95444 (34380) SS BOND : bond 0.01477 ( 45) SS BOND : angle 4.10010 ( 90) hydrogen bonds : bond 0.14000 ( 984) hydrogen bonds : angle 6.24625 ( 2691) link_NAG-ASN : bond 0.00729 ( 42) link_NAG-ASN : angle 4.86152 ( 126) *********************** 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 : 0.848 Fit side-chains REVERT: A 153 PHE cc_start: 0.7424 (OUTLIER) cc_final: 0.6608 (p90) 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: 0.1658 time to fit residues: 72.5660 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 : 0.882 ------------------------------------------------------------------------------- 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 197 optimal weight: 4.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 0.7980 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 0.6980 chunk 183 optimal weight: 3.9990 chunk 298 optimal weight: 0.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 HIS ** A 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 883 GLN A 917 GLN A 939 GLN B 181 HIS B 883 GLN B 896 ASN B 917 GLN C 883 GLN C 896 ASN C 917 GLN C 939 GLN C 984 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.126348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.099959 restraints weight = 31028.140| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 1.76 r_work: 0.2824 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2680 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.1284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 25392 Z= 0.164 Angle : 0.627 13.261 34596 Z= 0.321 Chirality : 0.049 0.315 3990 Planarity : 0.005 0.045 4392 Dihedral : 7.304 49.788 4275 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.01 % Allowed : 6.48 % Favored : 92.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.14), residues: 3045 helix: 1.21 (0.21), residues: 675 sheet: 1.01 (0.19), residues: 696 loop : -1.56 (0.13), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 38 TYR 0.019 0.001 TYR C1049 PHE 0.021 0.002 PHE B 130 TRP 0.012 0.002 TRP A 423 HIS 0.003 0.001 HIS A1065 Details of bonding type rmsd covalent geometry : bond 0.00400 (25305) covalent geometry : angle 0.58378 (34380) SS BOND : bond 0.00570 ( 45) SS BOND : angle 2.33977 ( 90) hydrogen bonds : bond 0.06127 ( 984) hydrogen bonds : angle 5.31303 ( 2691) link_NAG-ASN : bond 0.00475 ( 42) link_NAG-ASN : angle 3.31357 ( 126) *********************** 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 213 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 186 time to evaluate : 0.783 Fit side-chains REVERT: A 96 ASN cc_start: 0.7665 (t0) cc_final: 0.7059 (t0) REVERT: A 851 MET cc_start: 0.8831 (mtt) cc_final: 0.8534 (mtt) REVERT: B 758 ARG cc_start: 0.8512 (ttp-110) cc_final: 0.8096 (ttp-110) REVERT: C 417 MET cc_start: 0.9078 (ttp) cc_final: 0.8660 (ttm) REVERT: C 630 GLN cc_start: 0.9008 (tp40) cc_final: 0.8106 (tp40) REVERT: C 992 GLN cc_start: 0.8523 (mm-40) cc_final: 0.8257 (mm-40) REVERT: C 1105 SER cc_start: 0.9207 (t) cc_final: 0.8812 (m) outliers start: 27 outliers final: 18 residues processed: 208 average time/residue: 0.1624 time to fit residues: 54.4321 Evaluate side-chains 187 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 169 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain A residue 762 GLU Chi-restraints excluded: chain A residue 973 VAL Chi-restraints excluded: chain B residue 363 THR 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 B residue 1096 ILE Chi-restraints excluded: chain C residue 319 ILE Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 517 THR Chi-restraints excluded: chain C residue 600 ASP Chi-restraints excluded: chain C residue 646 TYR Chi-restraints excluded: chain C residue 729 THR Chi-restraints excluded: chain C residue 762 GLU 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 131 optimal weight: 2.9990 chunk 211 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 chunk 146 optimal weight: 0.7980 chunk 140 optimal weight: 1.9990 chunk 210 optimal weight: 0.6980 chunk 74 optimal weight: 9.9990 chunk 129 optimal weight: 0.7980 chunk 221 optimal weight: 2.9990 chunk 267 optimal weight: 0.9980 chunk 277 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 877 GLN B 181 HIS C 939 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.126442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.100188 restraints weight = 30923.311| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 1.75 r_work: 0.2786 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2642 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.1637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 25392 Z= 0.141 Angle : 0.572 12.910 34596 Z= 0.293 Chirality : 0.047 0.283 3990 Planarity : 0.004 0.040 4392 Dihedral : 6.294 53.783 4247 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.12 % Allowed : 8.61 % Favored : 90.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.14), residues: 3045 helix: 1.42 (0.21), residues: 693 sheet: 0.98 (0.19), residues: 711 loop : -1.50 (0.13), residues: 1641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 395 TYR 0.021 0.001 TYR C1049 PHE 0.016 0.001 PHE B 130 TRP 0.010 0.001 TRP A 423 HIS 0.002 0.001 HIS A1040 Details of bonding type rmsd covalent geometry : bond 0.00340 (25305) covalent geometry : angle 0.53127 (34380) SS BOND : bond 0.00470 ( 45) SS BOND : angle 2.30021 ( 90) hydrogen bonds : bond 0.05586 ( 984) hydrogen bonds : angle 5.11911 ( 2691) link_NAG-ASN : bond 0.00512 ( 42) link_NAG-ASN : angle 3.02374 ( 126) *********************** REFINEMENT MACRO_CYCLE 3 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 216 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 186 time to evaluate : 0.876 Fit side-chains REVERT: A 96 ASN cc_start: 0.7740 (t0) cc_final: 0.7345 (t0) REVERT: A 155 ASN cc_start: 0.7635 (t0) cc_final: 0.6342 (m-40) REVERT: A 851 MET cc_start: 0.8819 (mtt) cc_final: 0.8546 (mtt) REVERT: A 984 GLN cc_start: 0.8475 (tp40) cc_final: 0.8231 (tt0) REVERT: C 417 MET cc_start: 0.9128 (ttp) cc_final: 0.8707 (ttm) REVERT: C 630 GLN cc_start: 0.8970 (tp40) cc_final: 0.8439 (tp40) outliers start: 30 outliers final: 18 residues processed: 211 average time/residue: 0.1509 time to fit residues: 51.7257 Evaluate side-chains 182 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 164 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 722 MET 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 646 TYR Chi-restraints excluded: chain B residue 722 MET Chi-restraints excluded: chain B residue 729 THR Chi-restraints excluded: chain B residue 973 VAL Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 319 ILE Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 646 TYR Chi-restraints excluded: chain C residue 722 MET Chi-restraints excluded: chain C residue 762 GLU Chi-restraints excluded: chain C residue 958 VAL Chi-restraints excluded: chain C residue 973 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 29 optimal weight: 0.6980 chunk 50 optimal weight: 0.9980 chunk 211 optimal weight: 0.7980 chunk 83 optimal weight: 0.0370 chunk 185 optimal weight: 0.0980 chunk 300 optimal weight: 6.9990 chunk 53 optimal weight: 4.9990 chunk 263 optimal weight: 4.9990 chunk 267 optimal weight: 0.8980 chunk 95 optimal weight: 5.9990 chunk 73 optimal weight: 3.9990 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 181 HIS C 939 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.128274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.102084 restraints weight = 30863.880| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 1.72 r_work: 0.2865 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2731 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.086 25392 Z= 0.107 Angle : 0.538 14.378 34596 Z= 0.274 Chirality : 0.045 0.283 3990 Planarity : 0.004 0.038 4392 Dihedral : 5.826 59.721 4246 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.97 % Allowed : 9.29 % Favored : 89.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.14), residues: 3045 helix: 1.69 (0.21), residues: 690 sheet: 0.85 (0.20), residues: 618 loop : -1.31 (0.13), residues: 1737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 99 TYR 0.018 0.001 TYR A1049 PHE 0.012 0.001 PHE A 130 TRP 0.009 0.001 TRP C 423 HIS 0.001 0.000 HIS A 33 Details of bonding type rmsd covalent geometry : bond 0.00247 (25305) covalent geometry : angle 0.50059 (34380) SS BOND : bond 0.00616 ( 45) SS BOND : angle 2.11981 ( 90) hydrogen bonds : bond 0.04699 ( 984) hydrogen bonds : angle 4.96252 ( 2691) link_NAG-ASN : bond 0.00542 ( 42) link_NAG-ASN : angle 2.82159 ( 126) *********************** REFINEMENT MACRO_CYCLE 4 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 204 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 178 time to evaluate : 0.826 Fit side-chains REVERT: A 984 GLN cc_start: 0.8295 (tp40) cc_final: 0.8061 (tt0) REVERT: A 1089 ARG cc_start: 0.8160 (OUTLIER) cc_final: 0.7902 (ttp-170) REVERT: B 572 ASP cc_start: 0.7922 (m-30) cc_final: 0.7708 (m-30) REVERT: B 758 ARG cc_start: 0.8333 (ttp-110) cc_final: 0.7925 (ttp-110) REVERT: C 428 ILE cc_start: 0.8829 (mm) cc_final: 0.8518 (mt) REVERT: C 630 GLN cc_start: 0.8874 (tp40) cc_final: 0.8265 (tp40) REVERT: C 1006 LEU cc_start: 0.9114 (tp) cc_final: 0.8904 (tp) outliers start: 26 outliers final: 21 residues processed: 199 average time/residue: 0.1579 time to fit residues: 50.1446 Evaluate side-chains 185 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 163 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 722 MET Chi-restraints excluded: chain A residue 729 THR Chi-restraints excluded: chain A residue 848 THR Chi-restraints excluded: chain A residue 973 VAL Chi-restraints excluded: chain A residue 1089 ARG Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 502 GLU Chi-restraints excluded: chain B residue 646 TYR Chi-restraints excluded: chain B residue 762 GLU Chi-restraints excluded: chain B residue 877 GLN Chi-restraints excluded: chain B residue 973 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 646 TYR Chi-restraints excluded: chain C residue 762 GLU Chi-restraints excluded: chain C residue 958 VAL Chi-restraints excluded: chain C residue 973 VAL Chi-restraints excluded: chain C residue 1089 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 134 optimal weight: 1.9990 chunk 206 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 98 optimal weight: 6.9990 chunk 190 optimal weight: 4.9990 chunk 203 optimal weight: 1.9990 chunk 294 optimal weight: 0.6980 chunk 195 optimal weight: 0.9990 chunk 233 optimal weight: 0.6980 chunk 264 optimal weight: 0.9990 chunk 45 optimal weight: 5.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 ASN ** A 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 181 HIS C 939 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.126060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.100116 restraints weight = 30852.636| |-----------------------------------------------------------------------------| r_work (start): 0.3001 rms_B_bonded: 1.76 r_work: 0.2808 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2664 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 25392 Z= 0.141 Angle : 0.563 14.512 34596 Z= 0.286 Chirality : 0.047 0.282 3990 Planarity : 0.004 0.036 4392 Dihedral : 5.674 51.146 4245 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.42 % Allowed : 9.89 % Favored : 88.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.14), residues: 3045 helix: 1.66 (0.21), residues: 693 sheet: 0.84 (0.20), residues: 621 loop : -1.31 (0.13), residues: 1731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 395 TYR 0.020 0.001 TYR C1049 PHE 0.015 0.001 PHE C 83 TRP 0.016 0.001 TRP C 868 HIS 0.002 0.001 HIS B1046 Details of bonding type rmsd covalent geometry : bond 0.00344 (25305) covalent geometry : angle 0.52859 (34380) SS BOND : bond 0.00700 ( 45) SS BOND : angle 2.09949 ( 90) hydrogen bonds : bond 0.05424 ( 984) hydrogen bonds : angle 4.95431 ( 2691) link_NAG-ASN : bond 0.00489 ( 42) link_NAG-ASN : angle 2.74990 ( 126) *********************** REFINEMENT MACRO_CYCLE 5 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 207 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 169 time to evaluate : 0.876 Fit side-chains REVERT: A 984 GLN cc_start: 0.8506 (tp40) cc_final: 0.8242 (tt0) REVERT: A 1089 ARG cc_start: 0.8230 (OUTLIER) cc_final: 0.7972 (ttp-170) REVERT: B 758 ARG cc_start: 0.8542 (ttp-110) cc_final: 0.8120 (ttp-110) REVERT: B 768 LYS cc_start: 0.6985 (ptpt) cc_final: 0.6124 (pttm) outliers start: 38 outliers final: 32 residues processed: 201 average time/residue: 0.1554 time to fit residues: 49.8818 Evaluate side-chains 191 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 158 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 323 CYS Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 722 MET Chi-restraints excluded: chain A residue 729 THR Chi-restraints excluded: chain A residue 762 GLU Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 973 VAL Chi-restraints excluded: chain A residue 1089 ARG Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 323 CYS Chi-restraints excluded: chain B residue 502 GLU Chi-restraints excluded: chain B residue 646 TYR Chi-restraints excluded: chain B residue 722 MET Chi-restraints excluded: chain B residue 848 THR Chi-restraints excluded: chain B residue 877 GLN Chi-restraints excluded: chain B residue 973 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 323 CYS Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 455 ILE Chi-restraints excluded: chain C residue 646 TYR Chi-restraints excluded: chain C residue 722 MET Chi-restraints excluded: chain C residue 762 GLU Chi-restraints excluded: chain C residue 848 THR Chi-restraints excluded: chain C residue 958 VAL Chi-restraints excluded: chain C residue 973 VAL Chi-restraints excluded: chain C residue 1089 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 203 optimal weight: 6.9990 chunk 268 optimal weight: 0.6980 chunk 114 optimal weight: 5.9990 chunk 176 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 249 optimal weight: 0.6980 chunk 92 optimal weight: 4.9990 chunk 283 optimal weight: 0.0980 chunk 225 optimal weight: 0.7980 chunk 105 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 ASN ** A 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 181 HIS ** C 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 939 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.127767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.102041 restraints weight = 30938.594| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 1.69 r_work: 0.2837 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2698 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 25392 Z= 0.109 Angle : 0.522 15.065 34596 Z= 0.265 Chirality : 0.045 0.283 3990 Planarity : 0.004 0.036 4392 Dihedral : 5.363 50.237 4245 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.61 % Allowed : 10.30 % Favored : 88.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.14), residues: 3045 helix: 1.82 (0.21), residues: 693 sheet: 0.92 (0.20), residues: 615 loop : -1.25 (0.13), residues: 1737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 38 TYR 0.018 0.001 TYR C1049 PHE 0.011 0.001 PHE A 130 TRP 0.022 0.001 TRP C 868 HIS 0.001 0.000 HIS A 33 Details of bonding type rmsd covalent geometry : bond 0.00253 (25305) covalent geometry : angle 0.48971 (34380) SS BOND : bond 0.00580 ( 45) SS BOND : angle 1.87657 ( 90) hydrogen bonds : bond 0.04744 ( 984) hydrogen bonds : angle 4.85550 ( 2691) link_NAG-ASN : bond 0.00538 ( 42) link_NAG-ASN : angle 2.63423 ( 126) *********************** REFINEMENT MACRO_CYCLE 6 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 215 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 172 time to evaluate : 0.795 Fit side-chains REVERT: A 130 PHE cc_start: 0.8771 (OUTLIER) cc_final: 0.8559 (m-80) REVERT: A 984 GLN cc_start: 0.8340 (tp40) cc_final: 0.8115 (tt0) REVERT: A 1089 ARG cc_start: 0.8188 (OUTLIER) cc_final: 0.7920 (ttp-170) REVERT: B 758 ARG cc_start: 0.8382 (ttp-110) cc_final: 0.7953 (ttp-110) REVERT: B 768 LYS cc_start: 0.6972 (ptpt) cc_final: 0.6122 (pttm) REVERT: C 1006 LEU cc_start: 0.9117 (tp) cc_final: 0.8901 (tp) outliers start: 43 outliers final: 35 residues processed: 208 average time/residue: 0.1613 time to fit residues: 53.8616 Evaluate side-chains 198 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 161 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 130 PHE Chi-restraints excluded: chain A residue 155 ASN Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 323 CYS Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 722 MET Chi-restraints excluded: chain A residue 729 THR Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 848 THR Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 970 GLU Chi-restraints excluded: chain A residue 973 VAL Chi-restraints excluded: chain A residue 1089 ARG Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 323 CYS Chi-restraints excluded: chain B residue 502 GLU Chi-restraints excluded: chain B residue 646 TYR Chi-restraints excluded: chain B residue 722 MET Chi-restraints excluded: chain B residue 848 THR Chi-restraints excluded: chain B residue 877 GLN Chi-restraints excluded: chain B residue 973 VAL Chi-restraints excluded: chain B residue 1096 ILE Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 323 CYS Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 646 TYR Chi-restraints excluded: chain C residue 722 MET Chi-restraints excluded: chain C residue 762 GLU Chi-restraints excluded: chain C residue 848 THR Chi-restraints excluded: chain C residue 958 VAL Chi-restraints excluded: chain C residue 973 VAL Chi-restraints excluded: chain C residue 1089 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 285 optimal weight: 6.9990 chunk 12 optimal weight: 4.9990 chunk 247 optimal weight: 0.0040 chunk 198 optimal weight: 1.9990 chunk 259 optimal weight: 0.7980 chunk 7 optimal weight: 4.9990 chunk 257 optimal weight: 8.9990 chunk 39 optimal weight: 1.9990 chunk 250 optimal weight: 5.9990 chunk 222 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 overall best weight: 1.3598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 181 HIS C 181 HIS ** C 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 939 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.125491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.099614 restraints weight = 30988.215| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 1.73 r_work: 0.2780 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2641 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.2123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 25392 Z= 0.161 Angle : 0.573 15.399 34596 Z= 0.293 Chirality : 0.047 0.286 3990 Planarity : 0.004 0.036 4392 Dihedral : 5.496 52.156 4245 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.80 % Allowed : 10.56 % Favored : 87.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.14), residues: 3045 helix: 1.67 (0.21), residues: 696 sheet: 0.81 (0.20), residues: 621 loop : -1.28 (0.13), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B1021 TYR 0.021 0.001 TYR C1049 PHE 0.017 0.001 PHE C 83 TRP 0.023 0.002 TRP C 868 HIS 0.003 0.001 HIS B1065 Details of bonding type rmsd covalent geometry : bond 0.00400 (25305) covalent geometry : angle 0.54195 (34380) SS BOND : bond 0.00649 ( 45) SS BOND : angle 2.13232 ( 90) hydrogen bonds : bond 0.05705 ( 984) hydrogen bonds : angle 4.95225 ( 2691) link_NAG-ASN : bond 0.00474 ( 42) link_NAG-ASN : angle 2.62036 ( 126) *********************** REFINEMENT MACRO_CYCLE 7 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 220 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 172 time to evaluate : 0.614 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 130 PHE cc_start: 0.8845 (OUTLIER) cc_final: 0.8452 (m-80) REVERT: A 984 GLN cc_start: 0.8492 (tp40) cc_final: 0.8224 (tt0) REVERT: A 1089 ARG cc_start: 0.8185 (OUTLIER) cc_final: 0.7900 (ttp-170) REVERT: B 758 ARG cc_start: 0.8684 (ttp-110) cc_final: 0.8247 (ttp-110) REVERT: B 768 LYS cc_start: 0.6994 (ptpt) cc_final: 0.6125 (pttm) REVERT: C 417 MET cc_start: 0.9058 (ttp) cc_final: 0.8608 (ttm) REVERT: C 679 MET cc_start: 0.8441 (ptt) cc_final: 0.8122 (ptp) outliers start: 48 outliers final: 43 residues processed: 215 average time/residue: 0.1567 time to fit residues: 53.6833 Evaluate side-chains 208 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 163 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 130 PHE Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 323 CYS Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 646 TYR Chi-restraints excluded: chain A residue 722 MET Chi-restraints excluded: chain A residue 729 THR Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 762 GLU Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 969 CYS Chi-restraints excluded: chain A residue 970 GLU Chi-restraints excluded: chain A residue 973 VAL Chi-restraints excluded: chain A residue 1089 ARG Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 323 CYS Chi-restraints excluded: chain B residue 502 GLU Chi-restraints excluded: chain B residue 646 TYR Chi-restraints excluded: chain B residue 722 MET Chi-restraints excluded: chain B residue 762 GLU Chi-restraints excluded: chain B residue 848 THR Chi-restraints excluded: chain B residue 877 GLN Chi-restraints excluded: chain B residue 973 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 323 CYS Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 455 ILE Chi-restraints excluded: chain C residue 517 THR Chi-restraints excluded: chain C residue 600 ASP Chi-restraints excluded: chain C residue 646 TYR Chi-restraints excluded: chain C residue 722 MET Chi-restraints excluded: chain C residue 729 THR Chi-restraints excluded: chain C residue 762 GLU Chi-restraints excluded: chain C residue 848 THR Chi-restraints excluded: chain C residue 958 VAL Chi-restraints excluded: chain C residue 969 CYS Chi-restraints excluded: chain C residue 973 VAL Chi-restraints excluded: chain C residue 1089 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 285 optimal weight: 5.9990 chunk 184 optimal weight: 0.9990 chunk 87 optimal weight: 2.9990 chunk 178 optimal weight: 0.9980 chunk 289 optimal weight: 0.9990 chunk 156 optimal weight: 7.9990 chunk 217 optimal weight: 0.7980 chunk 139 optimal weight: 1.9990 chunk 259 optimal weight: 6.9990 chunk 166 optimal weight: 0.6980 chunk 108 optimal weight: 0.6980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 181 HIS ** C 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 939 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.126904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.101294 restraints weight = 30699.140| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 1.70 r_work: 0.2805 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2665 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.2184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 25392 Z= 0.123 Angle : 0.544 15.040 34596 Z= 0.278 Chirality : 0.046 0.284 3990 Planarity : 0.004 0.037 4392 Dihedral : 5.346 52.009 4245 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.69 % Allowed : 11.09 % Favored : 87.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.14), residues: 3045 helix: 1.81 (0.21), residues: 693 sheet: 0.84 (0.20), residues: 621 loop : -1.25 (0.13), residues: 1731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 38 TYR 0.024 0.001 TYR B 200 PHE 0.011 0.001 PHE B 83 TRP 0.024 0.001 TRP C 868 HIS 0.003 0.001 HIS B1065 Details of bonding type rmsd covalent geometry : bond 0.00294 (25305) covalent geometry : angle 0.51208 (34380) SS BOND : bond 0.00619 ( 45) SS BOND : angle 2.06609 ( 90) hydrogen bonds : bond 0.05076 ( 984) hydrogen bonds : angle 4.95522 ( 2691) link_NAG-ASN : bond 0.00528 ( 42) link_NAG-ASN : angle 2.56153 ( 126) *********************** REFINEMENT MACRO_CYCLE 8 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 215 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 170 time to evaluate : 0.799 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 541 SER cc_start: 0.8735 (t) cc_final: 0.8477 (p) REVERT: A 984 GLN cc_start: 0.8410 (tp40) cc_final: 0.8094 (tt0) REVERT: A 1089 ARG cc_start: 0.8183 (OUTLIER) cc_final: 0.7902 (ttp-170) REVERT: B 758 ARG cc_start: 0.8525 (ttp-110) cc_final: 0.8079 (ttp-110) REVERT: B 768 LYS cc_start: 0.6921 (ptpt) cc_final: 0.6050 (pttm) REVERT: B 1114 ILE cc_start: 0.9319 (tt) cc_final: 0.9022 (tt) REVERT: C 679 MET cc_start: 0.8418 (ptt) cc_final: 0.8131 (ptp) outliers start: 45 outliers final: 38 residues processed: 210 average time/residue: 0.1587 time to fit residues: 53.4622 Evaluate side-chains 205 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 166 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 323 CYS Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 646 TYR Chi-restraints excluded: chain A residue 722 MET Chi-restraints excluded: chain A residue 729 THR Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 762 GLU Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 969 CYS Chi-restraints excluded: chain A residue 970 GLU Chi-restraints excluded: chain A residue 973 VAL Chi-restraints excluded: chain A residue 1089 ARG Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 323 CYS Chi-restraints excluded: chain B residue 502 GLU Chi-restraints excluded: chain B residue 646 TYR Chi-restraints excluded: chain B residue 722 MET Chi-restraints excluded: chain B residue 762 GLU Chi-restraints excluded: chain B residue 848 THR Chi-restraints excluded: chain B residue 877 GLN Chi-restraints excluded: chain B residue 973 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 323 CYS Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 646 TYR Chi-restraints excluded: chain C residue 722 MET Chi-restraints excluded: chain C residue 762 GLU Chi-restraints excluded: chain C residue 848 THR Chi-restraints excluded: chain C residue 958 VAL Chi-restraints excluded: chain C residue 969 CYS Chi-restraints excluded: chain C residue 973 VAL Chi-restraints excluded: chain C residue 1089 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 224 optimal weight: 3.9990 chunk 80 optimal weight: 4.9990 chunk 69 optimal weight: 0.5980 chunk 51 optimal weight: 0.4980 chunk 47 optimal weight: 2.9990 chunk 20 optimal weight: 6.9990 chunk 5 optimal weight: 6.9990 chunk 277 optimal weight: 3.9990 chunk 142 optimal weight: 0.2980 chunk 173 optimal weight: 3.9990 chunk 50 optimal weight: 0.6980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 939 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.126417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.100164 restraints weight = 30916.122| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 1.73 r_work: 0.2801 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2662 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.2245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.093 25392 Z= 0.135 Angle : 0.557 15.049 34596 Z= 0.284 Chirality : 0.046 0.286 3990 Planarity : 0.004 0.037 4392 Dihedral : 5.341 52.336 4245 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.61 % Allowed : 11.31 % Favored : 87.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.14), residues: 3045 helix: 1.98 (0.21), residues: 675 sheet: 0.80 (0.20), residues: 624 loop : -1.24 (0.13), residues: 1746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 395 TYR 0.021 0.001 TYR B 200 PHE 0.013 0.001 PHE A 83 TRP 0.024 0.001 TRP C 868 HIS 0.005 0.001 HIS A1065 Details of bonding type rmsd covalent geometry : bond 0.00328 (25305) covalent geometry : angle 0.52647 (34380) SS BOND : bond 0.00670 ( 45) SS BOND : angle 2.05745 ( 90) hydrogen bonds : bond 0.05280 ( 984) hydrogen bonds : angle 4.98038 ( 2691) link_NAG-ASN : bond 0.00503 ( 42) link_NAG-ASN : angle 2.53386 ( 126) *********************** REFINEMENT MACRO_CYCLE 9 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 215 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 172 time to evaluate : 0.900 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 541 SER cc_start: 0.8771 (t) cc_final: 0.8503 (p) REVERT: A 984 GLN cc_start: 0.8418 (tp40) cc_final: 0.8100 (tt0) REVERT: A 1089 ARG cc_start: 0.8185 (OUTLIER) cc_final: 0.7909 (ttp-170) REVERT: A 1105 SER cc_start: 0.8781 (t) cc_final: 0.8318 (m) REVERT: B 299 ILE cc_start: 0.9256 (OUTLIER) cc_final: 0.9015 (tt) REVERT: B 758 ARG cc_start: 0.8668 (ttp-110) cc_final: 0.8229 (ttp-110) REVERT: B 768 LYS cc_start: 0.6928 (ptpt) cc_final: 0.6054 (pttm) REVERT: B 1114 ILE cc_start: 0.9292 (tt) cc_final: 0.9023 (tt) REVERT: C 1105 SER cc_start: 0.8986 (t) cc_final: 0.8434 (m) outliers start: 43 outliers final: 40 residues processed: 209 average time/residue: 0.1622 time to fit residues: 53.8990 Evaluate side-chains 209 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 167 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 323 CYS Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 646 TYR Chi-restraints excluded: chain A residue 722 MET Chi-restraints excluded: chain A residue 729 THR Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 762 GLU Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 969 CYS Chi-restraints excluded: chain A residue 970 GLU Chi-restraints excluded: chain A residue 973 VAL Chi-restraints excluded: chain A residue 1089 ARG Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 323 CYS Chi-restraints excluded: chain B residue 502 GLU Chi-restraints excluded: chain B residue 646 TYR Chi-restraints excluded: chain B residue 722 MET Chi-restraints excluded: chain B residue 762 GLU Chi-restraints excluded: chain B residue 848 THR Chi-restraints excluded: chain B residue 877 GLN Chi-restraints excluded: chain B residue 973 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 323 CYS Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 517 THR Chi-restraints excluded: chain C residue 646 TYR Chi-restraints excluded: chain C residue 722 MET Chi-restraints excluded: chain C residue 729 THR Chi-restraints excluded: chain C residue 762 GLU Chi-restraints excluded: chain C residue 848 THR Chi-restraints excluded: chain C residue 958 VAL Chi-restraints excluded: chain C residue 969 CYS Chi-restraints excluded: chain C residue 973 VAL Chi-restraints excluded: chain C residue 1089 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 15 optimal weight: 1.9990 chunk 158 optimal weight: 1.9990 chunk 255 optimal weight: 0.0570 chunk 250 optimal weight: 4.9990 chunk 27 optimal weight: 5.9990 chunk 113 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 241 optimal weight: 3.9990 chunk 161 optimal weight: 0.2980 chunk 21 optimal weight: 0.9990 chunk 270 optimal weight: 4.9990 overall best weight: 1.0704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 939 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.125953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.100247 restraints weight = 30976.556| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 1.73 r_work: 0.2792 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2649 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.2312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 25392 Z= 0.140 Angle : 0.561 15.004 34596 Z= 0.287 Chirality : 0.046 0.285 3990 Planarity : 0.004 0.037 4392 Dihedral : 5.339 53.278 4245 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.72 % Allowed : 11.20 % Favored : 87.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.14), residues: 3045 helix: 1.99 (0.21), residues: 672 sheet: 0.79 (0.20), residues: 624 loop : -1.23 (0.13), residues: 1749 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 38 TYR 0.021 0.001 TYR B 200 PHE 0.013 0.001 PHE B 83 TRP 0.027 0.001 TRP C 868 HIS 0.006 0.001 HIS A1065 Details of bonding type rmsd covalent geometry : bond 0.00342 (25305) covalent geometry : angle 0.53163 (34380) SS BOND : bond 0.00655 ( 45) SS BOND : angle 2.05056 ( 90) hydrogen bonds : bond 0.05368 ( 984) hydrogen bonds : angle 4.99553 ( 2691) link_NAG-ASN : bond 0.00502 ( 42) link_NAG-ASN : angle 2.51101 ( 126) ********************** REFINEMENT MACRO_CYCLE 10 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 219 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 173 time to evaluate : 0.703 Fit side-chains revert: symmetry clash REVERT: A 984 GLN cc_start: 0.8447 (tp40) cc_final: 0.8124 (tt0) REVERT: A 1089 ARG cc_start: 0.8201 (OUTLIER) cc_final: 0.7905 (ttp-170) REVERT: A 1105 SER cc_start: 0.8763 (t) cc_final: 0.8290 (m) REVERT: B 299 ILE cc_start: 0.9252 (OUTLIER) cc_final: 0.9019 (tt) REVERT: B 758 ARG cc_start: 0.8689 (ttp-110) cc_final: 0.8231 (ttp-110) REVERT: B 768 LYS cc_start: 0.6881 (ptpt) cc_final: 0.5983 (pttm) REVERT: B 1074 GLU cc_start: 0.8037 (pt0) cc_final: 0.7824 (pt0) REVERT: B 1114 ILE cc_start: 0.9314 (tt) cc_final: 0.9069 (tt) REVERT: C 1105 SER cc_start: 0.8976 (t) cc_final: 0.8394 (m) outliers start: 46 outliers final: 43 residues processed: 211 average time/residue: 0.1628 time to fit residues: 54.7793 Evaluate side-chains 212 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 167 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 323 CYS Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 646 TYR Chi-restraints excluded: chain A residue 722 MET Chi-restraints excluded: chain A residue 729 THR Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 762 GLU Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 969 CYS Chi-restraints excluded: chain A residue 970 GLU Chi-restraints excluded: chain A residue 973 VAL Chi-restraints excluded: chain A residue 1089 ARG Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 323 CYS Chi-restraints excluded: chain B residue 502 GLU Chi-restraints excluded: chain B residue 646 TYR Chi-restraints excluded: chain B residue 722 MET Chi-restraints excluded: chain B residue 762 GLU Chi-restraints excluded: chain B residue 848 THR Chi-restraints excluded: chain B residue 877 GLN Chi-restraints excluded: chain B residue 973 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 323 CYS Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 517 THR Chi-restraints excluded: chain C residue 646 TYR Chi-restraints excluded: chain C residue 722 MET Chi-restraints excluded: chain C residue 729 THR Chi-restraints excluded: chain C residue 762 GLU Chi-restraints excluded: chain C residue 848 THR Chi-restraints excluded: chain C residue 958 VAL Chi-restraints excluded: chain C residue 973 VAL Chi-restraints excluded: chain C residue 1089 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 266 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 258 optimal weight: 0.9990 chunk 85 optimal weight: 0.9990 chunk 304 optimal weight: 2.9990 chunk 111 optimal weight: 7.9990 chunk 238 optimal weight: 0.9980 chunk 179 optimal weight: 4.9990 chunk 117 optimal weight: 1.9990 chunk 26 optimal weight: 0.0870 chunk 28 optimal weight: 0.8980 overall best weight: 0.7962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 939 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.127177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.101561 restraints weight = 30835.943| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 1.65 r_work: 0.2821 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2683 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.2351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 25392 Z= 0.121 Angle : 0.542 14.814 34596 Z= 0.277 Chirality : 0.046 0.285 3990 Planarity : 0.004 0.038 4392 Dihedral : 5.217 52.863 4245 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.61 % Allowed : 11.27 % Favored : 87.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.15), residues: 3045 helix: 2.07 (0.21), residues: 672 sheet: 0.80 (0.20), residues: 654 loop : -1.22 (0.13), residues: 1719 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 38 TYR 0.020 0.001 TYR B 200 PHE 0.010 0.001 PHE A 130 TRP 0.030 0.001 TRP A 868 HIS 0.006 0.001 HIS B1065 Details of bonding type rmsd covalent geometry : bond 0.00288 (25305) covalent geometry : angle 0.51332 (34380) SS BOND : bond 0.00625 ( 45) SS BOND : angle 1.88974 ( 90) hydrogen bonds : bond 0.04949 ( 984) hydrogen bonds : angle 4.93486 ( 2691) link_NAG-ASN : bond 0.00521 ( 42) link_NAG-ASN : angle 2.46684 ( 126) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5407.52 seconds wall clock time: 93 minutes 11.18 seconds (5591.18 seconds total)