Starting phenix.real_space_refine on Wed May 21 21:47:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8h16_34426/05_2025/8h16_34426.cif Found real_map, /net/cci-nas-00/data/ceres_data/8h16_34426/05_2025/8h16_34426.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.35534 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8h16_34426/05_2025/8h16_34426.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8h16_34426/05_2025/8h16_34426.map" model { file = "/net/cci-nas-00/data/ceres_data/8h16_34426/05_2025/8h16_34426.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8h16_34426/05_2025/8h16_34426.cif" } resolution = 3.35534 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 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 111 5.16 5 C 13977 2.51 5 N 3603 2.21 5 O 4243 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 97 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 21934 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 7549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 966, 7549 Classifications: {'peptide': 966} Link IDs: {'PTRANS': 44, 'TRANS': 921} Chain breaks: 11 Chain: "A" Number of atoms: 6252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 805, 6252 Classifications: {'peptide': 805} Link IDs: {'PTRANS': 35, 'TRANS': 769} Chain breaks: 8 Chain: "C" Number of atoms: 7685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 983, 7685 Classifications: {'peptide': 983} Link IDs: {'PTRANS': 44, 'TRANS': 938} Chain breaks: 10 Chain: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "C" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Time building chain proxies: 11.35, per 1000 atoms: 0.52 Number of scatterers: 21934 At special positions: 0 Unit cell: (128.25, 129.6, 163.35, 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 111 16.00 O 4243 8.00 N 3603 7.00 C 13977 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=34, symmetry=0 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=2.03 Simple disulfide: pdb=" SG CYS B 378 " - pdb=" SG CYS B 511 " distance=2.05 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=2.04 Simple disulfide: pdb=" SG CYS B 725 " - pdb=" SG CYS B 731 " distance=2.04 Simple disulfide: pdb=" SG CYS B 822 " - pdb=" SG CYS B 833 " distance=2.05 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 A 128 " - pdb=" SG CYS A 159 " distance=2.04 Simple disulfide: pdb=" SG CYS A 278 " - pdb=" SG CYS A 288 " distance=2.03 Simple disulfide: pdb=" SG CYS A 524 " - pdb=" SG CYS A 576 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS A 725 " - pdb=" SG CYS A 731 " distance=2.03 Simple disulfide: pdb=" SG CYS A1014 " - pdb=" SG CYS A1025 " distance=2.01 Simple disulfide: pdb=" SG CYS A1064 " - pdb=" SG CYS A1108 " distance=2.04 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=2.02 Simple disulfide: pdb=" SG CYS C 323 " - pdb=" SG CYS C 348 " distance=2.02 Simple disulfide: pdb=" SG CYS C 366 " - pdb=" SG CYS C 419 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 511 " distance=2.05 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=2.01 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=2.04 Simple disulfide: pdb=" SG CYS C 725 " - pdb=" SG CYS C 731 " distance=2.03 Simple disulfide: pdb=" SG CYS C 822 " - pdb=" SG CYS C 833 " distance=2.03 Simple disulfide: pdb=" SG CYS C1014 " - pdb=" SG CYS C1025 " distance=2.01 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 A1080 " " NAG A1302 " - " ASN A 119 " " NAG A1303 " - " ASN A 158 " " NAG A1304 " - " ASN A 227 " " NAG A1305 " - " ASN A 269 " " NAG A1306 " - " ASN A 602 " " NAG A1307 " - " ASN A 691 " " NAG A1308 " - " ASN A 699 " " NAG A1309 " - " ASN A 783 " " NAG A1310 " - " ASN A1056 " " NAG A1311 " - " ASN A1116 " " NAG B1301 " - " ASN B1080 " " NAG B1302 " - " ASN B 269 " " NAG B1303 " - " ASN B 318 " " NAG B1304 " - " ASN B 602 " " NAG B1305 " - " ASN B 691 " " NAG B1306 " - " ASN B 699 " " NAG B1307 " - " ASN B 783 " " NAG B1308 " - " ASN B1056 " " NAG B1309 " - " ASN B1116 " " NAG C1301 " - " ASN C 65 " " NAG C1302 " - " ASN C1080 " " NAG C1303 " - " ASN C 119 " " NAG C1304 " - " ASN C 227 " " NAG C1305 " - " ASN C 269 " " NAG C1306 " - " ASN C 318 " " NAG C1307 " - " ASN C 602 " " NAG C1308 " - " ASN C 691 " " NAG C1309 " - " ASN C 699 " " NAG C1310 " - " ASN C 783 " " NAG C1311 " - " ASN C1056 " " NAG C1312 " - " ASN C1116 " Time building additional restraints: 5.62 Conformation dependent library (CDL) restraints added in 2.9 seconds 5380 Ramachandran restraints generated. 2690 Oldfield, 0 Emsley, 2690 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5164 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 42 sheets defined 26.8% alpha, 29.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.56 Creating SS restraints... Processing helix chain 'B' and resid 281 through 291 Processing helix chain 'B' and resid 324 through 330 removed outlier: 4.164A pdb=" N VAL B 328 " --> pdb=" O PRO B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 340 removed outlier: 3.990A pdb=" N TRP B 340 " --> pdb=" O VAL B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 357 removed outlier: 4.277A pdb=" N TYR B 356 " --> pdb=" O TYR B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 376 removed outlier: 4.213A pdb=" N ASN B 375 " --> pdb=" O THR B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 390 through 397 removed outlier: 3.929A pdb=" N VAL B 394 " --> pdb=" O GLY B 391 " (cutoff:3.500A) removed outlier: 3.867A 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 602 through 612 removed outlier: 3.580A pdb=" N VAL B 606 " --> pdb=" O ASN B 602 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N THR B 608 " --> pdb=" O THR B 604 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N HIS B 611 " --> pdb=" O SER B 607 " (cutoff:3.500A) Processing helix chain 'B' and resid 719 through 725 Processing helix chain 'B' and resid 728 through 736 removed outlier: 3.859A pdb=" N LEU B 736 " --> pdb=" O ALA B 732 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 739 No H-bonds generated for 'chain 'B' and resid 737 through 739' Processing helix chain 'B' and resid 741 through 765 removed outlier: 3.992A pdb=" N THR B 760 " --> pdb=" O GLN B 756 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ARG B 761 " --> pdb=" O ASP B 757 " (cutoff:3.500A) Processing helix chain 'B' and resid 798 through 808 removed outlier: 3.559A pdb=" N VAL B 808 " --> pdb=" O LEU B 804 " (cutoff:3.500A) Processing helix chain 'B' and resid 848 through 866 removed outlier: 3.551A pdb=" N TYR B 855 " --> pdb=" O MET B 851 " (cutoff:3.500A) Processing helix chain 'B' and resid 868 through 873 removed outlier: 4.408A pdb=" N ALA B 872 " --> pdb=" O TRP B 868 " (cutoff:3.500A) Processing helix chain 'B' and resid 879 through 891 removed outlier: 3.875A pdb=" N TYR B 886 " --> pdb=" O MET B 882 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ILE B 891 " --> pdb=" O ARG B 887 " (cutoff:3.500A) Processing helix chain 'B' and resid 894 through 901 removed outlier: 4.348A pdb=" N LEU B 898 " --> pdb=" O THR B 894 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N TYR B 899 " --> pdb=" O GLN B 895 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASN B 901 " --> pdb=" O VAL B 897 " (cutoff:3.500A) Processing helix chain 'B' and resid 901 through 922 Processing helix chain 'B' and resid 927 through 947 removed outlier: 4.040A pdb=" N VAL B 933 " --> pdb=" O LYS B 929 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N VAL B 934 " --> pdb=" O LEU B 930 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ASN B 937 " --> pdb=" O VAL B 933 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU B 944 " --> pdb=" O ALA B 940 " (cutoff:3.500A) Processing helix chain 'B' and resid 958 through 966 removed outlier: 3.819A pdb=" N ILE B 962 " --> pdb=" O VAL B 958 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU B 966 " --> pdb=" O ILE B 962 " (cutoff:3.500A) Processing helix chain 'B' and resid 967 through 1014 removed outlier: 3.633A pdb=" N VAL B 973 " --> pdb=" O VAL B 969 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ARG B 977 " --> pdb=" O VAL B 973 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LEU B 978 " --> pdb=" O GLN B 974 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N TYR B 989 " --> pdb=" O SER B 985 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLU B 999 " --> pdb=" O ILE B 995 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 291 Processing helix chain 'A' and resid 602 through 612 removed outlier: 4.134A pdb=" N THR A 608 " --> pdb=" O THR A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 719 through 725 Processing helix chain 'A' and resid 728 through 735 Processing helix chain 'A' and resid 740 through 765 removed outlier: 4.014A pdb=" N GLN A 744 " --> pdb=" O SER A 740 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ASP A 757 " --> pdb=" O ALA A 753 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR A 760 " --> pdb=" O GLN A 756 " (cutoff:3.500A) Processing helix chain 'A' and resid 798 through 808 removed outlier: 3.697A pdb=" N VAL A 808 " --> pdb=" O LEU A 804 " (cutoff:3.500A) Processing helix chain 'A' and resid 848 through 867 Processing helix chain 'A' and resid 868 through 873 removed outlier: 4.307A pdb=" N ALA A 872 " --> pdb=" O TRP A 868 " (cutoff:3.500A) Processing helix chain 'A' and resid 879 through 892 removed outlier: 3.779A pdb=" N ILE A 891 " --> pdb=" O ARG A 887 " (cutoff:3.500A) Processing helix chain 'A' and resid 894 through 901 removed outlier: 4.364A pdb=" N LEU A 898 " --> pdb=" O THR A 894 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N TYR A 899 " --> pdb=" O GLN A 895 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 923 removed outlier: 3.510A pdb=" N ILE A 905 " --> pdb=" O ASN A 901 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N THR A 923 " --> pdb=" O SER A 919 " (cutoff:3.500A) Processing helix chain 'A' and resid 927 through 947 removed outlier: 3.537A pdb=" N VAL A 934 " --> pdb=" O LEU A 930 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLN A 936 " --> pdb=" O ASP A 932 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ASN A 937 " --> pdb=" O VAL A 933 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU A 944 " --> pdb=" O ALA A 940 " (cutoff:3.500A) Processing helix chain 'A' and resid 958 through 966 removed outlier: 3.582A pdb=" N ILE A 962 " --> pdb=" O VAL A 958 " (cutoff:3.500A) Processing helix chain 'A' and resid 967 through 1015 removed outlier: 4.110A pdb=" N VAL A 973 " --> pdb=" O VAL A 969 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLN A 974 " --> pdb=" O GLU A 970 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ARG A 977 " --> pdb=" O VAL A 973 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU A 978 " --> pdb=" O GLN A 974 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLN A 984 " --> pdb=" O THR A 980 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N TYR A 989 " --> pdb=" O SER A 985 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ALA A 998 " --> pdb=" O LEU A 994 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLU A 999 " --> pdb=" O ILE A 995 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N SER A1003 " --> pdb=" O GLU A 999 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N THR A1009 " --> pdb=" O ASN A1005 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 291 Processing helix chain 'C' and resid 324 through 330 removed outlier: 3.982A pdb=" N VAL C 328 " --> pdb=" O PRO C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 336 through 340 removed outlier: 3.939A pdb=" N TRP C 340 " --> pdb=" O VAL C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 352 through 357 removed outlier: 4.068A pdb=" N TYR C 356 " --> pdb=" O TYR C 352 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 374 Processing helix chain 'C' and resid 403 through 409 Processing helix chain 'C' and resid 603 through 612 Processing helix chain 'C' and resid 719 through 725 Processing helix chain 'C' and resid 728 through 735 Processing helix chain 'C' and resid 736 through 739 removed outlier: 3.591A pdb=" N GLY C 739 " --> pdb=" O LEU C 736 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 736 through 739' Processing helix chain 'C' and resid 741 through 765 removed outlier: 3.930A pdb=" N ASP C 757 " --> pdb=" O ALA C 753 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ARG C 758 " --> pdb=" O ALA C 754 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N VAL C 763 " --> pdb=" O ASN C 759 " (cutoff:3.500A) Processing helix chain 'C' and resid 798 through 808 removed outlier: 3.526A pdb=" N VAL C 808 " --> pdb=" O LEU C 804 " (cutoff:3.500A) Processing helix chain 'C' and resid 848 through 866 removed outlier: 3.595A pdb=" N TYR C 855 " --> pdb=" O MET C 851 " (cutoff:3.500A) Processing helix chain 'C' and resid 868 through 872 Processing helix chain 'C' and resid 879 through 891 removed outlier: 3.746A pdb=" N ILE C 891 " --> pdb=" O ARG C 887 " (cutoff:3.500A) Processing helix chain 'C' and resid 894 through 901 removed outlier: 4.184A pdb=" N LEU C 898 " --> pdb=" O THR C 894 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASN C 901 " --> pdb=" O VAL C 897 " (cutoff:3.500A) Processing helix chain 'C' and resid 901 through 922 Processing helix chain 'C' and resid 927 through 947 removed outlier: 3.525A pdb=" N ASP C 932 " --> pdb=" O GLY C 928 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL C 933 " --> pdb=" O LYS C 929 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL C 934 " --> pdb=" O LEU C 930 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASN C 937 " --> pdb=" O VAL C 933 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR C 943 " --> pdb=" O GLN C 939 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU C 944 " --> pdb=" O ALA C 940 " (cutoff:3.500A) Processing helix chain 'C' and resid 958 through 966 removed outlier: 3.529A pdb=" N LEU C 966 " --> pdb=" O ILE C 962 " (cutoff:3.500A) Processing helix chain 'C' and resid 967 through 1015 removed outlier: 4.362A pdb=" N VAL C 973 " --> pdb=" O VAL C 969 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N GLN C 974 " --> pdb=" O GLU C 970 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLN C 984 " --> pdb=" O THR C 980 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N TYR C 989 " --> pdb=" O SER C 985 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ALA C 998 " --> pdb=" O LEU C 994 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLU C 999 " --> pdb=" O ILE C 995 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA C1002 " --> pdb=" O ALA C 998 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N SER C1003 " --> pdb=" O GLU C 999 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 32 through 35 removed outlier: 3.774A pdb=" N SER B 64 " --> pdb=" O SER B 35 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N ASN B 65 " --> pdb=" O TYR B 256 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N TYR B 256 " --> pdb=" O ASN B 65 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA B 251 " --> pdb=" O THR B 92 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU B 182 " --> pdb=" O GLN B 201 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N LYS B 198 " --> pdb=" O PRO B 218 " (cutoff:3.500A) removed outlier: 8.892A pdb=" N TYR B 200 " --> pdb=" O LEU B 216 " (cutoff:3.500A) removed outlier: 8.285A pdb=" N LEU B 216 " --> pdb=" O TYR B 200 " (cutoff:3.500A) removed outlier: 10.672A pdb=" N ASN B 214 " --> pdb=" O PRO B 202 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N ARG B 38 " --> pdb=" O ASN B 214 " (cutoff:3.500A) removed outlier: 9.214A pdb=" N LEU B 216 " --> pdb=" O ARG B 38 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N VAL B 40 " --> pdb=" O LEU B 216 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 52 through 59 removed outlier: 4.135A pdb=" N ASP B 274 " --> pdb=" O LYS B 265 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 81 through 82 removed outlier: 3.881A pdb=" N GLY B 104 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ARG B 232 " --> pdb=" O VAL B 102 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILE B 234 " --> pdb=" O GLY B 100 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N GLY B 100 " --> pdb=" O ILE B 234 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE B 125 " --> pdb=" O SER B 165 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 298 through 306 removed outlier: 5.512A pdb=" N ILE B 299 " --> pdb=" O THR B 585 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N THR B 585 " --> pdb=" O ILE B 299 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N GLN B 301 " --> pdb=" O VAL B 583 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N VAL B 583 " --> pdb=" O GLN B 301 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N GLY B 580 " --> pdb=" O GLN B 599 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 312 through 315 removed outlier: 5.769A pdb=" N ASP B 560 " --> pdb=" O ILE B 573 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 341 through 345 removed outlier: 3.666A pdb=" N GLU B 341 " --> pdb=" O SER B 386 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 378 through 379 removed outlier: 3.539A pdb=" N VAL B 510 " --> pdb=" O PHE B 379 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 439 through 441 Processing sheet with id=AA9, first strand: chain 'B' and resid 640 through 641 removed outlier: 6.698A pdb=" N ALA B 658 " --> pdb=" O PRO B 651 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 683 through 685 Processing sheet with id=AB2, first strand: chain 'B' and resid 693 through 710 removed outlier: 6.668A pdb=" N GLN B1053 " --> pdb=" O THR B 698 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N PHE B 700 " --> pdb=" O PRO B1051 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N ILE B 702 " --> pdb=" O TYR B1049 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N TYR B1049 " --> pdb=" O ILE B 702 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ILE B 704 " --> pdb=" O VAL B1047 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N VAL B1047 " --> pdb=" O ILE B 704 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N THR B 706 " --> pdb=" O LEU B1045 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N LEU B1045 " --> pdb=" O THR B 706 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N VAL B 708 " --> pdb=" O VAL B1043 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N VAL B1043 " --> pdb=" O VAL B 708 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N GLY B1041 " --> pdb=" O PRO B 710 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA B1038 " --> pdb=" O GLY B1041 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N MET B1032 " --> pdb=" O VAL B1047 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N TYR B1049 " --> pdb=" O HIS B1030 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N HIS B1030 " --> pdb=" O TYR B1049 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 693 through 710 removed outlier: 6.668A pdb=" N GLN B1053 " --> pdb=" O THR B 698 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N PHE B 700 " --> pdb=" O PRO B1051 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N ILE B 702 " --> pdb=" O TYR B1049 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N TYR B1049 " --> pdb=" O ILE B 702 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ILE B 704 " --> pdb=" O VAL B1047 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N VAL B1047 " --> pdb=" O ILE B 704 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N THR B 706 " --> pdb=" O LEU B1045 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N LEU B1045 " --> pdb=" O THR B 706 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N VAL B 708 " --> pdb=" O VAL B1043 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N VAL B1043 " --> pdb=" O VAL B 708 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N GLY B1041 " --> pdb=" O PRO B 710 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N THR B1058 " --> pdb=" O PHE B1079 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ALA B1060 " --> pdb=" O PHE B1077 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N PHE B1077 " --> pdb=" O ALA B1060 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 715 through 718 removed outlier: 4.603A pdb=" N LYS B 715 " --> pdb=" O LEU B 843 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 769 through 771 removed outlier: 5.716A pdb=" N MET B 770 " --> pdb=" O SER A 685 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'B' and resid 778 through 779 Processing sheet with id=AB7, first strand: chain 'B' and resid 1102 through 1104 Processing sheet with id=AB8, first strand: chain 'A' and resid 32 through 35 removed outlier: 3.703A pdb=" N SER A 64 " --> pdb=" O SER A 35 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N ASN A 65 " --> pdb=" O TYR A 256 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N TYR A 256 " --> pdb=" O ASN A 65 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N LYS A 198 " --> pdb=" O PRO A 218 " (cutoff:3.500A) removed outlier: 8.843A pdb=" N TYR A 200 " --> pdb=" O LEU A 216 " (cutoff:3.500A) removed outlier: 8.150A pdb=" N LEU A 216 " --> pdb=" O TYR A 200 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N VAL A 40 " --> pdb=" O LEU A 216 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 51 through 59 removed outlier: 3.510A pdb=" N THR A 51 " --> pdb=" O TYR A 266 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ASP A 274 " --> pdb=" O LYS A 265 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 81 through 82 removed outlier: 7.139A pdb=" N ASN A 230 " --> pdb=" O PHE A 103 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N PHE A 103 " --> pdb=" O ASN A 230 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ARG A 232 " --> pdb=" O TRP A 101 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N TRP A 101 " --> pdb=" O ARG A 232 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N ILE A 234 " --> pdb=" O ARG A 99 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ARG A 99 " --> pdb=" O ASN A 118 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N ASN A 118 " --> pdb=" O ARG A 99 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N SER A 113 " --> pdb=" O CYS A 128 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N PHE A 161 " --> pdb=" O ALA A 127 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 298 through 306 removed outlier: 6.656A pdb=" N VAL A 581 " --> pdb=" O THR A 302 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N ASN A 304 " --> pdb=" O GLY A 579 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N GLY A 579 " --> pdb=" O ASN A 304 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N GLY A 580 " --> pdb=" O GLN A 599 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 312 through 315 removed outlier: 5.318A pdb=" N ASP A 560 " --> pdb=" O ILE A 573 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N SER A 561 " --> pdb=" O GLY A 552 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 640 through 641 removed outlier: 6.589A pdb=" N ALA A 658 " --> pdb=" O PRO A 651 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 693 through 710 removed outlier: 6.649A pdb=" N THR A 693 " --> pdb=" O THR A1058 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N THR A1058 " --> pdb=" O THR A 693 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ALA A 695 " --> pdb=" O ASN A1056 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ASN A1056 " --> pdb=" O ALA A 695 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N GLU A1054 " --> pdb=" O PRO A 697 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N MET A1032 " --> pdb=" O VAL A1047 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N TYR A1049 " --> pdb=" O HIS A1030 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N HIS A1030 " --> pdb=" O TYR A1049 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 716 through 718 Processing sheet with id=AC7, first strand: chain 'A' and resid 769 through 771 Processing sheet with id=AC8, first strand: chain 'A' and resid 778 through 779 Processing sheet with id=AC9, first strand: chain 'A' and resid 1102 through 1104 Processing sheet with id=AD1, first strand: chain 'A' and resid 1076 through 1080 Processing sheet with id=AD2, first strand: chain 'C' and resid 32 through 35 removed outlier: 3.886A pdb=" N SER C 64 " --> pdb=" O SER C 35 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N ASN C 65 " --> pdb=" O TYR C 256 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N TYR C 256 " --> pdb=" O ASN C 65 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLU C 93 " --> pdb=" O HIS C 181 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N HIS C 181 " --> pdb=" O GLU C 93 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N LYS C 198 " --> pdb=" O PRO C 218 " (cutoff:3.500A) removed outlier: 9.058A pdb=" N TYR C 200 " --> pdb=" O LEU C 216 " (cutoff:3.500A) removed outlier: 8.508A pdb=" N LEU C 216 " --> pdb=" O TYR C 200 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N VAL C 40 " --> pdb=" O LEU C 216 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 51 through 59 removed outlier: 3.902A pdb=" N ASP C 274 " --> pdb=" O LYS C 265 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 81 through 82 removed outlier: 4.471A pdb=" N GLY C 100 " --> pdb=" O ILE C 234 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ARG C 99 " --> pdb=" O ASN C 118 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N ASN C 118 " --> pdb=" O ARG C 99 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N PHE C 161 " --> pdb=" O ALA C 127 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N ASN C 129 " --> pdb=" O CYS C 159 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N CYS C 159 " --> pdb=" O ASN C 129 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 298 through 305 removed outlier: 3.694A pdb=" N GLY C 298 " --> pdb=" O THR C 585 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N VAL C 581 " --> pdb=" O THR C 302 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N ASN C 304 " --> pdb=" O GLY C 579 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N GLY C 579 " --> pdb=" O ASN C 304 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N GLY C 580 " --> pdb=" O GLN C 599 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 312 through 315 removed outlier: 5.712A pdb=" N ASP C 560 " --> pdb=" O ILE C 573 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N SER C 561 " --> pdb=" O GLY C 552 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 341 through 345 removed outlier: 3.603A pdb=" N GLU C 341 " --> pdb=" O SER C 386 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 378 through 379 Processing sheet with id=AD9, first strand: chain 'C' and resid 439 through 441 Processing sheet with id=AE1, first strand: chain 'C' and resid 640 through 641 removed outlier: 6.521A pdb=" N ILE C 656 " --> pdb=" O ILE C 652 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 693 through 710 removed outlier: 6.561A pdb=" N THR C 693 " --> pdb=" O THR C1058 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N THR C1058 " --> pdb=" O THR C 693 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ALA C 695 " --> pdb=" O ASN C1056 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ASN C1056 " --> pdb=" O ALA C 695 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N GLU C1054 " --> pdb=" O PRO C 697 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N MET C1032 " --> pdb=" O VAL C1047 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N TYR C1049 " --> pdb=" O HIS C1030 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N HIS C1030 " --> pdb=" O TYR C1049 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 693 through 710 removed outlier: 6.561A pdb=" N THR C 693 " --> pdb=" O THR C1058 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N THR C1058 " --> pdb=" O THR C 693 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ALA C 695 " --> pdb=" O ASN C1056 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ASN C1056 " --> pdb=" O ALA C 695 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N GLU C1054 " --> pdb=" O PRO C 697 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N THR C1058 " --> pdb=" O PHE C1079 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ALA C1060 " --> pdb=" O PHE C1077 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N PHE C1077 " --> pdb=" O ALA C1060 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 717 through 718 Processing sheet with id=AE5, first strand: chain 'C' and resid 778 through 779 Processing sheet with id=AE6, first strand: chain 'C' and resid 1102 through 1104 932 hydrogen bonds defined for protein. 2574 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.33 Time building geometry restraints manager: 6.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 6987 1.35 - 1.47: 5787 1.47 - 1.60: 9467 1.60 - 1.72: 0 1.72 - 1.85: 152 Bond restraints: 22393 Sorted by residual: bond pdb=" C1 NAG C1304 " pdb=" O5 NAG C1304 " ideal model delta sigma weight residual 1.406 1.450 -0.044 2.00e-02 2.50e+03 4.76e+00 bond pdb=" CB CYS C 635 " pdb=" SG CYS C 635 " ideal model delta sigma weight residual 1.808 1.737 0.071 3.30e-02 9.18e+02 4.61e+00 bond pdb=" CB VAL B1047 " pdb=" CG1 VAL B1047 " ideal model delta sigma weight residual 1.521 1.451 0.070 3.30e-02 9.18e+02 4.48e+00 bond pdb=" C1 NAG A1302 " pdb=" O5 NAG A1302 " ideal model delta sigma weight residual 1.406 1.447 -0.041 2.00e-02 2.50e+03 4.14e+00 bond pdb=" C1 NAG A1304 " pdb=" O5 NAG A1304 " ideal model delta sigma weight residual 1.406 1.446 -0.040 2.00e-02 2.50e+03 3.91e+00 ... (remaining 22388 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.56: 29831 2.56 - 5.11: 527 5.11 - 7.67: 40 7.67 - 10.22: 12 10.22 - 12.78: 2 Bond angle restraints: 30412 Sorted by residual: angle pdb=" CA PRO B 218 " pdb=" N PRO B 218 " pdb=" CD PRO B 218 " ideal model delta sigma weight residual 112.00 104.25 7.75 1.40e+00 5.10e-01 3.06e+01 angle pdb=" C ILE C 652 " pdb=" N GLY C 653 " pdb=" CA GLY C 653 " ideal model delta sigma weight residual 122.54 115.60 6.94 1.35e+00 5.49e-01 2.64e+01 angle pdb=" C GLY C 653 " pdb=" N ALA C 654 " pdb=" CA ALA C 654 " ideal model delta sigma weight residual 122.40 128.75 -6.35 1.45e+00 4.76e-01 1.92e+01 angle pdb=" C LYS B 817 " pdb=" N GLN B 818 " pdb=" CA GLN B 818 " ideal model delta sigma weight residual 122.61 129.32 -6.71 1.56e+00 4.11e-01 1.85e+01 angle pdb=" N CYS B 511 " pdb=" CA CYS B 511 " pdb=" C CYS B 511 " ideal model delta sigma weight residual 108.79 115.34 -6.55 1.53e+00 4.27e-01 1.83e+01 ... (remaining 30407 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 12523 17.99 - 35.97: 1008 35.97 - 53.96: 188 53.96 - 71.94: 46 71.94 - 89.93: 12 Dihedral angle restraints: 13777 sinusoidal: 5770 harmonic: 8007 Sorted by residual: dihedral pdb=" CB CYS A 603 " pdb=" SG CYS A 603 " pdb=" SG CYS A 635 " pdb=" CB CYS A 635 " ideal model delta sinusoidal sigma weight residual -86.00 -156.80 70.80 1 1.00e+01 1.00e-02 6.44e+01 dihedral pdb=" CB CYS A 524 " pdb=" SG CYS A 524 " pdb=" SG CYS A 576 " pdb=" CB CYS A 576 " ideal model delta sinusoidal sigma weight residual -86.00 -17.77 -68.23 1 1.00e+01 1.00e-02 6.04e+01 dihedral pdb=" CB CYS A1064 " pdb=" SG CYS A1064 " pdb=" SG CYS A1108 " pdb=" CB CYS A1108 " ideal model delta sinusoidal sigma weight residual -86.00 -19.04 -66.96 1 1.00e+01 1.00e-02 5.84e+01 ... (remaining 13774 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.119: 3440 0.119 - 0.238: 118 0.238 - 0.357: 4 0.357 - 0.476: 3 0.476 - 0.595: 1 Chirality restraints: 3566 Sorted by residual: chirality pdb=" C1 NAG B1308 " pdb=" ND2 ASN B1056 " pdb=" C2 NAG B1308 " pdb=" O5 NAG B1308 " both_signs ideal model delta sigma weight residual False -2.40 -1.80 -0.60 2.00e-01 2.50e+01 8.85e+00 chirality pdb=" C1 NAG C1302 " pdb=" ND2 ASN C1080 " pdb=" C2 NAG C1302 " pdb=" O5 NAG C1302 " both_signs ideal model delta sigma weight residual False -2.40 -1.96 -0.44 2.00e-01 2.50e+01 4.93e+00 chirality pdb=" C1 NAG A1301 " pdb=" ND2 ASN A1080 " pdb=" C2 NAG A1301 " pdb=" O5 NAG A1301 " both_signs ideal model delta sigma weight residual False -2.40 -1.97 -0.43 2.00e-01 2.50e+01 4.72e+00 ... (remaining 3563 not shown) Planarity restraints: 3905 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS B 217 " -0.101 5.00e-02 4.00e+02 1.49e-01 3.53e+01 pdb=" N PRO B 218 " 0.257 5.00e-02 4.00e+02 pdb=" CA PRO B 218 " -0.080 5.00e-02 4.00e+02 pdb=" CD PRO B 218 " -0.076 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 81 " 0.055 5.00e-02 4.00e+02 8.49e-02 1.15e+01 pdb=" N PRO B 82 " -0.147 5.00e-02 4.00e+02 pdb=" CA PRO B 82 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO B 82 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 790 " 0.046 5.00e-02 4.00e+02 6.96e-02 7.76e+00 pdb=" N PRO A 791 " -0.120 5.00e-02 4.00e+02 pdb=" CA PRO A 791 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 791 " 0.039 5.00e-02 4.00e+02 ... (remaining 3902 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 3247 2.76 - 3.29: 18603 3.29 - 3.83: 32782 3.83 - 4.36: 39067 4.36 - 4.90: 71728 Nonbonded interactions: 165427 Sorted by model distance: nonbonded pdb=" O SER B 380 " pdb=" OG1 THR B 509 " model vdw 2.223 3.040 nonbonded pdb=" O ASP A 932 " pdb=" NE2 GLN A 936 " model vdw 2.238 3.120 nonbonded pdb=" OG SER B 685 " pdb=" OE1 GLN C 769 " model vdw 2.243 3.040 nonbonded pdb=" NZ LYS B 390 " pdb=" OD2 ASP B 392 " model vdw 2.281 3.120 nonbonded pdb=" OH TYR B 41 " pdb=" O LEU B 58 " model vdw 2.287 3.040 ... (remaining 165422 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'B' selection = (chain 'C' and (resid 31 through 118 or resid 123 through 129 or resid 163 throu \ gh 1123 or resid 1301 through 1309)) } 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: 6.630 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: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 47.740 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 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 : 0.006 0.075 22459 Z= 0.275 Angle : 0.906 22.197 30576 Z= 0.495 Chirality : 0.057 0.595 3566 Planarity : 0.007 0.149 3873 Dihedral : 13.411 89.929 8511 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.14), residues: 2690 helix: -0.60 (0.19), residues: 633 sheet: 0.95 (0.21), residues: 577 loop : -1.37 (0.13), residues: 1480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 101 HIS 0.008 0.001 HIS B1046 PHE 0.033 0.003 PHE A 888 TYR 0.030 0.003 TYR C 338 ARG 0.014 0.001 ARG B 183 Details of bonding type rmsd link_NAG-ASN : bond 0.00796 ( 32) link_NAG-ASN : angle 4.85529 ( 96) hydrogen bonds : bond 0.17350 ( 915) hydrogen bonds : angle 7.02314 ( 2574) SS BOND : bond 0.00864 ( 34) SS BOND : angle 2.00881 ( 68) covalent geometry : bond 0.00632 (22393) covalent geometry : angle 0.86133 (30412) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5380 Ramachandran restraints generated. 2690 Oldfield, 0 Emsley, 2690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5380 Ramachandran restraints generated. 2690 Oldfield, 0 Emsley, 2690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 2389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 218 time to evaluate : 2.263 Fit side-chains revert: symmetry clash REVERT: B 37 MET cc_start: 0.8956 (mtp) cc_final: 0.8666 (mtm) REVERT: B 183 ARG cc_start: 0.7042 (mtt90) cc_final: 0.6554 (mtm-85) REVERT: B 882 MET cc_start: 0.8823 (mtm) cc_final: 0.8583 (mtp) REVERT: B 886 TYR cc_start: 0.7700 (t80) cc_final: 0.7460 (t80) REVERT: C 532 LEU cc_start: 0.7680 (tp) cc_final: 0.7209 (mt) REVERT: C 591 SER cc_start: 0.8232 (t) cc_final: 0.8019 (t) REVERT: C 796 LYS cc_start: 0.7415 (ttpt) cc_final: 0.7066 (tptt) REVERT: C 1032 MET cc_start: 0.8849 (mtp) cc_final: 0.8422 (mtm) outliers start: 0 outliers final: 0 residues processed: 218 average time/residue: 0.3263 time to fit residues: 110.5924 Evaluate side-chains 179 residues out of total 2389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 2.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 231 optimal weight: 0.5980 chunk 207 optimal weight: 9.9990 chunk 115 optimal weight: 0.7980 chunk 70 optimal weight: 2.9990 chunk 140 optimal weight: 0.4980 chunk 110 optimal weight: 0.4980 chunk 214 optimal weight: 0.7980 chunk 83 optimal weight: 0.8980 chunk 130 optimal weight: 2.9990 chunk 159 optimal weight: 0.0370 chunk 248 optimal weight: 5.9990 overall best weight: 0.4858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 505 ASN B 523 GLN B 904 GLN C 661 HIS C 883 GLN C 915 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.148367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.119569 restraints weight = 25708.836| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 2.25 r_work: 0.2869 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.1156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 22459 Z= 0.101 Angle : 0.549 17.070 30576 Z= 0.278 Chirality : 0.045 0.540 3566 Planarity : 0.005 0.083 3873 Dihedral : 5.657 53.473 3611 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 0.54 % Allowed : 4.98 % Favored : 94.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.15), residues: 2690 helix: 0.88 (0.21), residues: 636 sheet: 1.09 (0.20), residues: 639 loop : -1.18 (0.14), residues: 1415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 423 HIS 0.002 0.000 HIS B1046 PHE 0.013 0.001 PHE A1103 TYR 0.017 0.001 TYR C 200 ARG 0.004 0.000 ARG A 544 Details of bonding type rmsd link_NAG-ASN : bond 0.00639 ( 32) link_NAG-ASN : angle 3.69647 ( 96) hydrogen bonds : bond 0.04381 ( 915) hydrogen bonds : angle 5.04720 ( 2574) SS BOND : bond 0.00341 ( 34) SS BOND : angle 1.17640 ( 68) covalent geometry : bond 0.00213 (22393) covalent geometry : angle 0.50679 (30412) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5380 Ramachandran restraints generated. 2690 Oldfield, 0 Emsley, 2690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5380 Ramachandran restraints generated. 2690 Oldfield, 0 Emsley, 2690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 2389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 208 time to evaluate : 2.238 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 37 MET cc_start: 0.9068 (mtp) cc_final: 0.8747 (mtm) REVERT: B 376 ASP cc_start: 0.8214 (t0) cc_final: 0.7813 (m-30) REVERT: B 560 ASP cc_start: 0.8353 (p0) cc_final: 0.8004 (p0) REVERT: B 709 MET cc_start: 0.9198 (mtp) cc_final: 0.8989 (mtp) REVERT: A 191 ASP cc_start: 0.7995 (m-30) cc_final: 0.7588 (t70) REVERT: A 554 ASP cc_start: 0.7069 (t0) cc_final: 0.6555 (t0) REVERT: C 122 ASN cc_start: 0.8474 (m110) cc_final: 0.8136 (m-40) REVERT: C 338 TYR cc_start: 0.8506 (p90) cc_final: 0.8247 (p90) REVERT: C 591 SER cc_start: 0.8327 (t) cc_final: 0.8092 (t) REVERT: C 768 LYS cc_start: 0.7651 (mmtm) cc_final: 0.7193 (mmpt) REVERT: C 790 ASP cc_start: 0.8360 (m-30) cc_final: 0.8134 (m-30) REVERT: C 796 LYS cc_start: 0.7246 (ttpt) cc_final: 0.6660 (tptt) REVERT: C 939 GLN cc_start: 0.8858 (mt0) cc_final: 0.8167 (mp10) REVERT: C 1032 MET cc_start: 0.9016 (mtp) cc_final: 0.8626 (mtm) outliers start: 13 outliers final: 10 residues processed: 215 average time/residue: 0.3026 time to fit residues: 104.1489 Evaluate side-chains 200 residues out of total 2389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 190 time to evaluate : 2.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 438 TYR Chi-restraints excluded: chain B residue 729 THR Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain A residue 1109 ASP Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 1110 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 251 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 154 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 252 optimal weight: 3.9990 chunk 71 optimal weight: 0.9980 chunk 238 optimal weight: 4.9990 chunk 102 optimal weight: 5.9990 chunk 227 optimal weight: 0.8980 chunk 242 optimal weight: 0.5980 chunk 110 optimal weight: 0.0870 overall best weight: 1.1160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 883 GLN C 915 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.144948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.114655 restraints weight = 25810.006| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 2.56 r_work: 0.2831 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.1210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 22459 Z= 0.138 Angle : 0.571 17.013 30576 Z= 0.290 Chirality : 0.046 0.526 3566 Planarity : 0.004 0.067 3873 Dihedral : 5.120 42.991 3611 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.13 % Allowed : 7.74 % Favored : 91.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.15), residues: 2690 helix: 1.23 (0.21), residues: 645 sheet: 1.04 (0.20), residues: 606 loop : -1.15 (0.14), residues: 1439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 423 HIS 0.005 0.001 HIS B1046 PHE 0.019 0.001 PHE A 83 TYR 0.016 0.001 TYR B1049 ARG 0.004 0.000 ARG A 544 Details of bonding type rmsd link_NAG-ASN : bond 0.00612 ( 32) link_NAG-ASN : angle 3.63972 ( 96) hydrogen bonds : bond 0.05160 ( 915) hydrogen bonds : angle 4.95174 ( 2574) SS BOND : bond 0.00399 ( 34) SS BOND : angle 1.34839 ( 68) covalent geometry : bond 0.00331 (22393) covalent geometry : angle 0.53107 (30412) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5380 Ramachandran restraints generated. 2690 Oldfield, 0 Emsley, 2690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5380 Ramachandran restraints generated. 2690 Oldfield, 0 Emsley, 2690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 2389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 194 time to evaluate : 2.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 37 MET cc_start: 0.9022 (mtp) cc_final: 0.8735 (mtm) REVERT: B 256 TYR cc_start: 0.7747 (m-80) cc_final: 0.7479 (m-10) REVERT: B 376 ASP cc_start: 0.8354 (t0) cc_final: 0.8112 (t0) REVERT: B 652 ILE cc_start: 0.9074 (OUTLIER) cc_final: 0.8856 (mt) REVERT: A 45 GLU cc_start: 0.7463 (tp30) cc_final: 0.6908 (pm20) REVERT: A 191 ASP cc_start: 0.8005 (m-30) cc_final: 0.7590 (t70) REVERT: A 554 ASP cc_start: 0.7143 (t0) cc_final: 0.6616 (t0) REVERT: A 936 GLN cc_start: 0.7445 (pt0) cc_final: 0.7126 (mm-40) REVERT: C 591 SER cc_start: 0.8378 (t) cc_final: 0.8128 (t) REVERT: C 768 LYS cc_start: 0.7636 (mmtm) cc_final: 0.7170 (mmpt) REVERT: C 796 LYS cc_start: 0.7509 (ttpt) cc_final: 0.6806 (tptt) REVERT: C 1032 MET cc_start: 0.9043 (mtp) cc_final: 0.8675 (mtm) outliers start: 27 outliers final: 21 residues processed: 215 average time/residue: 0.3137 time to fit residues: 107.6607 Evaluate side-chains 204 residues out of total 2389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 182 time to evaluate : 5.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 438 TYR Chi-restraints excluded: chain B residue 652 ILE Chi-restraints excluded: chain B residue 729 THR Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 570 ILE Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain A residue 1100 ASP Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 511 CYS Chi-restraints excluded: chain C residue 615 LEU Chi-restraints excluded: chain C residue 690 SER Chi-restraints excluded: chain C residue 958 VAL Chi-restraints excluded: chain C residue 1110 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 83 optimal weight: 0.7980 chunk 55 optimal weight: 0.7980 chunk 149 optimal weight: 2.9990 chunk 92 optimal weight: 0.1980 chunk 271 optimal weight: 4.9990 chunk 35 optimal weight: 9.9990 chunk 216 optimal weight: 3.9990 chunk 127 optimal weight: 3.9990 chunk 29 optimal weight: 0.4980 chunk 51 optimal weight: 0.0980 chunk 230 optimal weight: 4.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 230 ASN ** B 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 904 GLN C 357 ASN ** C 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 883 GLN C 915 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.148526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.119339 restraints weight = 25820.862| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 2.29 r_work: 0.2879 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.1551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 22459 Z= 0.090 Angle : 0.512 15.891 30576 Z= 0.255 Chirality : 0.044 0.513 3566 Planarity : 0.004 0.056 3873 Dihedral : 4.580 39.765 3611 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.30 % Allowed : 9.25 % Favored : 89.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.15), residues: 2690 helix: 1.74 (0.21), residues: 635 sheet: 1.03 (0.20), residues: 617 loop : -1.06 (0.14), residues: 1438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 423 HIS 0.003 0.000 HIS B 181 PHE 0.012 0.001 PHE A1103 TYR 0.016 0.001 TYR A1049 ARG 0.003 0.000 ARG A 544 Details of bonding type rmsd link_NAG-ASN : bond 0.00606 ( 32) link_NAG-ASN : angle 3.38907 ( 96) hydrogen bonds : bond 0.03856 ( 915) hydrogen bonds : angle 4.66779 ( 2574) SS BOND : bond 0.00272 ( 34) SS BOND : angle 1.05053 ( 68) covalent geometry : bond 0.00197 (22393) covalent geometry : angle 0.47409 (30412) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5380 Ramachandran restraints generated. 2690 Oldfield, 0 Emsley, 2690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5380 Ramachandran restraints generated. 2690 Oldfield, 0 Emsley, 2690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 2389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 210 time to evaluate : 2.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 37 MET cc_start: 0.9027 (mtp) cc_final: 0.8745 (mtm) REVERT: B 256 TYR cc_start: 0.7699 (m-80) cc_final: 0.7478 (m-10) REVERT: B 373 LYS cc_start: 0.7587 (mptt) cc_final: 0.7231 (mmmt) REVERT: B 376 ASP cc_start: 0.8350 (t0) cc_final: 0.8041 (t0) REVERT: B 769 GLN cc_start: 0.8119 (mp10) cc_final: 0.7853 (mp10) REVERT: A 45 GLU cc_start: 0.7349 (tp30) cc_final: 0.6949 (pm20) REVERT: A 191 ASP cc_start: 0.7950 (m-30) cc_final: 0.7592 (t70) REVERT: A 554 ASP cc_start: 0.7016 (t0) cc_final: 0.6499 (t0) REVERT: A 936 GLN cc_start: 0.7442 (pt0) cc_final: 0.7122 (mm-40) REVERT: C 494 TYR cc_start: 0.6685 (m-80) cc_final: 0.6484 (m-80) REVERT: C 591 SER cc_start: 0.8484 (t) cc_final: 0.8282 (t) REVERT: C 768 LYS cc_start: 0.7654 (mmtm) cc_final: 0.7222 (mmpt) REVERT: C 796 LYS cc_start: 0.7479 (ttpt) cc_final: 0.6842 (tptt) REVERT: C 921 THR cc_start: 0.6771 (OUTLIER) cc_final: 0.6479 (t) REVERT: C 939 GLN cc_start: 0.8888 (mt0) cc_final: 0.8112 (mp10) REVERT: C 1032 MET cc_start: 0.8996 (mtp) cc_final: 0.8612 (mtm) outliers start: 31 outliers final: 25 residues processed: 236 average time/residue: 0.3394 time to fit residues: 129.1623 Evaluate side-chains 217 residues out of total 2389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 191 time to evaluate : 2.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 438 TYR Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain B residue 544 ARG Chi-restraints excluded: chain B residue 822 CYS Chi-restraints excluded: chain B residue 1047 VAL Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 570 ILE Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 1100 ASP Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 511 CYS Chi-restraints excluded: chain C residue 616 THR Chi-restraints excluded: chain C residue 690 SER Chi-restraints excluded: chain C residue 921 THR Chi-restraints excluded: chain C residue 958 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 263 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 254 optimal weight: 3.9990 chunk 257 optimal weight: 2.9990 chunk 127 optimal weight: 0.7980 chunk 26 optimal weight: 4.9990 chunk 272 optimal weight: 2.9990 chunk 235 optimal weight: 0.6980 chunk 259 optimal weight: 0.8980 chunk 273 optimal weight: 5.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 181 HIS B 907 ASN ** C 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 786 GLN C 883 GLN C 915 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.142796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.112940 restraints weight = 25979.794| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 2.73 r_work: 0.2787 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.1421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 22459 Z= 0.187 Angle : 0.608 16.397 30576 Z= 0.309 Chirality : 0.048 0.526 3566 Planarity : 0.004 0.053 3873 Dihedral : 5.034 45.702 3611 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.05 % Allowed : 9.67 % Favored : 88.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.15), residues: 2690 helix: 1.32 (0.21), residues: 643 sheet: 0.99 (0.20), residues: 634 loop : -1.24 (0.14), residues: 1413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 423 HIS 0.007 0.001 HIS B1046 PHE 0.023 0.002 PHE A 83 TYR 0.017 0.002 TYR B1049 ARG 0.003 0.000 ARG A 620 Details of bonding type rmsd link_NAG-ASN : bond 0.00580 ( 32) link_NAG-ASN : angle 3.59208 ( 96) hydrogen bonds : bond 0.05720 ( 915) hydrogen bonds : angle 4.94416 ( 2574) SS BOND : bond 0.00503 ( 34) SS BOND : angle 1.48036 ( 68) covalent geometry : bond 0.00465 (22393) covalent geometry : angle 0.57151 (30412) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5380 Ramachandran restraints generated. 2690 Oldfield, 0 Emsley, 2690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5380 Ramachandran restraints generated. 2690 Oldfield, 0 Emsley, 2690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 2389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 196 time to evaluate : 2.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 37 MET cc_start: 0.9022 (mtp) cc_final: 0.8766 (mtm) REVERT: B 126 ARG cc_start: 0.5673 (tmm160) cc_final: 0.5067 (tpp80) REVERT: B 256 TYR cc_start: 0.7850 (m-80) cc_final: 0.7586 (m-10) REVERT: B 373 LYS cc_start: 0.7800 (mptt) cc_final: 0.7347 (mmmt) REVERT: B 376 ASP cc_start: 0.8404 (t0) cc_final: 0.8017 (t0) REVERT: B 770 MET cc_start: 0.8849 (mmm) cc_final: 0.8442 (mmm) REVERT: A 45 GLU cc_start: 0.7707 (tp30) cc_final: 0.7282 (pm20) REVERT: A 191 ASP cc_start: 0.8023 (m-30) cc_final: 0.7533 (t70) REVERT: A 554 ASP cc_start: 0.7092 (t0) cc_final: 0.6588 (t0) REVERT: A 936 GLN cc_start: 0.7386 (pt0) cc_final: 0.7093 (mm110) REVERT: C 494 TYR cc_start: 0.6639 (m-80) cc_final: 0.6211 (m-80) REVERT: C 591 SER cc_start: 0.8526 (t) cc_final: 0.8325 (t) REVERT: C 652 ILE cc_start: 0.9176 (OUTLIER) cc_final: 0.8906 (mt) REVERT: C 768 LYS cc_start: 0.7870 (mmtm) cc_final: 0.7393 (mmpt) REVERT: C 796 LYS cc_start: 0.7730 (ttpt) cc_final: 0.7005 (tptt) REVERT: C 932 ASP cc_start: 0.8495 (t0) cc_final: 0.8293 (t0) REVERT: C 1032 MET cc_start: 0.9051 (mtp) cc_final: 0.8653 (mtp) outliers start: 49 outliers final: 39 residues processed: 233 average time/residue: 0.3281 time to fit residues: 121.4488 Evaluate side-chains 229 residues out of total 2389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 189 time to evaluate : 2.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 438 TYR Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain B residue 544 ARG Chi-restraints excluded: chain B residue 616 THR Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain B residue 693 THR Chi-restraints excluded: chain B residue 729 THR Chi-restraints excluded: chain B residue 822 CYS Chi-restraints excluded: chain B residue 1047 VAL Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 292 SER Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 690 SER Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 913 ILE Chi-restraints excluded: chain A residue 1100 ASP Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 268 GLU Chi-restraints excluded: chain C residue 491 TYR Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 511 CYS Chi-restraints excluded: chain C residue 615 LEU Chi-restraints excluded: chain C residue 616 THR Chi-restraints excluded: chain C residue 648 CYS Chi-restraints excluded: chain C residue 652 ILE Chi-restraints excluded: chain C residue 690 SER Chi-restraints excluded: chain C residue 958 VAL Chi-restraints excluded: chain C residue 1110 VAL Chi-restraints excluded: chain C residue 1112 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 106 optimal weight: 6.9990 chunk 187 optimal weight: 3.9990 chunk 222 optimal weight: 0.6980 chunk 83 optimal weight: 0.9990 chunk 80 optimal weight: 2.9990 chunk 271 optimal weight: 1.9990 chunk 174 optimal weight: 5.9990 chunk 38 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 chunk 136 optimal weight: 0.8980 chunk 201 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 904 GLN ** C 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.145362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.115285 restraints weight = 25797.172| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 2.64 r_work: 0.2836 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.1570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 22459 Z= 0.115 Angle : 0.536 15.598 30576 Z= 0.270 Chirality : 0.045 0.514 3566 Planarity : 0.004 0.050 3873 Dihedral : 4.706 42.266 3611 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.97 % Allowed : 10.46 % Favored : 87.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.15), residues: 2690 helix: 1.52 (0.21), residues: 649 sheet: 0.95 (0.20), residues: 618 loop : -1.16 (0.14), residues: 1423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 423 HIS 0.004 0.001 HIS B1046 PHE 0.014 0.001 PHE A 83 TYR 0.015 0.001 TYR A1049 ARG 0.005 0.000 ARG A 544 Details of bonding type rmsd link_NAG-ASN : bond 0.00590 ( 32) link_NAG-ASN : angle 3.41563 ( 96) hydrogen bonds : bond 0.04500 ( 915) hydrogen bonds : angle 4.72620 ( 2574) SS BOND : bond 0.00350 ( 34) SS BOND : angle 1.20190 ( 68) covalent geometry : bond 0.00270 (22393) covalent geometry : angle 0.49837 (30412) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5380 Ramachandran restraints generated. 2690 Oldfield, 0 Emsley, 2690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5380 Ramachandran restraints generated. 2690 Oldfield, 0 Emsley, 2690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 2389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 192 time to evaluate : 2.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 37 MET cc_start: 0.9034 (mtp) cc_final: 0.8767 (mtm) REVERT: B 126 ARG cc_start: 0.5736 (tmm160) cc_final: 0.5079 (tpp80) REVERT: B 183 ARG cc_start: 0.6983 (ptp-170) cc_final: 0.6352 (ptp-110) REVERT: B 373 LYS cc_start: 0.7639 (mptt) cc_final: 0.7253 (mmmt) REVERT: B 376 ASP cc_start: 0.8225 (t0) cc_final: 0.7916 (t0) REVERT: B 770 MET cc_start: 0.8814 (mmm) cc_final: 0.8414 (mmm) REVERT: A 45 GLU cc_start: 0.7690 (tp30) cc_final: 0.7294 (pm20) REVERT: A 191 ASP cc_start: 0.8008 (m-30) cc_final: 0.7568 (t70) REVERT: A 554 ASP cc_start: 0.7159 (t0) cc_final: 0.6609 (t0) REVERT: A 936 GLN cc_start: 0.7391 (pt0) cc_final: 0.7129 (mm110) REVERT: C 494 TYR cc_start: 0.6527 (m-80) cc_final: 0.5935 (m-80) REVERT: C 591 SER cc_start: 0.8486 (t) cc_final: 0.8282 (t) REVERT: C 768 LYS cc_start: 0.7822 (mmtm) cc_final: 0.7262 (mmpt) REVERT: C 769 GLN cc_start: 0.7784 (mm-40) cc_final: 0.7533 (mt0) REVERT: C 796 LYS cc_start: 0.7654 (ttpt) cc_final: 0.6994 (tptt) REVERT: C 1032 MET cc_start: 0.8971 (mtp) cc_final: 0.8542 (mtp) outliers start: 47 outliers final: 36 residues processed: 229 average time/residue: 0.3280 time to fit residues: 119.8984 Evaluate side-chains 223 residues out of total 2389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 187 time to evaluate : 2.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 438 TYR Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain B residue 544 ARG Chi-restraints excluded: chain B residue 616 THR Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain B residue 822 CYS Chi-restraints excluded: chain B residue 1047 VAL Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 292 SER Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 690 SER Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 913 ILE Chi-restraints excluded: chain A residue 1100 ASP Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 491 TYR Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 511 CYS Chi-restraints excluded: chain C residue 615 LEU Chi-restraints excluded: chain C residue 616 THR Chi-restraints excluded: chain C residue 690 SER Chi-restraints excluded: chain C residue 958 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 110 optimal weight: 0.0050 chunk 254 optimal weight: 4.9990 chunk 187 optimal weight: 3.9990 chunk 163 optimal weight: 1.9990 chunk 132 optimal weight: 0.0270 chunk 226 optimal weight: 4.9990 chunk 108 optimal weight: 1.9990 chunk 133 optimal weight: 0.9980 chunk 169 optimal weight: 0.9990 chunk 136 optimal weight: 1.9990 chunk 126 optimal weight: 5.9990 overall best weight: 0.8056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 230 ASN ** B 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1117 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.145778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.115672 restraints weight = 25810.201| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 2.58 r_work: 0.2835 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.1683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 22459 Z= 0.111 Angle : 0.524 15.127 30576 Z= 0.264 Chirality : 0.045 0.503 3566 Planarity : 0.004 0.047 3873 Dihedral : 4.536 40.032 3611 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.26 % Allowed : 10.72 % Favored : 87.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.15), residues: 2690 helix: 1.68 (0.21), residues: 643 sheet: 1.02 (0.20), residues: 622 loop : -1.16 (0.14), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 868 HIS 0.004 0.001 HIS B1046 PHE 0.014 0.001 PHE A 83 TYR 0.019 0.001 TYR C 200 ARG 0.002 0.000 ARG A 620 Details of bonding type rmsd link_NAG-ASN : bond 0.00584 ( 32) link_NAG-ASN : angle 3.31512 ( 96) hydrogen bonds : bond 0.04370 ( 915) hydrogen bonds : angle 4.65606 ( 2574) SS BOND : bond 0.00349 ( 34) SS BOND : angle 1.14314 ( 68) covalent geometry : bond 0.00258 (22393) covalent geometry : angle 0.48842 (30412) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5380 Ramachandran restraints generated. 2690 Oldfield, 0 Emsley, 2690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5380 Ramachandran restraints generated. 2690 Oldfield, 0 Emsley, 2690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 2389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 197 time to evaluate : 2.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 37 MET cc_start: 0.9045 (mtp) cc_final: 0.8725 (mtm) REVERT: B 126 ARG cc_start: 0.5696 (tmm160) cc_final: 0.5011 (tpp-160) REVERT: B 183 ARG cc_start: 0.6894 (ptp-170) cc_final: 0.6321 (ptp-110) REVERT: B 256 TYR cc_start: 0.7926 (m-80) cc_final: 0.7647 (m-10) REVERT: B 373 LYS cc_start: 0.7659 (mptt) cc_final: 0.7264 (mmmt) REVERT: B 376 ASP cc_start: 0.8224 (t0) cc_final: 0.7929 (t0) REVERT: B 770 MET cc_start: 0.8813 (mmm) cc_final: 0.8435 (mmm) REVERT: B 792 LEU cc_start: 0.6901 (OUTLIER) cc_final: 0.6608 (tp) REVERT: A 45 GLU cc_start: 0.7729 (tp30) cc_final: 0.7348 (pm20) REVERT: A 191 ASP cc_start: 0.8034 (m-30) cc_final: 0.7585 (t70) REVERT: A 554 ASP cc_start: 0.7153 (t0) cc_final: 0.6607 (t0) REVERT: A 936 GLN cc_start: 0.7482 (pt0) cc_final: 0.7223 (mm110) REVERT: C 591 SER cc_start: 0.8475 (t) cc_final: 0.8268 (t) REVERT: C 768 LYS cc_start: 0.7826 (mmtm) cc_final: 0.7268 (mmpt) REVERT: C 769 GLN cc_start: 0.7873 (mm-40) cc_final: 0.7596 (mt0) REVERT: C 796 LYS cc_start: 0.7746 (ttpt) cc_final: 0.7020 (tptt) REVERT: C 1032 MET cc_start: 0.8962 (mtp) cc_final: 0.8736 (mtp) outliers start: 54 outliers final: 45 residues processed: 238 average time/residue: 0.3103 time to fit residues: 117.6921 Evaluate side-chains 234 residues out of total 2389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 188 time to evaluate : 2.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 438 TYR Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain B residue 544 ARG Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 616 THR Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain B residue 648 CYS Chi-restraints excluded: chain B residue 693 THR Chi-restraints excluded: chain B residue 729 THR Chi-restraints excluded: chain B residue 792 LEU Chi-restraints excluded: chain B residue 822 CYS Chi-restraints excluded: chain B residue 1047 VAL Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 292 SER Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 690 SER Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 913 ILE Chi-restraints excluded: chain A residue 1100 ASP Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 414 ASP Chi-restraints excluded: chain C residue 491 TYR Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 511 CYS Chi-restraints excluded: chain C residue 615 LEU Chi-restraints excluded: chain C residue 635 CYS Chi-restraints excluded: chain C residue 648 CYS Chi-restraints excluded: chain C residue 690 SER Chi-restraints excluded: chain C residue 958 VAL Chi-restraints excluded: chain C residue 1110 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 37 optimal weight: 4.9990 chunk 217 optimal weight: 5.9990 chunk 92 optimal weight: 0.7980 chunk 109 optimal weight: 2.9990 chunk 157 optimal weight: 0.6980 chunk 79 optimal weight: 3.9990 chunk 117 optimal weight: 0.5980 chunk 119 optimal weight: 5.9990 chunk 62 optimal weight: 0.0060 chunk 233 optimal weight: 0.7980 chunk 51 optimal weight: 0.6980 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.147335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.118052 restraints weight = 25796.720| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 2.26 r_work: 0.2876 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 22459 Z= 0.095 Angle : 0.506 14.401 30576 Z= 0.253 Chirality : 0.044 0.490 3566 Planarity : 0.004 0.046 3873 Dihedral : 4.338 37.693 3611 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.13 % Allowed : 10.76 % Favored : 87.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.16), residues: 2690 helix: 1.87 (0.22), residues: 638 sheet: 1.02 (0.20), residues: 627 loop : -1.11 (0.14), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 423 HIS 0.003 0.000 HIS B1046 PHE 0.012 0.001 PHE A1103 TYR 0.016 0.001 TYR A1049 ARG 0.008 0.000 ARG A 544 Details of bonding type rmsd link_NAG-ASN : bond 0.00583 ( 32) link_NAG-ASN : angle 3.20364 ( 96) hydrogen bonds : bond 0.03916 ( 915) hydrogen bonds : angle 4.55371 ( 2574) SS BOND : bond 0.00308 ( 34) SS BOND : angle 1.05631 ( 68) covalent geometry : bond 0.00212 (22393) covalent geometry : angle 0.47207 (30412) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5380 Ramachandran restraints generated. 2690 Oldfield, 0 Emsley, 2690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5380 Ramachandran restraints generated. 2690 Oldfield, 0 Emsley, 2690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 2389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 188 time to evaluate : 2.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 37 MET cc_start: 0.9013 (mtp) cc_final: 0.8745 (mtm) REVERT: B 107 MET cc_start: 0.7780 (OUTLIER) cc_final: 0.7361 (mmp) REVERT: B 126 ARG cc_start: 0.5701 (tmm160) cc_final: 0.4881 (tpp-160) REVERT: B 183 ARG cc_start: 0.6924 (ptp-170) cc_final: 0.6501 (ptp-110) REVERT: B 373 LYS cc_start: 0.7725 (mptt) cc_final: 0.7335 (mmmt) REVERT: B 376 ASP cc_start: 0.8205 (t0) cc_final: 0.7902 (t0) REVERT: B 770 MET cc_start: 0.8821 (mmm) cc_final: 0.8456 (mmm) REVERT: A 45 GLU cc_start: 0.7665 (tp30) cc_final: 0.7400 (pm20) REVERT: A 191 ASP cc_start: 0.7971 (m-30) cc_final: 0.7620 (t70) REVERT: A 554 ASP cc_start: 0.7084 (t0) cc_final: 0.6558 (t0) REVERT: A 936 GLN cc_start: 0.7478 (pt0) cc_final: 0.7251 (mm110) REVERT: C 591 SER cc_start: 0.8464 (t) cc_final: 0.8260 (t) REVERT: C 768 LYS cc_start: 0.7813 (mmtm) cc_final: 0.7277 (mmpt) REVERT: C 769 GLN cc_start: 0.7841 (mm-40) cc_final: 0.7573 (mt0) REVERT: C 796 LYS cc_start: 0.7747 (ttpt) cc_final: 0.7047 (tptt) REVERT: C 1032 MET cc_start: 0.8978 (mtp) cc_final: 0.8743 (mtp) outliers start: 51 outliers final: 43 residues processed: 229 average time/residue: 0.3127 time to fit residues: 114.4965 Evaluate side-chains 224 residues out of total 2389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 180 time to evaluate : 2.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 438 TYR Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain B residue 544 ARG Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 616 THR Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain B residue 648 CYS Chi-restraints excluded: chain B residue 729 THR Chi-restraints excluded: chain B residue 822 CYS Chi-restraints excluded: chain B residue 1047 VAL Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 292 SER Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 690 SER Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 1100 ASP Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 491 TYR Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 511 CYS Chi-restraints excluded: chain C residue 615 LEU Chi-restraints excluded: chain C residue 616 THR Chi-restraints excluded: chain C residue 648 CYS Chi-restraints excluded: chain C residue 684 ASP Chi-restraints excluded: chain C residue 690 SER Chi-restraints excluded: chain C residue 958 VAL Chi-restraints excluded: chain C residue 1110 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 167 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 158 optimal weight: 2.9990 chunk 264 optimal weight: 0.1980 chunk 1 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 212 optimal weight: 10.0000 chunk 106 optimal weight: 2.9990 chunk 190 optimal weight: 10.0000 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 181 HIS ** B 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 806 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.143388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.113544 restraints weight = 25852.711| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 2.69 r_work: 0.2816 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.1693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 22459 Z= 0.161 Angle : 0.576 14.565 30576 Z= 0.292 Chirality : 0.047 0.498 3566 Planarity : 0.004 0.047 3873 Dihedral : 4.771 42.454 3611 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.34 % Allowed : 10.97 % Favored : 86.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.15), residues: 2690 helix: 1.52 (0.21), residues: 640 sheet: 1.05 (0.20), residues: 625 loop : -1.21 (0.14), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 423 HIS 0.005 0.001 HIS B1046 PHE 0.021 0.002 PHE A 83 TYR 0.019 0.002 TYR C 200 ARG 0.008 0.000 ARG A 544 Details of bonding type rmsd link_NAG-ASN : bond 0.00557 ( 32) link_NAG-ASN : angle 3.36550 ( 96) hydrogen bonds : bond 0.05303 ( 915) hydrogen bonds : angle 4.81353 ( 2574) SS BOND : bond 0.00467 ( 34) SS BOND : angle 1.41425 ( 68) covalent geometry : bond 0.00397 (22393) covalent geometry : angle 0.54204 (30412) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5380 Ramachandran restraints generated. 2690 Oldfield, 0 Emsley, 2690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5380 Ramachandran restraints generated. 2690 Oldfield, 0 Emsley, 2690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 2389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 197 time to evaluate : 2.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 37 MET cc_start: 0.9012 (mtp) cc_final: 0.8735 (mtm) REVERT: B 183 ARG cc_start: 0.6848 (ptp-170) cc_final: 0.6412 (ptp-110) REVERT: B 373 LYS cc_start: 0.7965 (mptt) cc_final: 0.7420 (mmmt) REVERT: B 376 ASP cc_start: 0.8180 (t0) cc_final: 0.7911 (t0) REVERT: A 45 GLU cc_start: 0.7837 (tp30) cc_final: 0.7590 (pm20) REVERT: A 191 ASP cc_start: 0.7971 (m-30) cc_final: 0.7510 (t70) REVERT: A 554 ASP cc_start: 0.7054 (t0) cc_final: 0.6540 (t0) REVERT: A 936 GLN cc_start: 0.7424 (pt0) cc_final: 0.7166 (mm110) REVERT: C 551 PHE cc_start: 0.8739 (p90) cc_final: 0.8484 (p90) REVERT: C 591 SER cc_start: 0.8483 (t) cc_final: 0.8272 (t) REVERT: C 652 ILE cc_start: 0.9139 (OUTLIER) cc_final: 0.8875 (mt) REVERT: C 769 GLN cc_start: 0.7948 (mm-40) cc_final: 0.7642 (mt0) REVERT: C 796 LYS cc_start: 0.7892 (ttpt) cc_final: 0.7172 (tptt) REVERT: C 921 THR cc_start: 0.6711 (OUTLIER) cc_final: 0.6264 (t) REVERT: C 1032 MET cc_start: 0.8999 (mtp) cc_final: 0.8774 (mtp) outliers start: 56 outliers final: 47 residues processed: 240 average time/residue: 0.3130 time to fit residues: 120.0005 Evaluate side-chains 240 residues out of total 2389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 191 time to evaluate : 2.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 438 TYR Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain B residue 544 ARG Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 616 THR Chi-restraints excluded: chain B residue 646 TYR Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain B residue 648 CYS Chi-restraints excluded: chain B residue 693 THR Chi-restraints excluded: chain B residue 729 THR Chi-restraints excluded: chain B residue 822 CYS Chi-restraints excluded: chain B residue 1047 VAL Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 292 SER Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 690 SER Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 913 ILE Chi-restraints excluded: chain A residue 1099 THR Chi-restraints excluded: chain A residue 1100 ASP Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 491 TYR Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 511 CYS Chi-restraints excluded: chain C residue 615 LEU Chi-restraints excluded: chain C residue 616 THR Chi-restraints excluded: chain C residue 635 CYS Chi-restraints excluded: chain C residue 648 CYS Chi-restraints excluded: chain C residue 652 ILE Chi-restraints excluded: chain C residue 684 ASP Chi-restraints excluded: chain C residue 690 SER Chi-restraints excluded: chain C residue 921 THR Chi-restraints excluded: chain C residue 958 VAL Chi-restraints excluded: chain C residue 1110 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 163 optimal weight: 1.9990 chunk 166 optimal weight: 0.9980 chunk 148 optimal weight: 0.9980 chunk 262 optimal weight: 1.9990 chunk 250 optimal weight: 1.9990 chunk 204 optimal weight: 2.9990 chunk 224 optimal weight: 0.0970 chunk 138 optimal weight: 0.8980 chunk 33 optimal weight: 10.0000 chunk 150 optimal weight: 4.9990 chunk 195 optimal weight: 2.9990 overall best weight: 0.9980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 181 HIS ** B 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.145011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.114550 restraints weight = 25925.463| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 2.79 r_work: 0.2811 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.1776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 22459 Z= 0.125 Angle : 0.541 13.938 30576 Z= 0.273 Chirality : 0.045 0.484 3566 Planarity : 0.004 0.046 3873 Dihedral : 4.617 40.660 3611 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.26 % Allowed : 11.13 % Favored : 86.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.15), residues: 2690 helix: 1.62 (0.21), residues: 640 sheet: 0.94 (0.20), residues: 624 loop : -1.19 (0.14), residues: 1426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 423 HIS 0.005 0.001 HIS B1046 PHE 0.015 0.001 PHE A 83 TYR 0.015 0.001 TYR A1049 ARG 0.008 0.000 ARG A 544 Details of bonding type rmsd link_NAG-ASN : bond 0.00554 ( 32) link_NAG-ASN : angle 3.27743 ( 96) hydrogen bonds : bond 0.04612 ( 915) hydrogen bonds : angle 4.69351 ( 2574) SS BOND : bond 0.00382 ( 34) SS BOND : angle 1.24382 ( 68) covalent geometry : bond 0.00299 (22393) covalent geometry : angle 0.50719 (30412) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5380 Ramachandran restraints generated. 2690 Oldfield, 0 Emsley, 2690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5380 Ramachandran restraints generated. 2690 Oldfield, 0 Emsley, 2690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 2389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 196 time to evaluate : 2.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 37 MET cc_start: 0.9026 (mtp) cc_final: 0.8759 (mtm) REVERT: B 107 MET cc_start: 0.7938 (OUTLIER) cc_final: 0.7499 (mmp) REVERT: B 126 ARG cc_start: 0.5971 (ttp-170) cc_final: 0.5050 (tpp-160) REVERT: B 373 LYS cc_start: 0.7972 (mptt) cc_final: 0.7420 (mmmt) REVERT: B 376 ASP cc_start: 0.8228 (t0) cc_final: 0.7959 (t0) REVERT: B 770 MET cc_start: 0.8707 (mmm) cc_final: 0.8402 (mmm) REVERT: B 823 LEU cc_start: 0.6249 (OUTLIER) cc_final: 0.6044 (pp) REVERT: A 45 GLU cc_start: 0.7755 (tp30) cc_final: 0.7451 (pm20) REVERT: A 191 ASP cc_start: 0.7994 (m-30) cc_final: 0.7525 (t70) REVERT: A 554 ASP cc_start: 0.7241 (t0) cc_final: 0.6689 (t0) REVERT: A 936 GLN cc_start: 0.7428 (pt0) cc_final: 0.7153 (mm110) REVERT: C 591 SER cc_start: 0.8477 (t) cc_final: 0.8265 (t) REVERT: C 652 ILE cc_start: 0.9130 (OUTLIER) cc_final: 0.8850 (mt) REVERT: C 768 LYS cc_start: 0.7914 (mmtm) cc_final: 0.7379 (mmpt) REVERT: C 769 GLN cc_start: 0.7943 (mm-40) cc_final: 0.7639 (mt0) REVERT: C 796 LYS cc_start: 0.7894 (ttpt) cc_final: 0.7164 (tptt) REVERT: C 1032 MET cc_start: 0.8992 (mtp) cc_final: 0.8767 (mtp) outliers start: 54 outliers final: 48 residues processed: 238 average time/residue: 0.3029 time to fit residues: 115.3633 Evaluate side-chains 243 residues out of total 2389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 192 time to evaluate : 2.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 438 TYR Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain B residue 544 ARG Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 616 THR Chi-restraints excluded: chain B residue 646 TYR Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain B residue 648 CYS Chi-restraints excluded: chain B residue 693 THR Chi-restraints excluded: chain B residue 729 THR Chi-restraints excluded: chain B residue 822 CYS Chi-restraints excluded: chain B residue 823 LEU Chi-restraints excluded: chain B residue 1047 VAL Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 292 SER Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 690 SER Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 913 ILE Chi-restraints excluded: chain A residue 1099 THR Chi-restraints excluded: chain A residue 1100 ASP Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 491 TYR Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 511 CYS Chi-restraints excluded: chain C residue 615 LEU Chi-restraints excluded: chain C residue 616 THR Chi-restraints excluded: chain C residue 635 CYS Chi-restraints excluded: chain C residue 648 CYS Chi-restraints excluded: chain C residue 652 ILE Chi-restraints excluded: chain C residue 684 ASP Chi-restraints excluded: chain C residue 958 VAL Chi-restraints excluded: chain C residue 1110 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 213 optimal weight: 7.9990 chunk 207 optimal weight: 0.9990 chunk 225 optimal weight: 3.9990 chunk 1 optimal weight: 0.9990 chunk 202 optimal weight: 1.9990 chunk 131 optimal weight: 6.9990 chunk 88 optimal weight: 0.8980 chunk 172 optimal weight: 0.6980 chunk 11 optimal weight: 4.9990 chunk 46 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 181 HIS ** B 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.145094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.115188 restraints weight = 25898.519| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 2.66 r_work: 0.2838 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.1829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 22459 Z= 0.119 Angle : 0.534 13.444 30576 Z= 0.270 Chirality : 0.045 0.473 3566 Planarity : 0.004 0.045 3873 Dihedral : 4.547 39.350 3611 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.22 % Allowed : 11.34 % Favored : 86.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.15), residues: 2690 helix: 1.67 (0.21), residues: 634 sheet: 0.95 (0.20), residues: 624 loop : -1.21 (0.14), residues: 1432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 423 HIS 0.004 0.001 HIS B1046 PHE 0.015 0.001 PHE A 83 TYR 0.019 0.001 TYR C 200 ARG 0.008 0.000 ARG A 544 Details of bonding type rmsd link_NAG-ASN : bond 0.00551 ( 32) link_NAG-ASN : angle 3.21671 ( 96) hydrogen bonds : bond 0.04539 ( 915) hydrogen bonds : angle 4.66197 ( 2574) SS BOND : bond 0.00359 ( 34) SS BOND : angle 1.21243 ( 68) covalent geometry : bond 0.00283 (22393) covalent geometry : angle 0.50081 (30412) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8909.51 seconds wall clock time: 155 minutes 43.83 seconds (9343.83 seconds total)