Starting phenix.real_space_refine on Thu Jun 19 03:18:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8h16_34426/06_2025/8h16_34426.cif Found real_map, /net/cci-nas-00/data/ceres_data/8h16_34426/06_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_34426/06_2025/8h16_34426.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8h16_34426/06_2025/8h16_34426.map" model { file = "/net/cci-nas-00/data/ceres_data/8h16_34426/06_2025/8h16_34426.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8h16_34426/06_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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 12.37, per 1000 atoms: 0.56 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: 5.07 Conformation dependent library (CDL) restraints added in 2.7 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: 3.28 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: 9.38 Time building geometry restraints manager: 6.08 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: 1.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.800 Check model and map are aligned: 0.160 Set scattering table: 0.190 Process input model: 50.310 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.060 ------------------------------------------------------------------------------- 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 : 2.247 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: 0.3383 time to fit residues: 115.7554 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 : 2.462 ------------------------------------------------------------------------------- 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: 0.2876 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 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 : 3.000 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 37 MET cc_start: 0.9077 (mtp) cc_final: 0.8762 (mtm) REVERT: B 376 ASP cc_start: 0.8198 (t0) cc_final: 0.7819 (m-30) REVERT: B 560 ASP cc_start: 0.8353 (p0) cc_final: 0.8008 (p0) REVERT: B 709 MET cc_start: 0.9194 (mtp) cc_final: 0.8988 (mtp) REVERT: A 191 ASP cc_start: 0.7971 (m-30) cc_final: 0.7590 (t70) REVERT: A 554 ASP cc_start: 0.7070 (t0) cc_final: 0.6562 (t0) REVERT: C 122 ASN cc_start: 0.8480 (m110) cc_final: 0.8149 (m-40) REVERT: C 338 TYR cc_start: 0.8537 (p90) cc_final: 0.8276 (p90) REVERT: C 591 SER cc_start: 0.8321 (t) cc_final: 0.8086 (t) REVERT: C 768 LYS cc_start: 0.7641 (mmtm) cc_final: 0.7191 (mmpt) REVERT: C 790 ASP cc_start: 0.8359 (m-30) cc_final: 0.8130 (m-30) REVERT: C 796 LYS cc_start: 0.7265 (ttpt) cc_final: 0.6687 (tptt) REVERT: C 939 GLN cc_start: 0.8844 (mt0) cc_final: 0.8151 (mp10) REVERT: C 1032 MET cc_start: 0.9009 (mtp) cc_final: 0.8617 (mtm) outliers start: 13 outliers final: 10 residues processed: 215 average time/residue: 0.4345 time to fit residues: 151.5370 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 : 2.389 ------------------------------------------------------------------------------- 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: 1.9990 chunk 110 optimal weight: 0.0870 overall best weight: 1.3962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 907 ASN ** C 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 883 GLN C 915 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.143963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.115019 restraints weight = 25819.733| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 2.61 r_work: 0.2801 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.1169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 22459 Z= 0.161 Angle : 0.596 17.222 30576 Z= 0.303 Chirality : 0.047 0.530 3566 Planarity : 0.005 0.067 3873 Dihedral : 5.262 44.451 3611 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.21 % Allowed : 7.62 % Favored : 91.17 % 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: -0.13 (0.15), residues: 2690 helix: 1.10 (0.21), residues: 646 sheet: 1.02 (0.20), residues: 605 loop : -1.19 (0.14), residues: 1439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 423 HIS 0.006 0.001 HIS B1046 PHE 0.021 0.002 PHE A 83 TYR 0.018 0.002 TYR B1049 ARG 0.005 0.000 ARG A 544 Details of bonding type rmsd link_NAG-ASN : bond 0.00602 ( 32) link_NAG-ASN : angle 3.70920 ( 96) hydrogen bonds : bond 0.05543 ( 915) hydrogen bonds : angle 5.03043 ( 2574) SS BOND : bond 0.00453 ( 34) SS BOND : angle 1.45050 ( 68) covalent geometry : bond 0.00394 (22393) covalent geometry : angle 0.55563 (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 232 residues out of total 2389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 203 time to evaluate : 2.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 37 MET cc_start: 0.9023 (mtp) cc_final: 0.8710 (mtm) REVERT: B 126 ARG cc_start: 0.5760 (tmm160) cc_final: 0.5143 (tpp80) REVERT: B 256 TYR cc_start: 0.7791 (m-80) cc_final: 0.7511 (m-10) REVERT: B 306 ARG cc_start: 0.8022 (mmt90) cc_final: 0.7779 (mmt90) REVERT: B 376 ASP cc_start: 0.8341 (t0) cc_final: 0.8139 (t0) REVERT: A 45 GLU cc_start: 0.7534 (tp30) cc_final: 0.6959 (pm20) REVERT: A 191 ASP cc_start: 0.8003 (m-30) cc_final: 0.7523 (t70) REVERT: A 554 ASP cc_start: 0.7208 (t0) cc_final: 0.6682 (t0) REVERT: A 936 GLN cc_start: 0.7478 (pt0) cc_final: 0.7132 (mm-40) REVERT: C 338 TYR cc_start: 0.8606 (p90) cc_final: 0.8398 (p90) REVERT: C 768 LYS cc_start: 0.7668 (mmtm) cc_final: 0.7186 (mmpt) REVERT: C 796 LYS cc_start: 0.7607 (ttpt) cc_final: 0.6911 (tptt) REVERT: C 1032 MET cc_start: 0.9056 (mtp) cc_final: 0.8686 (mtm) outliers start: 29 outliers final: 23 residues processed: 224 average time/residue: 0.3310 time to fit residues: 118.2612 Evaluate side-chains 210 residues out of total 2389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 187 time to evaluate : 2.241 ------------------------------------------------------------------------------- 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 438 TYR Chi-restraints excluded: chain B residue 537 VAL 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 292 SER 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 690 SER 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: 0.9980 chunk 149 optimal weight: 2.9990 chunk 92 optimal weight: 0.9990 chunk 271 optimal weight: 4.9990 chunk 35 optimal weight: 10.0000 chunk 216 optimal weight: 0.8980 chunk 127 optimal weight: 4.9990 chunk 29 optimal weight: 0.1980 chunk 51 optimal weight: 0.8980 chunk 230 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 904 GLN C 357 ASN ** C 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.146466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.117383 restraints weight = 25886.522| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 2.34 r_work: 0.2845 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.1429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 22459 Z= 0.105 Angle : 0.533 16.242 30576 Z= 0.267 Chirality : 0.045 0.520 3566 Planarity : 0.004 0.057 3873 Dihedral : 4.784 42.171 3611 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.47 % Allowed : 9.17 % Favored : 89.37 % 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: 1.51 (0.21), residues: 644 sheet: 1.01 (0.20), residues: 615 loop : -1.13 (0.14), residues: 1431 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 0.016 0.001 TYR A1049 ARG 0.003 0.000 ARG A 544 Details of bonding type rmsd link_NAG-ASN : bond 0.00612 ( 32) link_NAG-ASN : angle 3.48627 ( 96) hydrogen bonds : bond 0.04332 ( 915) hydrogen bonds : angle 4.76093 ( 2574) SS BOND : bond 0.00315 ( 34) SS BOND : angle 1.16311 ( 68) covalent geometry : bond 0.00240 (22393) covalent geometry : angle 0.49461 (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 234 residues out of total 2389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 199 time to evaluate : 2.192 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 37 MET cc_start: 0.9048 (mtp) cc_final: 0.8736 (mtm) REVERT: B 256 TYR cc_start: 0.7741 (m-80) cc_final: 0.7527 (m-10) REVERT: B 306 ARG cc_start: 0.8033 (mmt90) cc_final: 0.7787 (mmt90) REVERT: B 373 LYS cc_start: 0.7564 (mptt) cc_final: 0.7232 (mmmt) REVERT: B 376 ASP cc_start: 0.8353 (t0) cc_final: 0.8102 (t0) REVERT: B 770 MET cc_start: 0.8806 (mmm) cc_final: 0.8421 (mmm) REVERT: A 45 GLU cc_start: 0.7472 (tp30) cc_final: 0.7104 (pm20) REVERT: A 191 ASP cc_start: 0.7978 (m-30) cc_final: 0.7600 (t70) REVERT: A 554 ASP cc_start: 0.7109 (t0) cc_final: 0.6603 (t0) REVERT: A 936 GLN cc_start: 0.7500 (pt0) cc_final: 0.7181 (mm-40) REVERT: C 768 LYS cc_start: 0.7652 (mmtm) cc_final: 0.7201 (mmpt) REVERT: C 796 LYS cc_start: 0.7552 (ttpt) cc_final: 0.6900 (tptt) REVERT: C 921 THR cc_start: 0.6863 (OUTLIER) cc_final: 0.6570 (t) REVERT: C 1032 MET cc_start: 0.8984 (mtp) cc_final: 0.8605 (mtm) outliers start: 35 outliers final: 30 residues processed: 226 average time/residue: 0.3170 time to fit residues: 115.1119 Evaluate side-chains 218 residues out of total 2389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 187 time to evaluate : 2.251 ------------------------------------------------------------------------------- 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 370 SER Chi-restraints excluded: chain B residue 438 TYR Chi-restraints excluded: chain B residue 544 ARG 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 533 THR Chi-restraints excluded: chain A residue 535 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 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 615 LEU 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: 0.4980 chunk 12 optimal weight: 0.9990 chunk 0 optimal weight: 9.9990 chunk 254 optimal weight: 3.9990 chunk 257 optimal weight: 2.9990 chunk 127 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 272 optimal weight: 2.9990 chunk 235 optimal weight: 0.6980 chunk 259 optimal weight: 1.9990 chunk 273 optimal weight: 4.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 181 HIS B 904 GLN ** C 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.143241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.113159 restraints weight = 25954.977| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 2.80 r_work: 0.2812 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.1423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 22459 Z= 0.163 Angle : 0.588 16.436 30576 Z= 0.297 Chirality : 0.047 0.526 3566 Planarity : 0.004 0.053 3873 Dihedral : 4.999 45.177 3611 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.18 % Allowed : 9.59 % Favored : 88.24 % 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: -0.11 (0.15), residues: 2690 helix: 1.31 (0.21), residues: 649 sheet: 0.94 (0.20), residues: 611 loop : -1.24 (0.14), residues: 1430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 423 HIS 0.005 0.001 HIS B1046 PHE 0.021 0.002 PHE A 83 TYR 0.017 0.002 TYR B1049 ARG 0.003 0.000 ARG A1021 Details of bonding type rmsd link_NAG-ASN : bond 0.00583 ( 32) link_NAG-ASN : angle 3.57824 ( 96) hydrogen bonds : bond 0.05385 ( 915) hydrogen bonds : angle 4.91002 ( 2574) SS BOND : bond 0.00464 ( 34) SS BOND : angle 1.41238 ( 68) covalent geometry : bond 0.00402 (22393) covalent geometry : angle 0.55013 (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 244 residues out of total 2389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 192 time to evaluate : 2.542 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 37 MET cc_start: 0.9016 (mtp) cc_final: 0.8738 (mtm) REVERT: B 126 ARG cc_start: 0.5658 (tmm160) cc_final: 0.5073 (tpp80) REVERT: B 256 TYR cc_start: 0.7801 (m-80) cc_final: 0.7542 (m-10) REVERT: B 306 ARG cc_start: 0.8000 (mmt90) cc_final: 0.7728 (mmt90) REVERT: B 373 LYS cc_start: 0.7712 (mptt) cc_final: 0.7250 (mmmt) REVERT: B 376 ASP cc_start: 0.8331 (t0) cc_final: 0.7958 (t0) REVERT: B 770 MET cc_start: 0.8851 (mmm) cc_final: 0.8459 (mmm) REVERT: A 45 GLU cc_start: 0.7694 (tp30) cc_final: 0.7305 (pm20) REVERT: A 191 ASP cc_start: 0.7989 (m-30) cc_final: 0.7509 (t70) REVERT: A 554 ASP cc_start: 0.7169 (t0) cc_final: 0.6628 (t0) REVERT: A 936 GLN cc_start: 0.7447 (pt0) cc_final: 0.7172 (mm110) REVERT: C 494 TYR cc_start: 0.6717 (m-80) cc_final: 0.6480 (m-80) REVERT: C 652 ILE cc_start: 0.9133 (OUTLIER) cc_final: 0.8855 (mt) REVERT: C 769 GLN cc_start: 0.7902 (mm-40) cc_final: 0.7612 (mt0) REVERT: C 796 LYS cc_start: 0.7729 (ttpt) cc_final: 0.7015 (tptt) REVERT: C 1032 MET cc_start: 0.9016 (mtp) cc_final: 0.8614 (mtp) outliers start: 52 outliers final: 43 residues processed: 234 average time/residue: 0.3272 time to fit residues: 122.9687 Evaluate side-chains 230 residues out of total 2389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 186 time to evaluate : 2.290 ------------------------------------------------------------------------------- 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 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 652 ILE 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 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 588 THR 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 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 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 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: 4.9990 chunk 222 optimal weight: 0.9990 chunk 83 optimal weight: 0.7980 chunk 80 optimal weight: 3.9990 chunk 271 optimal weight: 0.3980 chunk 174 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 31 optimal weight: 5.9990 chunk 136 optimal weight: 2.9990 chunk 201 optimal weight: 0.4980 overall best weight: 0.7384 ------------------------------------------------------------------------------- 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** B1117 ASN ** 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 = 0.3542 r_free = 0.3542 target = 0.146000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.116634 restraints weight = 25735.159| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 2.28 r_work: 0.2845 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.1593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 22459 Z= 0.106 Angle : 0.529 15.658 30576 Z= 0.265 Chirality : 0.045 0.513 3566 Planarity : 0.004 0.049 3873 Dihedral : 4.662 41.471 3611 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.22 % Allowed : 10.00 % Favored : 87.78 % 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: 0.08 (0.15), residues: 2690 helix: 1.60 (0.21), residues: 647 sheet: 0.96 (0.20), residues: 618 loop : -1.15 (0.14), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 423 HIS 0.004 0.001 HIS B1046 PHE 0.013 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 0.00595 ( 32) link_NAG-ASN : angle 3.39993 ( 96) hydrogen bonds : bond 0.04314 ( 915) hydrogen bonds : angle 4.69914 ( 2574) SS BOND : bond 0.00336 ( 34) SS BOND : angle 1.14732 ( 68) covalent geometry : bond 0.00243 (22393) covalent geometry : angle 0.49136 (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 246 residues out of total 2389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 193 time to evaluate : 2.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 37 MET cc_start: 0.9051 (mtp) cc_final: 0.8795 (mtm) REVERT: B 126 ARG cc_start: 0.5773 (tmm160) cc_final: 0.5119 (tpp80) REVERT: B 183 ARG cc_start: 0.7016 (ptp-170) cc_final: 0.6390 (ptp-110) REVERT: B 306 ARG cc_start: 0.8010 (mmt90) cc_final: 0.7749 (mmt90) REVERT: B 373 LYS cc_start: 0.7748 (mptt) cc_final: 0.7313 (mmmt) REVERT: B 376 ASP cc_start: 0.8223 (t0) cc_final: 0.7925 (t0) REVERT: B 770 MET cc_start: 0.8834 (mmm) cc_final: 0.8459 (mmm) REVERT: A 45 GLU cc_start: 0.7716 (tp30) cc_final: 0.7440 (pm20) REVERT: A 191 ASP cc_start: 0.7984 (m-30) cc_final: 0.7573 (t70) REVERT: A 554 ASP cc_start: 0.7101 (t0) cc_final: 0.6582 (t0) REVERT: A 936 GLN cc_start: 0.7486 (pt0) cc_final: 0.7246 (mm110) REVERT: C 494 TYR cc_start: 0.6750 (m-80) cc_final: 0.6344 (m-80) REVERT: C 768 LYS cc_start: 0.7915 (mmtm) cc_final: 0.7401 (mmpt) REVERT: C 769 GLN cc_start: 0.7863 (mm-40) cc_final: 0.7568 (mt0) REVERT: C 796 LYS cc_start: 0.7659 (ttpt) cc_final: 0.7046 (tptt) REVERT: C 921 THR cc_start: 0.6908 (OUTLIER) cc_final: 0.6560 (t) REVERT: C 1032 MET cc_start: 0.8962 (mtp) cc_final: 0.8537 (mtp) outliers start: 53 outliers final: 40 residues processed: 234 average time/residue: 0.3226 time to fit residues: 121.4785 Evaluate side-chains 230 residues out of total 2389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 189 time to evaluate : 2.433 ------------------------------------------------------------------------------- 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 332 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 544 ARG 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 652 ILE 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 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 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 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 921 THR Chi-restraints excluded: chain C residue 958 VAL Chi-restraints excluded: chain C residue 1110 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 110 optimal weight: 0.9990 chunk 254 optimal weight: 3.9990 chunk 187 optimal weight: 4.9990 chunk 163 optimal weight: 1.9990 chunk 132 optimal weight: 0.0670 chunk 226 optimal weight: 4.9990 chunk 108 optimal weight: 0.9980 chunk 133 optimal weight: 6.9990 chunk 169 optimal weight: 1.9990 chunk 136 optimal weight: 1.9990 chunk 126 optimal weight: 7.9990 overall best weight: 1.2124 ------------------------------------------------------------------------------- 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 = 0.3519 r_free = 0.3519 target = 0.143873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.114148 restraints weight = 25931.225| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 2.66 r_work: 0.2800 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.1588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 22459 Z= 0.143 Angle : 0.559 15.669 30576 Z= 0.283 Chirality : 0.046 0.514 3566 Planarity : 0.004 0.048 3873 Dihedral : 4.788 42.926 3611 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.30 % Allowed : 10.42 % Favored : 87.28 % 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: -0.02 (0.15), residues: 2690 helix: 1.45 (0.21), residues: 650 sheet: 0.94 (0.20), residues: 614 loop : -1.20 (0.14), residues: 1426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 868 HIS 0.005 0.001 HIS B1046 PHE 0.018 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 0.00580 ( 32) link_NAG-ASN : angle 3.44199 ( 96) hydrogen bonds : bond 0.04999 ( 915) hydrogen bonds : angle 4.79984 ( 2574) SS BOND : bond 0.00428 ( 34) SS BOND : angle 1.29972 ( 68) covalent geometry : bond 0.00348 (22393) covalent geometry : angle 0.52246 (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 252 residues out of total 2389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 197 time to evaluate : 2.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 37 MET cc_start: 0.9030 (mtp) cc_final: 0.8764 (mtm) REVERT: B 126 ARG cc_start: 0.5818 (tmm160) cc_final: 0.5058 (tpp-160) REVERT: B 183 ARG cc_start: 0.7031 (ptp-170) cc_final: 0.6422 (ptp-110) REVERT: B 256 TYR cc_start: 0.7977 (m-80) cc_final: 0.7694 (m-10) REVERT: B 306 ARG cc_start: 0.8030 (mmt90) cc_final: 0.7749 (mmt90) REVERT: B 373 LYS cc_start: 0.7922 (mptt) cc_final: 0.7404 (mmmt) REVERT: B 376 ASP cc_start: 0.8241 (t0) cc_final: 0.7963 (t0) REVERT: B 770 MET cc_start: 0.8843 (mmm) cc_final: 0.8476 (mmm) REVERT: A 45 GLU cc_start: 0.7894 (tp30) cc_final: 0.7510 (pm20) REVERT: A 191 ASP cc_start: 0.8005 (m-30) cc_final: 0.7523 (t70) REVERT: A 554 ASP cc_start: 0.7198 (t0) cc_final: 0.6652 (t0) REVERT: A 936 GLN cc_start: 0.7468 (pt0) cc_final: 0.7196 (mm110) REVERT: C 494 TYR cc_start: 0.6666 (m-80) cc_final: 0.6205 (m-80) REVERT: C 652 ILE cc_start: 0.9161 (OUTLIER) cc_final: 0.8878 (mt) REVERT: C 769 GLN cc_start: 0.7941 (mm-40) cc_final: 0.7638 (mt0) REVERT: C 796 LYS cc_start: 0.7757 (ttpt) cc_final: 0.7073 (tptt) REVERT: C 1032 MET cc_start: 0.8984 (mtp) cc_final: 0.8755 (mtp) outliers start: 55 outliers final: 48 residues processed: 240 average time/residue: 0.3301 time to fit residues: 127.3883 Evaluate side-chains 239 residues out of total 2389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 190 time to evaluate : 2.331 ------------------------------------------------------------------------------- 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 332 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 647 GLU Chi-restraints excluded: chain B residue 648 CYS Chi-restraints excluded: chain B residue 652 ILE 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 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 290 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 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: 2.9990 chunk 92 optimal weight: 0.2980 chunk 109 optimal weight: 4.9990 chunk 157 optimal weight: 0.4980 chunk 79 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 chunk 119 optimal weight: 5.9990 chunk 62 optimal weight: 3.9990 chunk 233 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.143283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.113177 restraints weight = 25960.309| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 2.75 r_work: 0.2798 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.1621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 22459 Z= 0.155 Angle : 0.574 15.432 30576 Z= 0.291 Chirality : 0.047 0.511 3566 Planarity : 0.004 0.047 3873 Dihedral : 4.890 44.218 3611 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.47 % Allowed : 10.51 % 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: -0.11 (0.15), residues: 2690 helix: 1.40 (0.21), residues: 643 sheet: 0.91 (0.20), residues: 616 loop : -1.27 (0.14), residues: 1431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 868 HIS 0.005 0.001 HIS B1046 PHE 0.019 0.002 PHE A 83 TYR 0.016 0.001 TYR B1049 ARG 0.008 0.000 ARG A 544 Details of bonding type rmsd link_NAG-ASN : bond 0.00563 ( 32) link_NAG-ASN : angle 3.48139 ( 96) hydrogen bonds : bond 0.05180 ( 915) hydrogen bonds : angle 4.84915 ( 2574) SS BOND : bond 0.00439 ( 34) SS BOND : angle 1.39742 ( 68) covalent geometry : bond 0.00382 (22393) covalent geometry : angle 0.53773 (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 253 residues out of total 2389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 194 time to evaluate : 2.505 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: 0.8780 (mtm) REVERT: B 126 ARG cc_start: 0.5657 (tmm160) cc_final: 0.4916 (tpp-160) REVERT: B 183 ARG cc_start: 0.6917 (ptp-170) cc_final: 0.6345 (ptp-110) REVERT: B 256 TYR cc_start: 0.7974 (m-80) cc_final: 0.7742 (m-10) REVERT: B 306 ARG cc_start: 0.8019 (mmt90) cc_final: 0.7662 (mmt90) REVERT: B 376 ASP cc_start: 0.8226 (t0) cc_final: 0.8013 (t0) REVERT: A 191 ASP cc_start: 0.7996 (m-30) cc_final: 0.7518 (t70) REVERT: A 554 ASP cc_start: 0.7251 (t0) cc_final: 0.6694 (t0) REVERT: A 936 GLN cc_start: 0.7477 (pt0) cc_final: 0.7203 (mm110) REVERT: C 494 TYR cc_start: 0.6485 (m-80) cc_final: 0.5821 (m-80) REVERT: C 652 ILE cc_start: 0.9177 (OUTLIER) cc_final: 0.8900 (mt) REVERT: C 769 GLN cc_start: 0.7962 (mm-40) cc_final: 0.7654 (mt0) REVERT: C 796 LYS cc_start: 0.7906 (ttpt) cc_final: 0.7193 (tptt) REVERT: C 921 THR cc_start: 0.6841 (OUTLIER) cc_final: 0.6479 (t) REVERT: C 1032 MET cc_start: 0.9000 (mtp) cc_final: 0.8773 (mtp) outliers start: 59 outliers final: 50 residues processed: 240 average time/residue: 0.3303 time to fit residues: 126.9067 Evaluate side-chains 243 residues out of total 2389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 191 time to evaluate : 2.260 ------------------------------------------------------------------------------- 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 647 GLU Chi-restraints excluded: chain B residue 648 CYS Chi-restraints excluded: chain B residue 652 ILE 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 215 THR 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 290 VAL Chi-restraints excluded: chain C residue 348 CYS 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 616 THR 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 Chi-restraints excluded: chain C residue 1112 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 167 optimal weight: 0.9980 chunk 27 optimal weight: 4.9990 chunk 76 optimal weight: 5.9990 chunk 21 optimal weight: 0.7980 chunk 158 optimal weight: 1.9990 chunk 264 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 77 optimal weight: 0.2980 chunk 212 optimal weight: 10.0000 chunk 106 optimal weight: 1.9990 chunk 190 optimal weight: 0.9980 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 = 0.3527 r_free = 0.3527 target = 0.144633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.114421 restraints weight = 25812.809| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 2.77 r_work: 0.2824 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.1719 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= 0.127 Angle : 0.546 14.982 30576 Z= 0.275 Chirality : 0.046 0.503 3566 Planarity : 0.004 0.046 3873 Dihedral : 4.727 41.745 3611 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.64 % Allowed : 10.59 % Favored : 86.77 % 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: -0.02 (0.15), residues: 2690 helix: 1.54 (0.21), residues: 643 sheet: 0.90 (0.20), residues: 623 loop : -1.22 (0.14), residues: 1424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 868 HIS 0.004 0.001 HIS B1046 PHE 0.015 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 0.00573 ( 32) link_NAG-ASN : angle 3.37375 ( 96) hydrogen bonds : bond 0.04682 ( 915) hydrogen bonds : angle 4.74524 ( 2574) SS BOND : bond 0.00383 ( 34) SS BOND : angle 1.27264 ( 68) covalent geometry : bond 0.00306 (22393) covalent geometry : angle 0.51026 (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 257 residues out of total 2389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 194 time to evaluate : 2.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 37 MET cc_start: 0.9026 (mtp) cc_final: 0.8767 (mtm) REVERT: B 256 TYR cc_start: 0.7923 (m-80) cc_final: 0.7715 (m-10) REVERT: B 306 ARG cc_start: 0.7997 (mmt90) cc_final: 0.7716 (mmt90) REVERT: B 376 ASP cc_start: 0.8226 (t0) cc_final: 0.8005 (t0) REVERT: B 770 MET cc_start: 0.8725 (mmm) cc_final: 0.8394 (mmm) REVERT: A 191 ASP cc_start: 0.7989 (m-30) cc_final: 0.7525 (t70) REVERT: A 224 LEU cc_start: 0.8146 (OUTLIER) cc_final: 0.7708 (pp) REVERT: A 554 ASP cc_start: 0.7203 (t0) cc_final: 0.6655 (t0) REVERT: A 936 GLN cc_start: 0.7503 (pt0) cc_final: 0.7247 (mm110) REVERT: C 652 ILE cc_start: 0.9128 (OUTLIER) cc_final: 0.8853 (mt) REVERT: C 769 GLN cc_start: 0.7958 (mm-40) cc_final: 0.7653 (mt0) REVERT: C 796 LYS cc_start: 0.7912 (ttpt) cc_final: 0.7186 (tptt) REVERT: C 921 THR cc_start: 0.6699 (OUTLIER) cc_final: 0.6319 (t) REVERT: C 1032 MET cc_start: 0.8974 (mtp) cc_final: 0.8750 (mtp) outliers start: 63 outliers final: 51 residues processed: 243 average time/residue: 0.3244 time to fit residues: 127.5504 Evaluate side-chains 244 residues out of total 2389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 190 time to evaluate : 2.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 VAL 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 332 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 647 GLU Chi-restraints excluded: chain B residue 648 CYS Chi-restraints excluded: chain B residue 652 ILE 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 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 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 290 VAL Chi-restraints excluded: chain C residue 348 CYS 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 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 921 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 163 optimal weight: 1.9990 chunk 166 optimal weight: 1.9990 chunk 148 optimal weight: 0.1980 chunk 262 optimal weight: 0.9980 chunk 250 optimal weight: 0.5980 chunk 204 optimal weight: 5.9990 chunk 224 optimal weight: 0.5980 chunk 138 optimal weight: 0.9980 chunk 33 optimal weight: 10.0000 chunk 150 optimal weight: 4.9990 chunk 195 optimal weight: 0.0470 overall best weight: 0.4878 ------------------------------------------------------------------------------- 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 883 GLN C 915 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.147719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.118165 restraints weight = 25870.586| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 2.39 r_work: 0.2877 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.1933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 22459 Z= 0.091 Angle : 0.504 13.907 30576 Z= 0.252 Chirality : 0.044 0.480 3566 Planarity : 0.004 0.044 3873 Dihedral : 4.320 36.596 3611 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.97 % Allowed : 11.39 % Favored : 86.65 % 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: 0.17 (0.16), residues: 2690 helix: 1.87 (0.22), residues: 641 sheet: 0.90 (0.20), residues: 630 loop : -1.14 (0.14), residues: 1419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 868 HIS 0.003 0.000 HIS B1046 PHE 0.012 0.001 PHE A1103 TYR 0.015 0.001 TYR A1049 ARG 0.008 0.000 ARG A 544 Details of bonding type rmsd link_NAG-ASN : bond 0.00579 ( 32) link_NAG-ASN : angle 3.17794 ( 96) hydrogen bonds : bond 0.03730 ( 915) hydrogen bonds : angle 4.52932 ( 2574) SS BOND : bond 0.00299 ( 34) SS BOND : angle 1.04604 ( 68) covalent geometry : bond 0.00202 (22393) covalent geometry : angle 0.47024 (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 244 residues out of total 2389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 197 time to evaluate : 2.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 37 MET cc_start: 0.9000 (mtp) cc_final: 0.8731 (mtm) REVERT: B 126 ARG cc_start: 0.5964 (ttp-170) cc_final: 0.5058 (tpp-160) REVERT: B 183 ARG cc_start: 0.7213 (ptp-170) cc_final: 0.6834 (ptp-110) REVERT: B 306 ARG cc_start: 0.7987 (mmt90) cc_final: 0.7740 (mmt90) REVERT: B 376 ASP cc_start: 0.8238 (t0) cc_final: 0.7994 (t0) REVERT: B 770 MET cc_start: 0.8644 (mmm) cc_final: 0.8387 (mmm) REVERT: A 191 ASP cc_start: 0.7974 (m-30) cc_final: 0.7590 (t70) REVERT: A 554 ASP cc_start: 0.7070 (t0) cc_final: 0.6527 (t0) REVERT: A 936 GLN cc_start: 0.7488 (pt0) cc_final: 0.7261 (mm110) REVERT: C 768 LYS cc_start: 0.7977 (mmtm) cc_final: 0.7458 (mmpt) REVERT: C 769 GLN cc_start: 0.7898 (mm-40) cc_final: 0.7653 (mt0) REVERT: C 796 LYS cc_start: 0.7846 (ttpt) cc_final: 0.7152 (tptt) REVERT: C 921 THR cc_start: 0.6551 (OUTLIER) cc_final: 0.6164 (t) REVERT: C 939 GLN cc_start: 0.8915 (mt0) cc_final: 0.8714 (mt0) REVERT: C 1032 MET cc_start: 0.8982 (mtp) cc_final: 0.8766 (mtp) outliers start: 47 outliers final: 41 residues processed: 236 average time/residue: 0.3188 time to fit residues: 121.0780 Evaluate side-chains 226 residues out of total 2389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 184 time to evaluate : 2.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 332 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 591 SER Chi-restraints excluded: chain B residue 616 THR Chi-restraints excluded: chain B residue 648 CYS Chi-restraints excluded: chain B residue 652 ILE Chi-restraints excluded: chain B residue 693 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 215 THR Chi-restraints excluded: chain A residue 224 LEU 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 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 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 635 CYS Chi-restraints excluded: chain C residue 648 CYS Chi-restraints excluded: chain C residue 684 ASP 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 213 optimal weight: 6.9990 chunk 207 optimal weight: 0.0980 chunk 225 optimal weight: 3.9990 chunk 1 optimal weight: 0.6980 chunk 202 optimal weight: 0.9990 chunk 131 optimal weight: 0.4980 chunk 88 optimal weight: 0.4980 chunk 172 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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** A 915 GLN C 786 GLN C 883 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.147207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.118124 restraints weight = 25848.400| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 2.29 r_work: 0.2870 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 22459 Z= 0.095 Angle : 0.508 13.551 30576 Z= 0.254 Chirality : 0.044 0.469 3566 Planarity : 0.004 0.045 3873 Dihedral : 4.249 35.625 3611 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.97 % Allowed : 11.59 % 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: 0.23 (0.16), residues: 2690 helix: 1.97 (0.21), residues: 635 sheet: 0.96 (0.20), residues: 620 loop : -1.11 (0.14), residues: 1435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 868 HIS 0.003 0.000 HIS B1046 PHE 0.012 0.001 PHE A1103 TYR 0.020 0.001 TYR C 200 ARG 0.009 0.000 ARG A 544 Details of bonding type rmsd link_NAG-ASN : bond 0.00576 ( 32) link_NAG-ASN : angle 3.13259 ( 96) hydrogen bonds : bond 0.03894 ( 915) hydrogen bonds : angle 4.50110 ( 2574) SS BOND : bond 0.00308 ( 34) SS BOND : angle 1.04619 ( 68) covalent geometry : bond 0.00214 (22393) covalent geometry : angle 0.47553 (30412) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9697.42 seconds wall clock time: 169 minutes 7.09 seconds (10147.09 seconds total)