Starting phenix.real_space_refine on Sat May 24 02:34:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v0q_42866/05_2025/8v0q_42866.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v0q_42866/05_2025/8v0q_42866.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8v0q_42866/05_2025/8v0q_42866.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v0q_42866/05_2025/8v0q_42866.map" model { file = "/net/cci-nas-00/data/ceres_data/8v0q_42866/05_2025/8v0q_42866.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v0q_42866/05_2025/8v0q_42866.cif" } resolution = 3.9 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= -0.001 sd= 0.020 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 114 5.16 5 C 15813 2.51 5 N 4068 2.21 5 O 4800 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 35 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 24795 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 8069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1035, 8069 Classifications: {'peptide': 1035} Link IDs: {'PTRANS': 51, 'TRANS': 983} Chain breaks: 7 Chain: "B" Number of atoms: 8069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1035, 8069 Classifications: {'peptide': 1035} Link IDs: {'PTRANS': 51, 'TRANS': 983} Chain breaks: 7 Chain: "C" Number of atoms: 8069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1035, 8069 Classifications: {'peptide': 1035} Link IDs: {'PTRANS': 51, 'TRANS': 983} Chain breaks: 7 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" 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: "B" 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: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 14.79, per 1000 atoms: 0.60 Number of scatterers: 24795 At special positions: 0 Unit cell: (137.16, 130.68, 174.96, 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 114 16.00 O 4800 8.00 N 4068 7.00 C 15813 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=40, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A 840 " - pdb=" SG CYS A 851 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.05 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B 840 " - pdb=" SG CYS B 851 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.05 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C 840 " - pdb=" SG CYS C 851 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " 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=2, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 282 " " NAG A1303 " - " ASN A 331 " " NAG A1304 " - " ASN A 343 " " NAG A1305 " - " ASN A 616 " " NAG A1306 " - " ASN A 709 " " NAG A1307 " - " ASN A1074 " " NAG A1308 " - " ASN A1134 " " NAG A1309 " - " ASN A 165 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 165 " " NAG B1303 " - " ASN B 282 " " NAG B1304 " - " ASN B 331 " " NAG B1305 " - " ASN B 343 " " NAG B1306 " - " ASN B 616 " " NAG B1307 " - " ASN B 709 " " NAG B1308 " - " ASN B1074 " " NAG B1309 " - " ASN B1134 " " NAG B1310 " - " ASN B 234 " " NAG B1311 " - " ASN C 234 " " NAG C1301 " - " ASN A 234 " " NAG C1302 " - " ASN C 61 " " NAG C1303 " - " ASN C 282 " " NAG C1304 " - " ASN C 331 " " NAG C1305 " - " ASN C 343 " " NAG C1306 " - " ASN C 616 " " NAG C1307 " - " ASN C 709 " " NAG C1308 " - " ASN C1074 " " NAG C1309 " - " ASN C1134 " " NAG C1310 " - " ASN C 165 " " NAG D 1 " - " ASN A 717 " " NAG E 1 " - " ASN A 801 " " NAG F 1 " - " ASN B 717 " " NAG G 1 " - " ASN B 801 " " NAG H 1 " - " ASN C 717 " " NAG I 1 " - " ASN C 801 " Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.88 Conformation dependent library (CDL) restraints added in 3.0 seconds 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5814 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 49 sheets defined 24.3% alpha, 23.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.91 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 406 through 410 removed outlier: 3.556A pdb=" N ILE A 410 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 422 Processing helix chain 'A' and resid 737 through 743 removed outlier: 3.723A pdb=" N CYS A 743 " --> pdb=" O THR A 739 " (cutoff:3.500A) Processing helix chain 'A' and resid 747 through 755 removed outlier: 3.568A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.565A pdb=" N GLU A 773 " --> pdb=" O GLY A 769 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLN A 774 " --> pdb=" O ILE A 770 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LYS A 776 " --> pdb=" O VAL A 772 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 825 Processing helix chain 'A' and resid 848 through 856 removed outlier: 4.003A pdb=" N ALA A 852 " --> pdb=" O ASP A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.654A pdb=" N ILE A 870 " --> pdb=" O THR A 866 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA A 871 " --> pdb=" O ASP A 867 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR A 883 " --> pdb=" O ALA A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.979A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 removed outlier: 3.717A pdb=" N ARG A 905 " --> pdb=" O GLN A 901 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASN A 907 " --> pdb=" O ALA A 903 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLY A 908 " --> pdb=" O TYR A 904 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.672A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.645A pdb=" N GLN A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ASN A 955 " --> pdb=" O VAL A 951 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLN A 965 " --> pdb=" O THR A 961 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.672A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.399A pdb=" N VAL A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 3.786A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.588A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 372 removed outlier: 3.538A pdb=" N PHE B 371 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 410 removed outlier: 3.578A pdb=" N GLN B 409 " --> pdb=" O GLU B 406 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ILE B 410 " --> pdb=" O VAL B 407 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 406 through 410' Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'B' and resid 502 through 506 removed outlier: 3.806A pdb=" N GLN B 506 " --> pdb=" O VAL B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 757 removed outlier: 3.515A pdb=" N GLY B 757 " --> pdb=" O LEU B 753 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 4.033A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 4.006A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 848 through 855 removed outlier: 3.633A pdb=" N ALA B 852 " --> pdb=" O ASP B 848 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 897 through 910 Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.749A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU B 918 " --> pdb=" O ASN B 914 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 913 through 918' Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.604A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU B 984 " --> pdb=" O ILE B 980 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.149A pdb=" N VAL B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1147 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 341 Processing helix chain 'C' and resid 364 through 371 removed outlier: 3.807A pdb=" N VAL C 367 " --> pdb=" O ASP C 364 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N TYR C 369 " --> pdb=" O SER C 366 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASN C 370 " --> pdb=" O VAL C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 389 removed outlier: 3.571A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 407 No H-bonds generated for 'chain 'C' and resid 405 through 407' Processing helix chain 'C' and resid 417 through 422 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 757 removed outlier: 3.595A pdb=" N GLY C 757 " --> pdb=" O LEU C 753 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 4.052A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.582A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 848 through 856 removed outlier: 3.864A pdb=" N ALA C 852 " --> pdb=" O ASP C 848 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 884 removed outlier: 3.561A pdb=" N ILE C 870 " --> pdb=" O THR C 866 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 910 Processing helix chain 'C' and resid 913 through 918 removed outlier: 3.877A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU C 918 " --> pdb=" O ASN C 914 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 913 through 918' Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 4.190A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 3.626A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.691A pdb=" N GLY C 548 " --> pdb=" O PHE C 541 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N PHE C 541 " --> pdb=" O GLY C 548 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.708A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA5, first strand: chain 'A' and resid 92 through 94 Processing sheet with id=AA6, first strand: chain 'A' and resid 92 through 94 removed outlier: 3.674A pdb=" N ILE A 203 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 101 through 104 removed outlier: 6.617A pdb=" N LEU A 241 " --> pdb=" O ARG A 102 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 311 through 316 removed outlier: 3.563A pdb=" N THR A 599 " --> pdb=" O GLY A 311 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N THR A 315 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N TYR A 612 " --> pdb=" O CYS A 649 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 325 through 326 removed outlier: 5.358A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.790A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS A 378 " --> pdb=" O VAL A 433 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 452 through 453 Processing sheet with id=AB3, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB4, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.343A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.485A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N SER A 691 " --> pdb=" O GLN A 675 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N GLN A 675 " --> pdb=" O SER A 691 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE A 664 " --> pdb=" O ALA A 672 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 701 through 702 removed outlier: 7.111A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 712 through 713 Processing sheet with id=AB7, first strand: chain 'A' and resid 717 through 728 removed outlier: 6.735A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLU A 725 " --> pdb=" O PHE A1062 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 717 through 728 removed outlier: 6.735A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLU A 725 " --> pdb=" O PHE A1062 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLY A1059 " --> pdb=" O ALA A1056 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ALA A1056 " --> pdb=" O GLY A1059 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AC1, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.354A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 26 through 31 removed outlier: 3.556A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG B 190 " --> pdb=" O SER B 94 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N PHE B 194 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 26 through 31 removed outlier: 3.556A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG B 190 " --> pdb=" O SER B 94 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LYS B 195 " --> pdb=" O LYS B 202 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LYS B 202 " --> pdb=" O LYS B 195 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE B 197 " --> pdb=" O TYR B 200 " (cutoff:3.500A) removed outlier: 8.114A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU B 226 " --> pdb=" O ILE B 203 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 52 through 55 removed outlier: 3.693A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG B 273 " --> pdb=" O ASP B 53 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N PHE B 55 " --> pdb=" O GLN B 271 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.596A pdb=" N GLY B 107 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU B 241 " --> pdb=" O GLY B 103 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 118 through 119 removed outlier: 3.818A pdb=" N VAL B 127 " --> pdb=" O LEU B 118 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 311 through 319 removed outlier: 3.669A pdb=" N THR B 599 " --> pdb=" O GLY B 311 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N THR B 315 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 325 through 328 removed outlier: 7.045A pdb=" N ILE B 326 " --> pdb=" O ASN B 542 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N PHE B 541 " --> pdb=" O GLY B 548 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.712A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.819A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD3, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.788A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.568A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 701 through 702 removed outlier: 6.391A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.532A pdb=" N ILE B 714 " --> pdb=" O LYS B1073 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 718 through 722 Processing sheet with id=AD8, first strand: chain 'B' and resid 718 through 722 removed outlier: 3.582A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AE1, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AE2, first strand: chain 'C' and resid 27 through 30 removed outlier: 8.173A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N TYR C 265 " --> pdb=" O PHE C 65 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLU C 191 " --> pdb=" O LYS C 206 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS C 206 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.893A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.965A pdb=" N LEU C 84 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ASN C 121 " --> pdb=" O ARG C 102 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 311 through 317 removed outlier: 4.554A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N CYS C 649 " --> pdb=" O TYR C 612 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLY C 648 " --> pdb=" O THR C 645 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N PHE C 643 " --> pdb=" O LEU C 650 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.575A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE8, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.611A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.273A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.423A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER C 691 " --> pdb=" O GLN C 675 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLN C 675 " --> pdb=" O SER C 691 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.635A pdb=" N ILE C 714 " --> pdb=" O LYS C1073 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 718 through 728 removed outlier: 3.856A pdb=" N SER C 721 " --> pdb=" O THR C1066 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLU C 725 " --> pdb=" O PHE C1062 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AF4, first strand: chain 'C' and resid 1120 through 1122 909 hydrogen bonds defined for protein. 2502 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 10.49 Time building geometry restraints manager: 6.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7859 1.34 - 1.47: 6366 1.47 - 1.60: 10978 1.60 - 1.72: 0 1.72 - 1.85: 141 Bond restraints: 25344 Sorted by residual: bond pdb=" C1 NAG B1304 " pdb=" O5 NAG B1304 " ideal model delta sigma weight residual 1.406 1.506 -0.100 2.00e-02 2.50e+03 2.51e+01 bond pdb=" C1 NAG A1303 " pdb=" O5 NAG A1303 " ideal model delta sigma weight residual 1.406 1.459 -0.053 2.00e-02 2.50e+03 6.90e+00 bond pdb=" C1 NAG C1302 " pdb=" O5 NAG C1302 " ideal model delta sigma weight residual 1.406 1.454 -0.048 2.00e-02 2.50e+03 5.88e+00 bond pdb=" C1 NAG B1311 " pdb=" O5 NAG B1311 " ideal model delta sigma weight residual 1.406 1.454 -0.048 2.00e-02 2.50e+03 5.86e+00 bond pdb=" C1 NAG A1304 " pdb=" O5 NAG A1304 " ideal model delta sigma weight residual 1.406 1.453 -0.047 2.00e-02 2.50e+03 5.48e+00 ... (remaining 25339 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.99: 34053 2.99 - 5.99: 354 5.99 - 8.98: 47 8.98 - 11.97: 11 11.97 - 14.96: 5 Bond angle restraints: 34470 Sorted by residual: angle pdb=" C LEU C 945 " pdb=" N GLY C 946 " pdb=" CA GLY C 946 " ideal model delta sigma weight residual 119.98 126.18 -6.20 1.11e+00 8.12e-01 3.11e+01 angle pdb=" C LEU A 518 " pdb=" N HIS A 519 " pdb=" CA HIS A 519 " ideal model delta sigma weight residual 121.54 130.45 -8.91 1.91e+00 2.74e-01 2.18e+01 angle pdb=" C LEU A 518 " pdb=" CA LEU A 518 " pdb=" CB LEU A 518 " ideal model delta sigma weight residual 115.79 110.44 5.35 1.19e+00 7.06e-01 2.02e+01 angle pdb=" C SER A 116 " pdb=" N LEU A 117 " pdb=" CA LEU A 117 " ideal model delta sigma weight residual 120.82 127.39 -6.57 1.47e+00 4.63e-01 2.00e+01 angle pdb=" CB MET C1050 " pdb=" CG MET C1050 " pdb=" SD MET C1050 " ideal model delta sigma weight residual 112.70 126.07 -13.37 3.00e+00 1.11e-01 1.98e+01 ... (remaining 34465 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.92: 14455 21.92 - 43.84: 1037 43.84 - 65.77: 127 65.77 - 87.69: 36 87.69 - 109.61: 5 Dihedral angle restraints: 15660 sinusoidal: 6627 harmonic: 9033 Sorted by residual: dihedral pdb=" CA TYR B 91 " pdb=" C TYR B 91 " pdb=" N PHE B 92 " pdb=" CA PHE B 92 " ideal model delta harmonic sigma weight residual -180.00 -132.40 -47.60 0 5.00e+00 4.00e-02 9.06e+01 dihedral pdb=" CA LYS B 462 " pdb=" C LYS B 462 " pdb=" N PRO B 463 " pdb=" CA PRO B 463 " ideal model delta harmonic sigma weight residual -180.00 -136.95 -43.05 0 5.00e+00 4.00e-02 7.41e+01 dihedral pdb=" CB CYS A 662 " pdb=" SG CYS A 662 " pdb=" SG CYS A 671 " pdb=" CB CYS A 671 " ideal model delta sinusoidal sigma weight residual -86.00 -18.25 -67.75 1 1.00e+01 1.00e-02 5.96e+01 ... (remaining 15657 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.124: 3945 0.124 - 0.248: 90 0.248 - 0.373: 9 0.373 - 0.497: 2 0.497 - 0.621: 1 Chirality restraints: 4047 Sorted by residual: chirality pdb=" C1 NAG A1301 " pdb=" ND2 ASN A 61 " pdb=" C2 NAG A1301 " pdb=" O5 NAG A1301 " both_signs ideal model delta sigma weight residual False -2.40 -1.78 -0.62 2.00e-01 2.50e+01 9.64e+00 chirality pdb=" CB ILE A 105 " pdb=" CA ILE A 105 " pdb=" CG1 ILE A 105 " pdb=" CG2 ILE A 105 " both_signs ideal model delta sigma weight residual False 2.64 2.25 0.39 2.00e-01 2.50e+01 3.82e+00 chirality pdb=" C2 NAG C1301 " pdb=" C1 NAG C1301 " pdb=" C3 NAG C1301 " pdb=" N2 NAG C1301 " both_signs ideal model delta sigma weight residual False -2.49 -2.11 -0.38 2.00e-01 2.50e+01 3.58e+00 ... (remaining 4044 not shown) Planarity restraints: 4434 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR B 91 " 0.019 2.00e-02 2.50e+03 3.73e-02 1.39e+01 pdb=" C TYR B 91 " -0.064 2.00e-02 2.50e+03 pdb=" O TYR B 91 " 0.024 2.00e-02 2.50e+03 pdb=" N PHE B 92 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA C 520 " 0.042 5.00e-02 4.00e+02 6.31e-02 6.38e+00 pdb=" N PRO C 521 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO C 521 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO C 521 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU C 118 " 0.012 2.00e-02 2.50e+03 2.43e-02 5.89e+00 pdb=" C LEU C 118 " -0.042 2.00e-02 2.50e+03 pdb=" O LEU C 118 " 0.016 2.00e-02 2.50e+03 pdb=" N ILE C 119 " 0.014 2.00e-02 2.50e+03 ... (remaining 4431 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 6318 2.80 - 3.33: 20145 3.33 - 3.85: 39830 3.85 - 4.38: 42999 4.38 - 4.90: 77033 Nonbonded interactions: 186325 Sorted by model distance: nonbonded pdb=" OH TYR A 37 " pdb=" O LEU A 54 " model vdw 2.279 3.040 nonbonded pdb=" O ASP B 294 " pdb=" OG SER B 297 " model vdw 2.287 3.040 nonbonded pdb=" O GLU B 661 " pdb=" OH TYR B 695 " model vdw 2.300 3.040 nonbonded pdb=" O VAL A 308 " pdb=" OG1 THR A 602 " model vdw 2.303 3.040 nonbonded pdb=" O THR C 393 " pdb=" OG1 THR C 523 " model vdw 2.304 3.040 ... (remaining 186320 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 'A' selection = (chain 'B' and (resid 24 through 1147 or resid 1301 through 1309)) selection = (chain 'C' and (resid 24 through 1147 or resid 1301 through 1309)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.330 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: 0.910 Check model and map are aligned: 0.170 Set scattering table: 0.230 Process input model: 55.360 Find NCS groups from input model: 1.380 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.100 25428 Z= 0.218 Angle : 0.853 19.090 34676 Z= 0.425 Chirality : 0.055 0.621 4047 Planarity : 0.006 0.068 4398 Dihedral : 14.492 109.610 9726 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.68 % Favored : 95.29 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.65 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.14), residues: 3057 helix: -0.68 (0.17), residues: 665 sheet: -0.08 (0.21), residues: 539 loop : -1.80 (0.13), residues: 1853 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 64 HIS 0.006 0.001 HIS B 519 PHE 0.036 0.002 PHE A 201 TYR 0.018 0.001 TYR A 453 ARG 0.017 0.001 ARG C1107 Details of bonding type rmsd link_NAG-ASN : bond 0.00652 ( 36) link_NAG-ASN : angle 4.00754 ( 108) link_BETA1-4 : bond 0.00645 ( 6) link_BETA1-4 : angle 1.49273 ( 18) hydrogen bonds : bond 0.22872 ( 873) hydrogen bonds : angle 8.28533 ( 2502) SS BOND : bond 0.00427 ( 40) SS BOND : angle 1.60354 ( 80) covalent geometry : bond 0.00439 (25344) covalent geometry : angle 0.82083 (34470) Misc. bond : bond 0.00884 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 262 time to evaluate : 2.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 ASP cc_start: 0.8511 (m-30) cc_final: 0.8299 (m-30) REVERT: A 353 TRP cc_start: 0.8791 (p-90) cc_final: 0.7161 (p-90) REVERT: B 740 MET cc_start: 0.7769 (mmt) cc_final: 0.7442 (mmt) REVERT: B 1019 ARG cc_start: 0.7610 (ttp80) cc_final: 0.7321 (ttp80) REVERT: C 549 THR cc_start: 0.8336 (m) cc_final: 0.8022 (p) REVERT: C 979 ASP cc_start: 0.8681 (m-30) cc_final: 0.8459 (m-30) outliers start: 0 outliers final: 0 residues processed: 262 average time/residue: 0.3337 time to fit residues: 141.8780 Evaluate side-chains 183 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 183 time to evaluate : 2.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 260 optimal weight: 5.9990 chunk 234 optimal weight: 8.9990 chunk 129 optimal weight: 6.9990 chunk 80 optimal weight: 0.9980 chunk 157 optimal weight: 0.9980 chunk 125 optimal weight: 0.9990 chunk 242 optimal weight: 20.0000 chunk 93 optimal weight: 3.9990 chunk 147 optimal weight: 3.9990 chunk 180 optimal weight: 5.9990 chunk 280 optimal weight: 4.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 405 ASN A 564 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 542 ASN ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 GLN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 448 ASN C 926 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.132888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.097789 restraints weight = 57953.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.097575 restraints weight = 36967.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.098221 restraints weight = 32079.114| |-----------------------------------------------------------------------------| r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.1359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 25428 Z= 0.189 Angle : 0.653 13.503 34676 Z= 0.327 Chirality : 0.047 0.477 4047 Planarity : 0.004 0.045 4398 Dihedral : 8.366 98.233 4200 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.68 % Favored : 95.29 % Rotamer: Outliers : 0.78 % Allowed : 8.02 % Favored : 91.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.65 % Twisted General : 0.07 % 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: -1.13 (0.14), residues: 3057 helix: 0.81 (0.20), residues: 675 sheet: -0.19 (0.21), residues: 578 loop : -1.63 (0.14), residues: 1804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 436 HIS 0.004 0.001 HIS A1048 PHE 0.022 0.002 PHE A 906 TYR 0.020 0.001 TYR A1067 ARG 0.005 0.000 ARG C1107 Details of bonding type rmsd link_NAG-ASN : bond 0.00501 ( 36) link_NAG-ASN : angle 2.81266 ( 108) link_BETA1-4 : bond 0.00626 ( 6) link_BETA1-4 : angle 1.18195 ( 18) hydrogen bonds : bond 0.05440 ( 873) hydrogen bonds : angle 5.74810 ( 2502) SS BOND : bond 0.00350 ( 40) SS BOND : angle 1.30799 ( 80) covalent geometry : bond 0.00432 (25344) covalent geometry : angle 0.63241 (34470) Misc. bond : bond 0.00113 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 188 time to evaluate : 2.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 353 TRP cc_start: 0.8842 (p-90) cc_final: 0.7509 (p-90) REVERT: B 87 ASN cc_start: 0.7153 (t0) cc_final: 0.6928 (t0) REVERT: B 91 TYR cc_start: 0.7864 (t80) cc_final: 0.7576 (t80) REVERT: B 740 MET cc_start: 0.7924 (mmt) cc_final: 0.7555 (mmt) REVERT: C 453 TYR cc_start: 0.7449 (p90) cc_final: 0.6982 (p90) REVERT: C 979 ASP cc_start: 0.8574 (m-30) cc_final: 0.8050 (m-30) outliers start: 21 outliers final: 15 residues processed: 202 average time/residue: 0.3251 time to fit residues: 107.2123 Evaluate side-chains 185 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 170 time to evaluate : 2.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 888 PHE Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 909 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 227 optimal weight: 0.9990 chunk 160 optimal weight: 0.8980 chunk 167 optimal weight: 0.8980 chunk 142 optimal weight: 0.6980 chunk 156 optimal weight: 3.9990 chunk 287 optimal weight: 0.7980 chunk 284 optimal weight: 2.9990 chunk 133 optimal weight: 6.9990 chunk 294 optimal weight: 3.9990 chunk 239 optimal weight: 10.0000 chunk 104 optimal weight: 5.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN ** C 239 GLN ** 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 = 0.4002 r_free = 0.4002 target = 0.134553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.100186 restraints weight = 58091.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.098753 restraints weight = 38799.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.099775 restraints weight = 30931.699| |-----------------------------------------------------------------------------| r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.1554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 25428 Z= 0.111 Angle : 0.570 13.501 34676 Z= 0.279 Chirality : 0.045 0.478 4047 Planarity : 0.004 0.044 4398 Dihedral : 7.807 95.393 4200 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.99 % Favored : 95.98 % Rotamer: Outliers : 0.71 % Allowed : 10.32 % Favored : 88.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.75 (0.15), residues: 3057 helix: 1.45 (0.20), residues: 672 sheet: -0.11 (0.20), residues: 595 loop : -1.47 (0.14), residues: 1790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 64 HIS 0.004 0.001 HIS B 66 PHE 0.028 0.001 PHE A 106 TYR 0.020 0.001 TYR A1067 ARG 0.003 0.000 ARG B 905 Details of bonding type rmsd link_NAG-ASN : bond 0.00473 ( 36) link_NAG-ASN : angle 2.70092 ( 108) link_BETA1-4 : bond 0.00308 ( 6) link_BETA1-4 : angle 1.03341 ( 18) hydrogen bonds : bond 0.04614 ( 873) hydrogen bonds : angle 5.21960 ( 2502) SS BOND : bond 0.00297 ( 40) SS BOND : angle 1.07775 ( 80) covalent geometry : bond 0.00248 (25344) covalent geometry : angle 0.54841 (34470) Misc. bond : bond 0.00219 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 189 time to evaluate : 2.861 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 353 TRP cc_start: 0.8820 (p-90) cc_final: 0.7821 (p-90) REVERT: A 731 MET cc_start: 0.8545 (ptp) cc_final: 0.8077 (ptp) REVERT: A 1039 ARG cc_start: 0.7555 (mtp180) cc_final: 0.7171 (mtm-85) REVERT: B 87 ASN cc_start: 0.7074 (t0) cc_final: 0.6710 (t0) REVERT: B 740 MET cc_start: 0.7859 (mmt) cc_final: 0.7457 (mmt) REVERT: B 869 MET cc_start: 0.9048 (OUTLIER) cc_final: 0.8715 (mtm) REVERT: B 1051 SER cc_start: 0.9048 (m) cc_final: 0.8814 (p) REVERT: C 453 TYR cc_start: 0.7559 (p90) cc_final: 0.7042 (p90) REVERT: C 900 MET cc_start: 0.8528 (mtm) cc_final: 0.8256 (mtm) REVERT: C 979 ASP cc_start: 0.8658 (m-30) cc_final: 0.8188 (m-30) outliers start: 19 outliers final: 10 residues processed: 204 average time/residue: 0.3608 time to fit residues: 117.8662 Evaluate side-chains 191 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 180 time to evaluate : 2.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 1061 VAL Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 888 PHE Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 457 ARG Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain C residue 938 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 94 optimal weight: 0.2980 chunk 204 optimal weight: 1.9990 chunk 212 optimal weight: 9.9990 chunk 61 optimal weight: 0.6980 chunk 64 optimal weight: 0.9990 chunk 210 optimal weight: 0.9980 chunk 98 optimal weight: 9.9990 chunk 186 optimal weight: 3.9990 chunk 101 optimal weight: 5.9990 chunk 112 optimal weight: 10.0000 chunk 36 optimal weight: 20.0000 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 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 = 0.4001 r_free = 0.4001 target = 0.134479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.099926 restraints weight = 58507.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.099779 restraints weight = 34561.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.100675 restraints weight = 31442.884| |-----------------------------------------------------------------------------| r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.1791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 25428 Z= 0.112 Angle : 0.556 12.910 34676 Z= 0.272 Chirality : 0.045 0.467 4047 Planarity : 0.004 0.046 4398 Dihedral : 7.392 90.311 4200 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.22 % Favored : 95.75 % Rotamer: Outliers : 1.08 % Allowed : 11.99 % Favored : 86.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.56 (0.15), residues: 3057 helix: 1.80 (0.21), residues: 660 sheet: -0.08 (0.20), residues: 599 loop : -1.38 (0.14), residues: 1798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 436 HIS 0.003 0.001 HIS B 66 PHE 0.021 0.001 PHE A 106 TYR 0.018 0.001 TYR A1067 ARG 0.003 0.000 ARG B 905 Details of bonding type rmsd link_NAG-ASN : bond 0.00442 ( 36) link_NAG-ASN : angle 2.63409 ( 108) link_BETA1-4 : bond 0.00235 ( 6) link_BETA1-4 : angle 1.10005 ( 18) hydrogen bonds : bond 0.04314 ( 873) hydrogen bonds : angle 4.97982 ( 2502) SS BOND : bond 0.00285 ( 40) SS BOND : angle 1.02335 ( 80) covalent geometry : bond 0.00255 (25344) covalent geometry : angle 0.53458 (34470) Misc. bond : bond 0.00240 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 188 time to evaluate : 2.912 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 353 TRP cc_start: 0.9063 (p-90) cc_final: 0.7747 (p-90) REVERT: A 697 MET cc_start: 0.7145 (tpt) cc_final: 0.6785 (mmm) REVERT: B 87 ASN cc_start: 0.7236 (t0) cc_final: 0.6865 (t0) REVERT: B 392 PHE cc_start: 0.7627 (m-10) cc_final: 0.7336 (m-10) REVERT: B 740 MET cc_start: 0.7829 (mmt) cc_final: 0.7468 (mmt) REVERT: B 869 MET cc_start: 0.9128 (OUTLIER) cc_final: 0.8842 (mtm) REVERT: C 453 TYR cc_start: 0.7529 (p90) cc_final: 0.7021 (p90) REVERT: C 900 MET cc_start: 0.8532 (OUTLIER) cc_final: 0.8146 (mtm) REVERT: C 902 MET cc_start: 0.8834 (mmt) cc_final: 0.8483 (mmt) REVERT: C 979 ASP cc_start: 0.8668 (m-30) cc_final: 0.8143 (m-30) REVERT: C 1033 VAL cc_start: 0.8643 (t) cc_final: 0.8412 (p) outliers start: 29 outliers final: 17 residues processed: 208 average time/residue: 0.3478 time to fit residues: 118.7220 Evaluate side-chains 193 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 174 time to evaluate : 2.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 1061 VAL Chi-restraints excluded: chain B residue 168 PHE Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 888 PHE Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 938 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 188 optimal weight: 1.9990 chunk 164 optimal weight: 0.8980 chunk 224 optimal weight: 0.3980 chunk 61 optimal weight: 0.6980 chunk 17 optimal weight: 8.9990 chunk 126 optimal weight: 7.9990 chunk 70 optimal weight: 2.9990 chunk 53 optimal weight: 0.0770 chunk 119 optimal weight: 7.9990 chunk 291 optimal weight: 0.0770 chunk 238 optimal weight: 0.0270 overall best weight: 0.2554 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 955 ASN ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1135 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.135488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.102369 restraints weight = 58577.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.099878 restraints weight = 38005.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.101298 restraints weight = 31685.507| |-----------------------------------------------------------------------------| r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 25428 Z= 0.092 Angle : 0.538 12.708 34676 Z= 0.262 Chirality : 0.044 0.464 4047 Planarity : 0.003 0.048 4398 Dihedral : 7.061 84.684 4200 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.73 % Favored : 96.24 % Rotamer: Outliers : 0.97 % Allowed : 13.21 % Favored : 85.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.40 (0.15), residues: 3057 helix: 2.05 (0.21), residues: 658 sheet: -0.01 (0.20), residues: 599 loop : -1.31 (0.14), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 436 HIS 0.002 0.000 HIS B 66 PHE 0.030 0.001 PHE A 106 TYR 0.027 0.001 TYR B 91 ARG 0.004 0.000 ARG C1107 Details of bonding type rmsd link_NAG-ASN : bond 0.00437 ( 36) link_NAG-ASN : angle 2.59719 ( 108) link_BETA1-4 : bond 0.00327 ( 6) link_BETA1-4 : angle 1.05833 ( 18) hydrogen bonds : bond 0.03968 ( 873) hydrogen bonds : angle 4.80210 ( 2502) SS BOND : bond 0.00306 ( 40) SS BOND : angle 1.12783 ( 80) covalent geometry : bond 0.00198 (25344) covalent geometry : angle 0.51633 (34470) Misc. bond : bond 0.00467 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 188 time to evaluate : 2.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 353 TRP cc_start: 0.9060 (p-90) cc_final: 0.7727 (p-90) REVERT: A 501 TYR cc_start: 0.8209 (m-10) cc_final: 0.7713 (m-10) REVERT: A 697 MET cc_start: 0.6915 (tpt) cc_final: 0.6535 (mmm) REVERT: B 87 ASN cc_start: 0.7212 (t0) cc_final: 0.6791 (t0) REVERT: B 392 PHE cc_start: 0.7723 (m-10) cc_final: 0.7428 (m-10) REVERT: B 740 MET cc_start: 0.7816 (mmt) cc_final: 0.7465 (mmt) REVERT: B 869 MET cc_start: 0.9095 (OUTLIER) cc_final: 0.8858 (mtm) REVERT: C 453 TYR cc_start: 0.7607 (p90) cc_final: 0.7067 (p90) REVERT: C 869 MET cc_start: 0.7769 (mpp) cc_final: 0.7467 (mpp) REVERT: C 900 MET cc_start: 0.8596 (OUTLIER) cc_final: 0.8238 (mtm) REVERT: C 902 MET cc_start: 0.8860 (mmt) cc_final: 0.8535 (mmt) REVERT: C 979 ASP cc_start: 0.8623 (m-30) cc_final: 0.8081 (m-30) REVERT: C 1033 VAL cc_start: 0.8588 (t) cc_final: 0.8356 (p) outliers start: 26 outliers final: 17 residues processed: 205 average time/residue: 0.3236 time to fit residues: 109.0785 Evaluate side-chains 193 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 174 time to evaluate : 2.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 1061 VAL Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 457 ARG Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 938 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 195 optimal weight: 1.9990 chunk 58 optimal weight: 5.9990 chunk 183 optimal weight: 2.9990 chunk 138 optimal weight: 4.9990 chunk 113 optimal weight: 9.9990 chunk 134 optimal weight: 4.9990 chunk 233 optimal weight: 0.0770 chunk 292 optimal weight: 3.9990 chunk 268 optimal weight: 2.9990 chunk 208 optimal weight: 8.9990 chunk 129 optimal weight: 7.9990 overall best weight: 2.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 955 ASN ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 339 HIS ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 388 ASN C 914 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.131194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.096179 restraints weight = 58079.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.095681 restraints weight = 35242.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.096476 restraints weight = 33212.397| |-----------------------------------------------------------------------------| r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.2190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 25428 Z= 0.196 Angle : 0.619 13.973 34676 Z= 0.305 Chirality : 0.046 0.440 4047 Planarity : 0.004 0.045 4398 Dihedral : 7.056 75.098 4200 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.04 % Favored : 94.93 % Rotamer: Outliers : 1.86 % Allowed : 13.59 % Favored : 84.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.51 (0.15), residues: 3057 helix: 1.82 (0.20), residues: 657 sheet: -0.15 (0.20), residues: 610 loop : -1.29 (0.14), residues: 1790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 436 HIS 0.005 0.001 HIS C1048 PHE 0.023 0.002 PHE A 106 TYR 0.021 0.001 TYR B 91 ARG 0.004 0.000 ARG B 905 Details of bonding type rmsd link_NAG-ASN : bond 0.00477 ( 36) link_NAG-ASN : angle 2.69457 ( 108) link_BETA1-4 : bond 0.00309 ( 6) link_BETA1-4 : angle 1.26916 ( 18) hydrogen bonds : bond 0.04803 ( 873) hydrogen bonds : angle 4.99799 ( 2502) SS BOND : bond 0.00387 ( 40) SS BOND : angle 1.55183 ( 80) covalent geometry : bond 0.00461 (25344) covalent geometry : angle 0.59672 (34470) Misc. bond : bond 0.00144 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 192 time to evaluate : 2.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 353 TRP cc_start: 0.9098 (p-90) cc_final: 0.7760 (p-90) REVERT: A 501 TYR cc_start: 0.8275 (m-10) cc_final: 0.7729 (m-10) REVERT: B 87 ASN cc_start: 0.7528 (t0) cc_final: 0.7116 (t0) REVERT: B 392 PHE cc_start: 0.7881 (m-10) cc_final: 0.7661 (m-10) REVERT: B 869 MET cc_start: 0.9072 (OUTLIER) cc_final: 0.8624 (mtm) REVERT: C 453 TYR cc_start: 0.7539 (p90) cc_final: 0.7023 (p90) REVERT: C 900 MET cc_start: 0.8608 (mtm) cc_final: 0.8326 (mtm) REVERT: C 979 ASP cc_start: 0.8587 (m-30) cc_final: 0.7991 (m-30) outliers start: 50 outliers final: 40 residues processed: 229 average time/residue: 0.3263 time to fit residues: 120.5642 Evaluate side-chains 222 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 181 time to evaluate : 2.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 1061 VAL Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 168 PHE Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 888 PHE Chi-restraints excluded: chain B residue 1014 ARG Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 457 ARG Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 909 ILE Chi-restraints excluded: chain C residue 938 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 103 optimal weight: 20.0000 chunk 57 optimal weight: 6.9990 chunk 143 optimal weight: 5.9990 chunk 210 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 80 optimal weight: 0.6980 chunk 99 optimal weight: 5.9990 chunk 274 optimal weight: 0.9990 chunk 284 optimal weight: 3.9990 chunk 293 optimal weight: 6.9990 chunk 211 optimal weight: 7.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** 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 = 0.3947 r_free = 0.3947 target = 0.130405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.095396 restraints weight = 58385.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.095027 restraints weight = 35362.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.095927 restraints weight = 32522.154| |-----------------------------------------------------------------------------| r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.2453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 25428 Z= 0.187 Angle : 0.629 12.633 34676 Z= 0.309 Chirality : 0.046 0.443 4047 Planarity : 0.004 0.049 4398 Dihedral : 6.909 59.859 4200 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.97 % Favored : 95.00 % Rotamer: Outliers : 1.93 % Allowed : 14.81 % Favored : 83.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.65 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.15), residues: 3057 helix: 1.60 (0.20), residues: 671 sheet: -0.25 (0.20), residues: 610 loop : -1.27 (0.14), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 104 HIS 0.004 0.001 HIS C1048 PHE 0.025 0.002 PHE A 106 TYR 0.028 0.001 TYR B 91 ARG 0.005 0.000 ARG B 905 Details of bonding type rmsd link_NAG-ASN : bond 0.00493 ( 36) link_NAG-ASN : angle 2.79093 ( 108) link_BETA1-4 : bond 0.00321 ( 6) link_BETA1-4 : angle 1.20483 ( 18) hydrogen bonds : bond 0.04900 ( 873) hydrogen bonds : angle 5.01740 ( 2502) SS BOND : bond 0.00469 ( 40) SS BOND : angle 1.52014 ( 80) covalent geometry : bond 0.00440 (25344) covalent geometry : angle 0.60585 (34470) Misc. bond : bond 0.00198 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 181 time to evaluate : 2.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.3279 (mmm) cc_final: 0.2990 (mmm) REVERT: A 501 TYR cc_start: 0.8257 (m-10) cc_final: 0.7527 (m-10) REVERT: A 697 MET cc_start: 0.7157 (tpt) cc_final: 0.6601 (mmm) REVERT: B 87 ASN cc_start: 0.7540 (t0) cc_final: 0.7132 (t0) REVERT: B 543 PHE cc_start: 0.8233 (m-10) cc_final: 0.8018 (m-10) REVERT: B 740 MET cc_start: 0.7857 (mmt) cc_final: 0.7404 (mmt) REVERT: B 869 MET cc_start: 0.9138 (OUTLIER) cc_final: 0.8706 (mtm) REVERT: C 453 TYR cc_start: 0.7686 (p90) cc_final: 0.7132 (p90) REVERT: C 900 MET cc_start: 0.8631 (OUTLIER) cc_final: 0.8422 (mtm) REVERT: C 979 ASP cc_start: 0.8576 (m-30) cc_final: 0.7977 (m-30) outliers start: 52 outliers final: 45 residues processed: 217 average time/residue: 0.3224 time to fit residues: 115.3218 Evaluate side-chains 220 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 173 time to evaluate : 2.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 106 PHE Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 1061 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 168 PHE Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 888 PHE Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1014 ARG Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 457 ARG Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 909 ILE Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain C residue 1001 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 270 optimal weight: 0.7980 chunk 188 optimal weight: 2.9990 chunk 295 optimal weight: 2.9990 chunk 275 optimal weight: 0.5980 chunk 53 optimal weight: 3.9990 chunk 125 optimal weight: 2.9990 chunk 151 optimal weight: 8.9990 chunk 7 optimal weight: 10.0000 chunk 199 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 132 optimal weight: 0.3980 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** 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 = 0.3958 r_free = 0.3958 target = 0.131400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.096436 restraints weight = 58394.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.096243 restraints weight = 35119.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.097044 restraints weight = 31793.991| |-----------------------------------------------------------------------------| r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.2555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 25428 Z= 0.139 Angle : 0.586 13.444 34676 Z= 0.286 Chirality : 0.045 0.440 4047 Planarity : 0.004 0.057 4398 Dihedral : 6.679 59.939 4200 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.55 % Favored : 95.42 % Rotamer: Outliers : 1.52 % Allowed : 15.55 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.15), residues: 3057 helix: 1.83 (0.20), residues: 670 sheet: -0.21 (0.20), residues: 612 loop : -1.19 (0.14), residues: 1775 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 104 HIS 0.003 0.001 HIS B 66 PHE 0.020 0.001 PHE A 106 TYR 0.031 0.001 TYR B 91 ARG 0.004 0.000 ARG C1019 Details of bonding type rmsd link_NAG-ASN : bond 0.00432 ( 36) link_NAG-ASN : angle 2.74823 ( 108) link_BETA1-4 : bond 0.00275 ( 6) link_BETA1-4 : angle 1.09776 ( 18) hydrogen bonds : bond 0.04508 ( 873) hydrogen bonds : angle 4.85015 ( 2502) SS BOND : bond 0.00338 ( 40) SS BOND : angle 1.33939 ( 80) covalent geometry : bond 0.00325 (25344) covalent geometry : angle 0.56313 (34470) Misc. bond : bond 0.00246 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 178 time to evaluate : 2.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 420 ASP cc_start: 0.8512 (m-30) cc_final: 0.8233 (m-30) REVERT: A 501 TYR cc_start: 0.8379 (m-10) cc_final: 0.7657 (m-10) REVERT: A 697 MET cc_start: 0.6874 (tpt) cc_final: 0.6354 (mmm) REVERT: B 87 ASN cc_start: 0.7657 (t0) cc_final: 0.7246 (t0) REVERT: B 740 MET cc_start: 0.7848 (mmt) cc_final: 0.7433 (mmt) REVERT: B 869 MET cc_start: 0.9073 (OUTLIER) cc_final: 0.8678 (mtm) REVERT: C 453 TYR cc_start: 0.7663 (p90) cc_final: 0.7122 (p90) REVERT: C 900 MET cc_start: 0.8625 (OUTLIER) cc_final: 0.8385 (mtm) REVERT: C 979 ASP cc_start: 0.8536 (m-30) cc_final: 0.7940 (m-30) outliers start: 41 outliers final: 35 residues processed: 208 average time/residue: 0.3432 time to fit residues: 117.3915 Evaluate side-chains 207 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 170 time to evaluate : 2.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 1061 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 168 PHE Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 888 PHE Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1014 ARG Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain C residue 1001 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 85 optimal weight: 0.7980 chunk 220 optimal weight: 5.9990 chunk 219 optimal weight: 8.9990 chunk 151 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 chunk 134 optimal weight: 9.9990 chunk 118 optimal weight: 0.9990 chunk 231 optimal weight: 3.9990 chunk 222 optimal weight: 4.9990 chunk 31 optimal weight: 7.9990 chunk 79 optimal weight: 2.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** 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 = 0.3946 r_free = 0.3946 target = 0.130214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.095325 restraints weight = 58595.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.094618 restraints weight = 36788.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.095544 restraints weight = 33239.567| |-----------------------------------------------------------------------------| r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.2718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 25428 Z= 0.164 Angle : 0.618 13.252 34676 Z= 0.302 Chirality : 0.045 0.433 4047 Planarity : 0.004 0.055 4398 Dihedral : 6.586 59.729 4200 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.20 % Favored : 94.77 % Rotamer: Outliers : 1.60 % Allowed : 15.85 % Favored : 82.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.65 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.15), residues: 3057 helix: 1.74 (0.20), residues: 670 sheet: -0.27 (0.20), residues: 610 loop : -1.23 (0.14), residues: 1777 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 104 HIS 0.004 0.001 HIS B 66 PHE 0.023 0.001 PHE A 106 TYR 0.032 0.001 TYR B 91 ARG 0.004 0.000 ARG B 905 Details of bonding type rmsd link_NAG-ASN : bond 0.00465 ( 36) link_NAG-ASN : angle 2.73529 ( 108) link_BETA1-4 : bond 0.00284 ( 6) link_BETA1-4 : angle 1.19042 ( 18) hydrogen bonds : bond 0.04754 ( 873) hydrogen bonds : angle 4.92653 ( 2502) SS BOND : bond 0.00366 ( 40) SS BOND : angle 1.50711 ( 80) covalent geometry : bond 0.00385 (25344) covalent geometry : angle 0.59602 (34470) Misc. bond : bond 0.00373 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 179 time to evaluate : 2.704 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 VAL cc_start: 0.9038 (OUTLIER) cc_final: 0.8817 (m) REVERT: A 177 MET cc_start: 0.4546 (mmm) cc_final: 0.4264 (mmm) REVERT: A 353 TRP cc_start: 0.9067 (p-90) cc_final: 0.7851 (p-90) REVERT: A 420 ASP cc_start: 0.8541 (m-30) cc_final: 0.8258 (m-30) REVERT: A 501 TYR cc_start: 0.8410 (m-10) cc_final: 0.7683 (m-10) REVERT: A 697 MET cc_start: 0.7124 (tpt) cc_final: 0.6643 (mmm) REVERT: B 87 ASN cc_start: 0.7743 (t0) cc_final: 0.7324 (t0) REVERT: B 869 MET cc_start: 0.9066 (OUTLIER) cc_final: 0.8660 (mtm) REVERT: C 453 TYR cc_start: 0.7687 (p90) cc_final: 0.7113 (p90) REVERT: C 900 MET cc_start: 0.8662 (OUTLIER) cc_final: 0.8452 (mtm) REVERT: C 979 ASP cc_start: 0.8585 (m-30) cc_final: 0.7926 (m-30) outliers start: 43 outliers final: 37 residues processed: 212 average time/residue: 0.3305 time to fit residues: 115.3446 Evaluate side-chains 214 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 174 time to evaluate : 2.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 1061 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 168 PHE Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 888 PHE Chi-restraints excluded: chain B residue 1014 ARG Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 457 ARG Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain C residue 1001 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 75 optimal weight: 0.0870 chunk 278 optimal weight: 4.9990 chunk 159 optimal weight: 0.0470 chunk 57 optimal weight: 0.5980 chunk 41 optimal weight: 1.9990 chunk 118 optimal weight: 6.9990 chunk 241 optimal weight: 20.0000 chunk 195 optimal weight: 3.9990 chunk 232 optimal weight: 20.0000 chunk 217 optimal weight: 20.0000 chunk 196 optimal weight: 0.8980 overall best weight: 0.7258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.132676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.098357 restraints weight = 58145.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.097772 restraints weight = 34421.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.098689 restraints weight = 32430.237| |-----------------------------------------------------------------------------| r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.2709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 25428 Z= 0.104 Angle : 0.578 14.183 34676 Z= 0.279 Chirality : 0.045 0.437 4047 Planarity : 0.004 0.058 4398 Dihedral : 6.378 59.629 4200 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.25 % Favored : 95.71 % Rotamer: Outliers : 1.26 % Allowed : 16.41 % Favored : 82.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.65 % Twisted General : 0.03 % 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: -0.28 (0.15), residues: 3057 helix: 2.04 (0.21), residues: 675 sheet: -0.14 (0.20), residues: 617 loop : -1.14 (0.14), residues: 1765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 104 HIS 0.002 0.000 HIS B 66 PHE 0.021 0.001 PHE A 106 TYR 0.037 0.001 TYR B 91 ARG 0.005 0.000 ARG C1019 Details of bonding type rmsd link_NAG-ASN : bond 0.00418 ( 36) link_NAG-ASN : angle 2.58510 ( 108) link_BETA1-4 : bond 0.00395 ( 6) link_BETA1-4 : angle 1.00279 ( 18) hydrogen bonds : bond 0.04128 ( 873) hydrogen bonds : angle 4.71827 ( 2502) SS BOND : bond 0.00308 ( 40) SS BOND : angle 1.20831 ( 80) covalent geometry : bond 0.00236 (25344) covalent geometry : angle 0.55754 (34470) Misc. bond : bond 0.00395 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 187 time to evaluate : 2.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.4734 (mmm) cc_final: 0.4454 (mmm) REVERT: A 353 TRP cc_start: 0.9049 (p-90) cc_final: 0.7813 (p-90) REVERT: A 501 TYR cc_start: 0.8385 (m-10) cc_final: 0.7647 (m-10) REVERT: A 697 MET cc_start: 0.7051 (tpt) cc_final: 0.6561 (mmm) REVERT: A 731 MET cc_start: 0.8890 (ptp) cc_final: 0.8521 (ptp) REVERT: A 1041 ASP cc_start: 0.7990 (m-30) cc_final: 0.7688 (t0) REVERT: A 1045 LYS cc_start: 0.7790 (mmtt) cc_final: 0.7492 (mmtt) REVERT: B 87 ASN cc_start: 0.7794 (t0) cc_final: 0.7387 (t0) REVERT: B 740 MET cc_start: 0.7731 (mmt) cc_final: 0.7365 (mmt) REVERT: B 869 MET cc_start: 0.9035 (OUTLIER) cc_final: 0.8661 (mtm) REVERT: C 396 TYR cc_start: 0.8172 (m-80) cc_final: 0.7671 (m-80) REVERT: C 453 TYR cc_start: 0.7716 (p90) cc_final: 0.7181 (p90) REVERT: C 900 MET cc_start: 0.8569 (OUTLIER) cc_final: 0.8326 (mtm) REVERT: C 979 ASP cc_start: 0.8580 (m-30) cc_final: 0.7952 (m-30) outliers start: 34 outliers final: 30 residues processed: 212 average time/residue: 0.3228 time to fit residues: 113.8443 Evaluate side-chains 204 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 172 time to evaluate : 2.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 1061 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 168 PHE Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain C residue 1001 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 171 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 40 optimal weight: 6.9990 chunk 241 optimal weight: 20.0000 chunk 83 optimal weight: 0.0050 chunk 42 optimal weight: 9.9990 chunk 160 optimal weight: 10.0000 chunk 130 optimal weight: 8.9990 chunk 240 optimal weight: 10.0000 chunk 75 optimal weight: 0.7980 chunk 246 optimal weight: 0.9980 overall best weight: 0.9598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN A 125 ASN A 901 GLN ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.132373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.097863 restraints weight = 58196.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.097351 restraints weight = 35180.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.098213 restraints weight = 32481.672| |-----------------------------------------------------------------------------| r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.2797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 25428 Z= 0.111 Angle : 0.576 13.577 34676 Z= 0.279 Chirality : 0.044 0.427 4047 Planarity : 0.004 0.079 4398 Dihedral : 6.298 59.643 4200 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.48 % Favored : 95.49 % Rotamer: Outliers : 1.48 % Allowed : 16.56 % Favored : 81.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.65 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.15), residues: 3057 helix: 2.05 (0.20), residues: 676 sheet: -0.06 (0.20), residues: 605 loop : -1.15 (0.14), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 104 HIS 0.003 0.000 HIS B 66 PHE 0.022 0.001 PHE A 106 TYR 0.037 0.001 TYR B 91 ARG 0.012 0.000 ARG B 237 Details of bonding type rmsd link_NAG-ASN : bond 0.00411 ( 36) link_NAG-ASN : angle 2.55352 ( 108) link_BETA1-4 : bond 0.00262 ( 6) link_BETA1-4 : angle 1.05171 ( 18) hydrogen bonds : bond 0.04109 ( 873) hydrogen bonds : angle 4.73157 ( 2502) SS BOND : bond 0.00311 ( 40) SS BOND : angle 1.20779 ( 80) covalent geometry : bond 0.00254 (25344) covalent geometry : angle 0.55655 (34470) Misc. bond : bond 0.00273 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6066.34 seconds wall clock time: 108 minutes 16.09 seconds (6496.09 seconds total)