Starting phenix.real_space_refine on Sat Jun 21 13:52:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tp2_26046/06_2025/7tp2_26046.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tp2_26046/06_2025/7tp2_26046.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.72 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7tp2_26046/06_2025/7tp2_26046.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tp2_26046/06_2025/7tp2_26046.map" model { file = "/net/cci-nas-00/data/ceres_data/7tp2_26046/06_2025/7tp2_26046.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tp2_26046/06_2025/7tp2_26046.cif" } resolution = 3.72 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= -0.003 sd= 0.132 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 105 5.16 5 C 15691 2.51 5 N 4036 2.21 5 O 4831 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 24663 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 7947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1017, 7947 Classifications: {'peptide': 1017} Link IDs: {'PTRANS': 48, 'TRANS': 968} Chain breaks: 7 Chain: "B" Number of atoms: 7946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1017, 7946 Classifications: {'peptide': 1017} Link IDs: {'PTRANS': 48, 'TRANS': 968} Chain breaks: 7 Chain: "C" Number of atoms: 7916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1013, 7916 Classifications: {'peptide': 1013} Link IDs: {'PTRANS': 48, 'TRANS': 964} 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: "J" 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: "K" 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: "L" 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: "M" 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: "N" 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: "O" 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: "P" 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: "Q" 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: 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: "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: 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 Time building chain proxies: 13.92, per 1000 atoms: 0.56 Number of scatterers: 24663 At special positions: 0 Unit cell: (131.76, 142.56, 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 105 16.00 O 4831 8.00 N 4036 7.00 C 15691 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.01 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=2.05 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.01 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=2.04 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.02 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.02 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=1.98 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.02 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.02 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=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.02 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 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=2.04 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.02 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.01 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.04 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.02 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=2.04 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=2.02 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied 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 J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 282 " " NAG A1304 " - " ASN A 331 " " NAG A1305 " - " ASN A 343 " " NAG A1306 " - " ASN A 603 " " NAG A1307 " - " ASN A 616 " " NAG A1308 " - " ASN A 657 " " NAG A1309 " - " ASN A 709 " " NAG A1310 " - " ASN A1074 " " NAG A1311 " - " ASN A 165 " " NAG B1301 " - " ASN B 331 " " NAG B1302 " - " ASN B 343 " " NAG B1303 " - " ASN B 603 " " NAG B1304 " - " ASN B 61 " " NAG B1305 " - " ASN B 657 " " NAG B1306 " - " ASN B 122 " " NAG B1307 " - " ASN B 282 " " NAG B1308 " - " ASN B 165 " " NAG B1309 " - " ASN B 616 " " NAG B1310 " - " ASN B 709 " " NAG B1311 " - " ASN B1074 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 282 " " NAG C1303 " - " ASN C 331 " " NAG C1304 " - " ASN C 603 " " NAG C1305 " - " ASN C1074 " " NAG C1306 " - " ASN C 343 " " NAG C1307 " - " ASN C 616 " " NAG C1308 " - " ASN C 165 " " NAG C1309 " - " ASN C 657 " " NAG C1310 " - " ASN C 709 " " NAG C1311 " - " ASN C 122 " " NAG D 1 " - " ASN A 234 " " NAG E 1 " - " ASN A 717 " " NAG F 1 " - " ASN A 801 " " NAG G 1 " - " ASN A1098 " " NAG H 1 " - " ASN A1134 " " NAG I 1 " - " ASN B 234 " " NAG J 1 " - " ASN B 801 " " NAG K 1 " - " ASN B1134 " " NAG L 1 " - " ASN B 717 " " NAG M 1 " - " ASN B1098 " " NAG N 1 " - " ASN C 234 " " NAG O 1 " - " ASN C1098 " " NAG P 1 " - " ASN C1134 " " NAG Q 1 " - " ASN C 801 " Time building additional restraints: 5.89 Conformation dependent library (CDL) restraints added in 3.1 seconds 5998 Ramachandran restraints generated. 2999 Oldfield, 0 Emsley, 2999 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5710 Finding SS restraints... Secondary structure from input PDB file: 82 helices and 47 sheets defined 28.0% alpha, 26.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.66 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.834A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 383 through 387 Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.571A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 498 through 502 Processing helix chain 'A' and resid 616 through 620 removed outlier: 3.766A pdb=" N VAL A 620 " --> pdb=" O CYS A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 633 through 638 removed outlier: 4.320A pdb=" N SER A 637 " --> pdb=" O ARG A 634 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.532A pdb=" N GLN A 774 " --> pdb=" O ILE A 770 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.505A pdb=" N LEU A 821 " --> pdb=" O PHE A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.732A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 918 Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.757A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N THR A 941 " --> pdb=" O SER A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.689A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (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: 3.992A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1032 removed outlier: 5.214A pdb=" N VAL A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER A1021 " --> pdb=" O GLU A1017 " (cutoff:3.500A) Processing helix chain 'A' and resid 1127 through 1129 No H-bonds generated for 'chain 'A' and resid 1127 through 1129' Processing helix chain 'A' and resid 1141 through 1147 removed outlier: 3.514A pdb=" N ASP A1146 " --> pdb=" O PRO A1143 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 Processing helix chain 'B' and resid 364 through 370 Processing helix chain 'B' and resid 383 through 387 Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.123A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 619 through 624 Processing helix chain 'B' and resid 633 through 638 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 756 removed outlier: 3.699A pdb=" N LEU B 754 " --> pdb=" O SER B 750 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N TYR B 756 " --> pdb=" O LEU B 752 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.718A pdb=" N LEU B 763 " --> pdb=" O PHE B 759 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLU B 773 " --> pdb=" O GLY B 769 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 801 through 805 removed outlier: 4.526A pdb=" N GLN B 804 " --> pdb=" O ASN B 801 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 825 Processing helix chain 'B' and resid 866 through 885 removed outlier: 3.538A pdb=" N GLY B 885 " --> pdb=" O THR B 881 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.531A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.729A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.749A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' 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: 3.679A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.669A pdb=" N VAL B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) Processing helix chain 'B' and resid 1116 through 1118 No H-bonds generated for 'chain 'B' and resid 1116 through 1118' Processing helix chain 'B' and resid 1143 through 1147 Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.512A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 383 through 389 removed outlier: 3.505A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.058A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 616 through 620 Processing helix chain 'C' and resid 634 through 639 removed outlier: 3.618A pdb=" N THR C 638 " --> pdb=" O ARG C 634 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 5.951A pdb=" N ASN C 764 " --> pdb=" O CYS C 760 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 801 through 805 removed outlier: 4.475A pdb=" N GLN C 804 " --> pdb=" O ASN C 801 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.564A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 918 removed outlier: 3.595A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.596A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.499A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) 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 removed outlier: 3.912A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.556A pdb=" N VAL C 991 " --> pdb=" O VAL C 987 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASP C 994 " --> pdb=" O GLU C 990 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 removed outlier: 4.137A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.490A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 8.891A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.033A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 4.029A 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 removed outlier: 5.566A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.509A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.300A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.837A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.805A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.005A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.510A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 702 through 704 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 715 Processing sheet with id=AB5, first strand: chain 'A' and resid 718 through 728 removed outlier: 6.099A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB7, first strand: chain 'A' and resid 788 through 790 removed outlier: 6.133A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.619A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AC1, first strand: chain 'B' and resid 28 through 30 removed outlier: 7.690A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N THR B 95 " --> pdb=" O ALA B 264 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 47 through 55 removed outlier: 7.190A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC4, first strand: chain 'B' and resid 141 through 142 removed outlier: 5.818A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.247A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 325 through 328 Processing sheet with id=AC7, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AC8, first strand: chain 'B' and resid 452 through 453 Processing sheet with id=AC9, first strand: chain 'B' and resid 553 through 554 removed outlier: 6.663A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.650A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 702 through 703 Processing sheet with id=AD3, first strand: chain 'B' and resid 711 through 715 Processing sheet with id=AD4, first strand: chain 'B' and resid 718 through 728 removed outlier: 3.501A pdb=" N ALA B1056 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD6, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.713A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AD8, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.411A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.861A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 84 through 85 removed outlier: 5.502A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.860A pdb=" N ARG C 237 " --> pdb=" O PHE C 106 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N PHE C 106 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N GLN C 239 " --> pdb=" O TRP C 104 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N TRP C 104 " --> pdb=" O GLN C 239 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N LEU C 241 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL C 126 " --> pdb=" O SER C 172 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 311 through 319 removed outlier: 6.767A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AE5, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.517A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 452 through 453 Processing sheet with id=AE7, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.643A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.643A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA C1056 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.643A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AF2, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.741A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) 1037 hydrogen bonds defined for protein. 2781 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: 10.67 Time building geometry restraints manager: 6.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 7293 1.34 - 1.46: 4378 1.46 - 1.58: 13399 1.58 - 1.70: 0 1.70 - 1.83: 129 Bond restraints: 25199 Sorted by residual: bond pdb=" C5 NAG D 1 " pdb=" O5 NAG D 1 " ideal model delta sigma weight residual 1.413 1.491 -0.078 2.00e-02 2.50e+03 1.50e+01 bond pdb=" C5 NAG N 2 " pdb=" O5 NAG N 2 " ideal model delta sigma weight residual 1.413 1.490 -0.077 2.00e-02 2.50e+03 1.50e+01 bond pdb=" C5 NAG A1302 " pdb=" O5 NAG A1302 " ideal model delta sigma weight residual 1.413 1.488 -0.075 2.00e-02 2.50e+03 1.40e+01 bond pdb=" C5 NAG Q 2 " pdb=" O5 NAG Q 2 " ideal model delta sigma weight residual 1.413 1.488 -0.075 2.00e-02 2.50e+03 1.40e+01 bond pdb=" C5 NAG A1308 " pdb=" O5 NAG A1308 " ideal model delta sigma weight residual 1.413 1.488 -0.075 2.00e-02 2.50e+03 1.39e+01 ... (remaining 25194 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.53: 33840 4.53 - 9.06: 434 9.06 - 13.59: 4 13.59 - 18.12: 0 18.12 - 22.64: 1 Bond angle restraints: 34279 Sorted by residual: angle pdb=" CA VAL B 622 " pdb=" CB VAL B 622 " pdb=" CG1 VAL B 622 " ideal model delta sigma weight residual 110.40 133.04 -22.64 1.70e+00 3.46e-01 1.77e+02 angle pdb=" N CYS C 391 " pdb=" CA CYS C 391 " pdb=" C CYS C 391 " ideal model delta sigma weight residual 108.96 119.30 -10.34 1.49e+00 4.50e-01 4.82e+01 angle pdb=" N CYS A 391 " pdb=" CA CYS A 391 " pdb=" C CYS A 391 " ideal model delta sigma weight residual 108.96 118.49 -9.53 1.49e+00 4.50e-01 4.09e+01 angle pdb=" N CYS B 391 " pdb=" CA CYS B 391 " pdb=" C CYS B 391 " ideal model delta sigma weight residual 108.96 118.12 -9.16 1.49e+00 4.50e-01 3.78e+01 angle pdb=" CA PHE C 559 " pdb=" CB PHE C 559 " pdb=" CG PHE C 559 " ideal model delta sigma weight residual 113.80 119.45 -5.65 1.00e+00 1.00e+00 3.20e+01 ... (remaining 34274 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.72: 14555 17.72 - 35.44: 991 35.44 - 53.16: 157 53.16 - 70.88: 56 70.88 - 88.60: 32 Dihedral angle restraints: 15791 sinusoidal: 6926 harmonic: 8865 Sorted by residual: dihedral pdb=" CB CYS C1082 " pdb=" SG CYS C1082 " pdb=" SG CYS C1126 " pdb=" CB CYS C1126 " ideal model delta sinusoidal sigma weight residual -86.00 -144.24 58.24 1 1.00e+01 1.00e-02 4.55e+01 dihedral pdb=" CA PHE A 135 " pdb=" C PHE A 135 " pdb=" N CYS A 136 " pdb=" CA CYS A 136 " ideal model delta harmonic sigma weight residual 180.00 149.99 30.01 0 5.00e+00 4.00e-02 3.60e+01 dihedral pdb=" CA ARG C 214 " pdb=" C ARG C 214 " pdb=" N ASP C 215 " pdb=" CA ASP C 215 " ideal model delta harmonic sigma weight residual 180.00 -150.01 -29.99 0 5.00e+00 4.00e-02 3.60e+01 ... (remaining 15788 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.309: 4063 0.309 - 0.618: 17 0.618 - 0.926: 0 0.926 - 1.235: 0 1.235 - 1.544: 1 Chirality restraints: 4081 Sorted by residual: chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.59 0.19 2.00e-02 2.50e+03 9.44e+01 chirality pdb=" C1 NAG P 2 " pdb=" O4 NAG P 1 " pdb=" C2 NAG P 2 " pdb=" O5 NAG P 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.58 0.18 2.00e-02 2.50e+03 8.43e+01 chirality pdb=" C1 NAG N 2 " pdb=" O4 NAG N 1 " pdb=" C2 NAG N 2 " pdb=" O5 NAG N 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.58 0.18 2.00e-02 2.50e+03 8.25e+01 ... (remaining 4078 not shown) Planarity restraints: 4397 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 343 " -0.139 2.00e-02 2.50e+03 1.50e-01 2.80e+02 pdb=" CG ASN A 343 " 0.073 2.00e-02 2.50e+03 pdb=" OD1 ASN A 343 " 0.013 2.00e-02 2.50e+03 pdb=" ND2 ASN A 343 " 0.234 2.00e-02 2.50e+03 pdb=" C1 NAG A1305 " -0.181 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 603 " -0.134 2.00e-02 2.50e+03 1.44e-01 2.58e+02 pdb=" CG ASN C 603 " 0.079 2.00e-02 2.50e+03 pdb=" OD1 ASN C 603 " 0.002 2.00e-02 2.50e+03 pdb=" ND2 ASN C 603 " 0.223 2.00e-02 2.50e+03 pdb=" C1 NAG C1304 " -0.170 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 709 " 0.138 2.00e-02 2.50e+03 1.43e-01 2.57e+02 pdb=" CG ASN B 709 " -0.091 2.00e-02 2.50e+03 pdb=" OD1 ASN B 709 " -0.002 2.00e-02 2.50e+03 pdb=" ND2 ASN B 709 " -0.215 2.00e-02 2.50e+03 pdb=" C1 NAG B1310 " 0.171 2.00e-02 2.50e+03 ... (remaining 4394 not shown) Histogram of nonbonded interaction distances: 2.53 - 3.00: 13167 3.00 - 3.48: 24558 3.48 - 3.95: 40506 3.95 - 4.43: 44853 4.43 - 4.90: 74536 Nonbonded interactions: 197620 Sorted by model distance: nonbonded pdb=" OD1 ASP C 364 " pdb=" OG SER C 366 " model vdw 2.529 3.040 nonbonded pdb=" OE2 GLU B 298 " pdb=" OG1 THR B 315 " model vdw 2.532 3.040 nonbonded pdb=" OD1 ASP A 364 " pdb=" OG SER A 366 " model vdw 2.535 3.040 nonbonded pdb=" OG SER B 813 " pdb=" OE1 GLU B 868 " model vdw 2.539 3.040 nonbonded pdb=" OE2 GLU A 918 " pdb=" OG SER C1123 " model vdw 2.547 3.040 ... (remaining 197615 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' and (resid 27 through 623 or resid 633 through 1147 or resid 1301 thr \ ough 1311)) selection = (chain 'B' and (resid 27 through 623 or resid 633 through 1147 or resid 1301 thr \ ough 1311)) selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' } 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: 1.660 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: 0.010 Extract box with map and model: 1.030 Check model and map are aligned: 0.200 Set scattering table: 0.240 Process input model: 55.210 Find NCS groups from input model: 1.520 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 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 : 0.014 0.078 25299 Z= 0.761 Angle : 1.790 22.645 34540 Z= 1.167 Chirality : 0.102 1.544 4081 Planarity : 0.015 0.185 4350 Dihedral : 13.200 88.601 9964 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 0.21 Ramachandran Plot: Outliers : 0.40 % Allowed : 7.17 % Favored : 92.43 % Rotamer: Outliers : 1.32 % Allowed : 4.25 % Favored : 94.44 % Cbeta Deviations : 0.21 % 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: -1.34 (0.14), residues: 2999 helix: -0.91 (0.16), residues: 697 sheet: 0.04 (0.21), residues: 507 loop : -1.17 (0.14), residues: 1795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.116 0.019 TRP C 436 HIS 0.009 0.002 HIS C1048 PHE 0.068 0.012 PHE C 497 TYR 0.190 0.021 TYR B 707 ARG 0.021 0.001 ARG C 466 Details of bonding type rmsd link_NAG-ASN : bond 0.00880 ( 47) link_NAG-ASN : angle 4.50047 ( 141) link_BETA1-4 : bond 0.02366 ( 14) link_BETA1-4 : angle 4.70816 ( 42) hydrogen bonds : bond 0.16621 ( 1021) hydrogen bonds : angle 8.39642 ( 2781) SS BOND : bond 0.01209 ( 39) SS BOND : angle 1.88200 ( 78) covalent geometry : bond 0.01351 (25199) covalent geometry : angle 1.76337 (34279) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5998 Ramachandran restraints generated. 2999 Oldfield, 0 Emsley, 2999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5998 Ramachandran restraints generated. 2999 Oldfield, 0 Emsley, 2999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 40 time to evaluate : 2.576 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 697 MET cc_start: 0.8734 (ptm) cc_final: 0.8452 (ptp) REVERT: A 740 MET cc_start: 0.8301 (ttt) cc_final: 0.8022 (ttt) REVERT: A 869 MET cc_start: 0.8679 (mtt) cc_final: 0.8351 (mtm) REVERT: B 1029 MET cc_start: 0.9456 (tpp) cc_final: 0.9187 (tpp) REVERT: C 457 ARG cc_start: 0.8103 (OUTLIER) cc_final: 0.7743 (ptm-80) REVERT: C 459 SER cc_start: 0.8975 (OUTLIER) cc_final: 0.8740 (p) REVERT: C 641 ASN cc_start: 0.7452 (OUTLIER) cc_final: 0.7217 (p0) REVERT: C 646 ARG cc_start: 0.7728 (OUTLIER) cc_final: 0.6922 (tpm170) outliers start: 35 outliers final: 8 residues processed: 75 average time/residue: 0.3586 time to fit residues: 44.9651 Evaluate side-chains 40 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 28 time to evaluate : 2.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain C residue 142 ASP Chi-restraints excluded: chain C residue 457 ARG Chi-restraints excluded: chain C residue 459 SER Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 646 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 255 optimal weight: 6.9990 chunk 229 optimal weight: 5.9990 chunk 127 optimal weight: 5.9990 chunk 78 optimal weight: 1.9990 chunk 154 optimal weight: 7.9990 chunk 122 optimal weight: 1.9990 chunk 237 optimal weight: 0.5980 chunk 91 optimal weight: 3.9990 chunk 144 optimal weight: 20.0000 chunk 176 optimal weight: 1.9990 chunk 275 optimal weight: 1.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 641 ASN A 675 GLN A1048 HIS A1083 HIS C 207 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.044377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.033074 restraints weight = 211736.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.033916 restraints weight = 113899.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.034465 restraints weight = 77376.821| |-----------------------------------------------------------------------------| r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.1544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.113 25299 Z= 0.146 Angle : 0.705 11.010 34540 Z= 0.367 Chirality : 0.047 0.326 4081 Planarity : 0.004 0.051 4350 Dihedral : 7.180 51.211 4562 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.33 % Favored : 96.47 % Rotamer: Outliers : 0.98 % Allowed : 4.96 % Favored : 94.06 % 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: -0.36 (0.15), residues: 2999 helix: 1.10 (0.20), residues: 683 sheet: -0.11 (0.19), residues: 649 loop : -0.85 (0.15), residues: 1667 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 64 HIS 0.006 0.001 HIS C1048 PHE 0.023 0.002 PHE C 392 TYR 0.019 0.002 TYR C 451 ARG 0.004 0.001 ARG B 995 Details of bonding type rmsd link_NAG-ASN : bond 0.00333 ( 47) link_NAG-ASN : angle 3.41426 ( 141) link_BETA1-4 : bond 0.00450 ( 14) link_BETA1-4 : angle 2.05616 ( 42) hydrogen bonds : bond 0.05545 ( 1021) hydrogen bonds : angle 6.26108 ( 2781) SS BOND : bond 0.00927 ( 39) SS BOND : angle 1.68882 ( 78) covalent geometry : bond 0.00298 (25199) covalent geometry : angle 0.66375 (34279) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5998 Ramachandran restraints generated. 2999 Oldfield, 0 Emsley, 2999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5998 Ramachandran restraints generated. 2999 Oldfield, 0 Emsley, 2999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 29 time to evaluate : 2.671 Fit side-chains revert: symmetry clash REVERT: A 461 LEU cc_start: 0.8066 (OUTLIER) cc_final: 0.7662 (mm) REVERT: C 646 ARG cc_start: 0.7698 (OUTLIER) cc_final: 0.7193 (tpm170) outliers start: 26 outliers final: 11 residues processed: 55 average time/residue: 0.3269 time to fit residues: 33.4959 Evaluate side-chains 40 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 27 time to evaluate : 2.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 646 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 283 optimal weight: 9.9990 chunk 272 optimal weight: 5.9990 chunk 172 optimal weight: 0.9990 chunk 186 optimal weight: 9.9990 chunk 24 optimal weight: 20.0000 chunk 28 optimal weight: 2.9990 chunk 82 optimal weight: 10.0000 chunk 128 optimal weight: 9.9990 chunk 114 optimal weight: 6.9990 chunk 103 optimal weight: 6.9990 chunk 140 optimal weight: 30.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.043431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.031985 restraints weight = 214350.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.032802 restraints weight = 117183.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.033333 restraints weight = 80332.484| |-----------------------------------------------------------------------------| r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 25299 Z= 0.213 Angle : 0.662 9.797 34540 Z= 0.339 Chirality : 0.045 0.279 4081 Planarity : 0.004 0.044 4350 Dihedral : 6.555 56.270 4552 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.10 % Favored : 95.73 % Rotamer: Outliers : 1.39 % Allowed : 5.30 % Favored : 93.31 % 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: -0.27 (0.15), residues: 2999 helix: 1.48 (0.20), residues: 686 sheet: -0.24 (0.19), residues: 626 loop : -0.85 (0.15), residues: 1687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 64 HIS 0.005 0.001 HIS C1058 PHE 0.019 0.002 PHE B 347 TYR 0.024 0.002 TYR C1067 ARG 0.005 0.001 ARG A1039 Details of bonding type rmsd link_NAG-ASN : bond 0.00451 ( 47) link_NAG-ASN : angle 2.66437 ( 141) link_BETA1-4 : bond 0.00306 ( 14) link_BETA1-4 : angle 1.66657 ( 42) hydrogen bonds : bond 0.04845 ( 1021) hydrogen bonds : angle 5.93617 ( 2781) SS BOND : bond 0.00534 ( 39) SS BOND : angle 1.26428 ( 78) covalent geometry : bond 0.00488 (25199) covalent geometry : angle 0.63632 (34279) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5998 Ramachandran restraints generated. 2999 Oldfield, 0 Emsley, 2999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5998 Ramachandran restraints generated. 2999 Oldfield, 0 Emsley, 2999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 27 time to evaluate : 2.892 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 461 LEU cc_start: 0.8091 (OUTLIER) cc_final: 0.7708 (mm) REVERT: A 869 MET cc_start: 0.8640 (mtt) cc_final: 0.7982 (mtm) REVERT: C 329 PHE cc_start: 0.8056 (OUTLIER) cc_final: 0.7821 (t80) REVERT: C 646 ARG cc_start: 0.7744 (OUTLIER) cc_final: 0.7337 (tpm170) REVERT: C 740 MET cc_start: 0.8531 (tpt) cc_final: 0.8229 (tpt) outliers start: 37 outliers final: 19 residues processed: 62 average time/residue: 0.3290 time to fit residues: 37.5110 Evaluate side-chains 49 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 27 time to evaluate : 2.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 604 THR Chi-restraints excluded: chain C residue 646 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 217 optimal weight: 9.9990 chunk 27 optimal weight: 5.9990 chunk 19 optimal weight: 10.0000 chunk 231 optimal weight: 3.9990 chunk 31 optimal weight: 6.9990 chunk 65 optimal weight: 0.9980 chunk 283 optimal weight: 5.9990 chunk 109 optimal weight: 8.9990 chunk 249 optimal weight: 0.0070 chunk 15 optimal weight: 30.0000 chunk 210 optimal weight: 3.9990 overall best weight: 3.0004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 115 GLN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.043694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.032248 restraints weight = 213446.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.033070 restraints weight = 115524.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.033585 restraints weight = 78611.357| |-----------------------------------------------------------------------------| r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.2388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 25299 Z= 0.142 Angle : 0.577 11.326 34540 Z= 0.297 Chirality : 0.043 0.246 4081 Planarity : 0.003 0.041 4350 Dihedral : 6.098 55.735 4550 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.27 % Favored : 96.63 % Rotamer: Outliers : 1.39 % Allowed : 6.05 % Favored : 92.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.15), residues: 2999 helix: 1.77 (0.20), residues: 689 sheet: -0.11 (0.19), residues: 628 loop : -0.83 (0.15), residues: 1682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 64 HIS 0.003 0.001 HIS A 66 PHE 0.013 0.001 PHE B 456 TYR 0.021 0.001 TYR C1067 ARG 0.004 0.000 ARG C 466 Details of bonding type rmsd link_NAG-ASN : bond 0.00216 ( 47) link_NAG-ASN : angle 2.18353 ( 141) link_BETA1-4 : bond 0.00365 ( 14) link_BETA1-4 : angle 1.44295 ( 42) hydrogen bonds : bond 0.04267 ( 1021) hydrogen bonds : angle 5.60748 ( 2781) SS BOND : bond 0.00374 ( 39) SS BOND : angle 1.05966 ( 78) covalent geometry : bond 0.00318 (25199) covalent geometry : angle 0.55714 (34279) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5998 Ramachandran restraints generated. 2999 Oldfield, 0 Emsley, 2999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5998 Ramachandran restraints generated. 2999 Oldfield, 0 Emsley, 2999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 28 time to evaluate : 2.974 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 461 LEU cc_start: 0.8100 (OUTLIER) cc_final: 0.7736 (mm) REVERT: A 657 ASN cc_start: 0.8615 (OUTLIER) cc_final: 0.8308 (m-40) REVERT: A 869 MET cc_start: 0.8696 (mtt) cc_final: 0.7981 (mtm) REVERT: C 329 PHE cc_start: 0.7988 (OUTLIER) cc_final: 0.7776 (t80) REVERT: C 646 ARG cc_start: 0.7806 (OUTLIER) cc_final: 0.7310 (tpm170) REVERT: C 740 MET cc_start: 0.8542 (tpt) cc_final: 0.8223 (tpt) outliers start: 37 outliers final: 19 residues processed: 62 average time/residue: 0.3198 time to fit residues: 36.9686 Evaluate side-chains 50 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 27 time to evaluate : 2.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 657 ASN Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 604 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 646 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 185 optimal weight: 7.9990 chunk 11 optimal weight: 20.0000 chunk 209 optimal weight: 30.0000 chunk 93 optimal weight: 0.9990 chunk 16 optimal weight: 20.0000 chunk 197 optimal weight: 8.9990 chunk 103 optimal weight: 10.0000 chunk 184 optimal weight: 0.4980 chunk 121 optimal weight: 8.9990 chunk 115 optimal weight: 7.9990 chunk 152 optimal weight: 2.9990 overall best weight: 4.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 121 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 = 0.3408 r_free = 0.3408 target = 0.043348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.031872 restraints weight = 212727.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.032691 restraints weight = 114043.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.033204 restraints weight = 77555.222| |-----------------------------------------------------------------------------| r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.2650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 25299 Z= 0.183 Angle : 0.589 8.793 34540 Z= 0.302 Chirality : 0.043 0.222 4081 Planarity : 0.004 0.039 4350 Dihedral : 5.946 56.694 4550 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.10 % Favored : 95.80 % Rotamer: Outliers : 1.77 % Allowed : 6.80 % Favored : 91.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.15), residues: 2999 helix: 1.78 (0.20), residues: 688 sheet: -0.06 (0.19), residues: 613 loop : -0.82 (0.15), residues: 1698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 64 HIS 0.004 0.001 HIS C1058 PHE 0.012 0.001 PHE C 92 TYR 0.022 0.001 TYR C1067 ARG 0.003 0.000 ARG A1039 Details of bonding type rmsd link_NAG-ASN : bond 0.00341 ( 47) link_NAG-ASN : angle 2.11114 ( 141) link_BETA1-4 : bond 0.00273 ( 14) link_BETA1-4 : angle 1.41932 ( 42) hydrogen bonds : bond 0.04249 ( 1021) hydrogen bonds : angle 5.56908 ( 2781) SS BOND : bond 0.00377 ( 39) SS BOND : angle 1.41567 ( 78) covalent geometry : bond 0.00415 (25199) covalent geometry : angle 0.56952 (34279) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5998 Ramachandran restraints generated. 2999 Oldfield, 0 Emsley, 2999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5998 Ramachandran restraints generated. 2999 Oldfield, 0 Emsley, 2999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 29 time to evaluate : 2.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 461 LEU cc_start: 0.8098 (OUTLIER) cc_final: 0.7780 (mm) REVERT: A 657 ASN cc_start: 0.8684 (OUTLIER) cc_final: 0.8407 (m-40) REVERT: A 869 MET cc_start: 0.8628 (mtt) cc_final: 0.7907 (mtm) REVERT: B 697 MET cc_start: 0.9056 (OUTLIER) cc_final: 0.8732 (ttm) REVERT: C 329 PHE cc_start: 0.8218 (OUTLIER) cc_final: 0.8014 (t80) REVERT: C 646 ARG cc_start: 0.7832 (OUTLIER) cc_final: 0.7328 (tpm170) REVERT: C 740 MET cc_start: 0.8549 (tpt) cc_final: 0.8154 (tpt) outliers start: 47 outliers final: 28 residues processed: 73 average time/residue: 0.3237 time to fit residues: 42.7540 Evaluate side-chains 60 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 27 time to evaluate : 2.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 657 ASN Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 604 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 638 THR Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 1094 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 75 optimal weight: 3.9990 chunk 239 optimal weight: 10.0000 chunk 190 optimal weight: 0.9990 chunk 162 optimal weight: 3.9990 chunk 46 optimal weight: 10.0000 chunk 184 optimal weight: 8.9990 chunk 175 optimal weight: 4.9990 chunk 240 optimal weight: 9.9990 chunk 143 optimal weight: 10.0000 chunk 156 optimal weight: 9.9990 chunk 21 optimal weight: 8.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1106 GLN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1135 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.043125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.031693 restraints weight = 213828.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.032496 restraints weight = 116521.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.033007 restraints weight = 79915.144| |-----------------------------------------------------------------------------| r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.2837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 25299 Z= 0.197 Angle : 0.589 8.707 34540 Z= 0.302 Chirality : 0.043 0.211 4081 Planarity : 0.004 0.041 4350 Dihedral : 5.949 56.889 4550 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.87 % Favored : 96.07 % Rotamer: Outliers : 1.47 % Allowed : 8.00 % Favored : 90.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.15), residues: 2999 helix: 1.70 (0.20), residues: 700 sheet: -0.09 (0.19), residues: 625 loop : -0.86 (0.15), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 64 HIS 0.004 0.001 HIS C1058 PHE 0.013 0.001 PHE C1089 TYR 0.032 0.001 TYR B 473 ARG 0.006 0.000 ARG B 214 Details of bonding type rmsd link_NAG-ASN : bond 0.00315 ( 47) link_NAG-ASN : angle 2.00661 ( 141) link_BETA1-4 : bond 0.00277 ( 14) link_BETA1-4 : angle 1.37712 ( 42) hydrogen bonds : bond 0.04244 ( 1021) hydrogen bonds : angle 5.53222 ( 2781) SS BOND : bond 0.00375 ( 39) SS BOND : angle 1.15126 ( 78) covalent geometry : bond 0.00448 (25199) covalent geometry : angle 0.57255 (34279) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5998 Ramachandran restraints generated. 2999 Oldfield, 0 Emsley, 2999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5998 Ramachandran restraints generated. 2999 Oldfield, 0 Emsley, 2999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 27 time to evaluate : 2.995 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 461 LEU cc_start: 0.8066 (OUTLIER) cc_final: 0.7743 (mm) REVERT: A 657 ASN cc_start: 0.8660 (OUTLIER) cc_final: 0.8374 (m-40) REVERT: A 869 MET cc_start: 0.8668 (mtt) cc_final: 0.7927 (mtm) REVERT: B 697 MET cc_start: 0.9057 (OUTLIER) cc_final: 0.8733 (ttm) REVERT: C 329 PHE cc_start: 0.8199 (OUTLIER) cc_final: 0.7996 (t80) REVERT: C 646 ARG cc_start: 0.7847 (OUTLIER) cc_final: 0.7345 (tpm170) REVERT: C 740 MET cc_start: 0.8523 (tpt) cc_final: 0.8102 (tpt) outliers start: 39 outliers final: 26 residues processed: 63 average time/residue: 0.3247 time to fit residues: 38.5839 Evaluate side-chains 57 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 26 time to evaluate : 2.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 657 ASN Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 604 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 896 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 77 optimal weight: 1.9990 chunk 106 optimal weight: 10.0000 chunk 298 optimal weight: 2.9990 chunk 277 optimal weight: 6.9990 chunk 62 optimal weight: 3.9990 chunk 212 optimal weight: 30.0000 chunk 225 optimal weight: 20.0000 chunk 295 optimal weight: 6.9990 chunk 249 optimal weight: 7.9990 chunk 190 optimal weight: 0.9990 chunk 80 optimal weight: 7.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1088 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.043332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.031913 restraints weight = 214869.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.032731 restraints weight = 116401.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.033267 restraints weight = 79590.728| |-----------------------------------------------------------------------------| r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.3008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 25299 Z= 0.156 Angle : 0.546 8.703 34540 Z= 0.281 Chirality : 0.043 0.202 4081 Planarity : 0.003 0.043 4350 Dihedral : 5.709 56.048 4549 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.83 % Favored : 96.10 % Rotamer: Outliers : 1.24 % Allowed : 8.64 % Favored : 90.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.01 (0.15), residues: 2999 helix: 1.88 (0.20), residues: 700 sheet: -0.09 (0.19), residues: 640 loop : -0.80 (0.15), residues: 1659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 64 HIS 0.003 0.001 HIS C1048 PHE 0.012 0.001 PHE B 456 TYR 0.021 0.001 TYR C1067 ARG 0.004 0.000 ARG B 457 Details of bonding type rmsd link_NAG-ASN : bond 0.00222 ( 47) link_NAG-ASN : angle 1.82617 ( 141) link_BETA1-4 : bond 0.00308 ( 14) link_BETA1-4 : angle 1.27799 ( 42) hydrogen bonds : bond 0.03962 ( 1021) hydrogen bonds : angle 5.38299 ( 2781) SS BOND : bond 0.00354 ( 39) SS BOND : angle 1.01343 ( 78) covalent geometry : bond 0.00352 (25199) covalent geometry : angle 0.53113 (34279) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5998 Ramachandran restraints generated. 2999 Oldfield, 0 Emsley, 2999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5998 Ramachandran restraints generated. 2999 Oldfield, 0 Emsley, 2999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 27 time to evaluate : 2.595 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 461 LEU cc_start: 0.8145 (OUTLIER) cc_final: 0.7836 (mm) REVERT: A 657 ASN cc_start: 0.8681 (OUTLIER) cc_final: 0.8421 (m-40) REVERT: A 869 MET cc_start: 0.8684 (mtt) cc_final: 0.7994 (mtm) REVERT: B 697 MET cc_start: 0.9049 (OUTLIER) cc_final: 0.8793 (ttm) REVERT: C 224 GLU cc_start: 0.8557 (OUTLIER) cc_final: 0.8273 (pm20) REVERT: C 329 PHE cc_start: 0.8224 (OUTLIER) cc_final: 0.8015 (t80) REVERT: C 646 ARG cc_start: 0.7853 (OUTLIER) cc_final: 0.7351 (tpm170) REVERT: C 740 MET cc_start: 0.8489 (tpt) cc_final: 0.8055 (tpt) outliers start: 33 outliers final: 21 residues processed: 59 average time/residue: 0.3044 time to fit residues: 33.3036 Evaluate side-chains 53 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 26 time to evaluate : 2.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 657 ASN Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 604 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 646 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 130 optimal weight: 5.9990 chunk 253 optimal weight: 2.9990 chunk 279 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 chunk 195 optimal weight: 4.9990 chunk 269 optimal weight: 6.9990 chunk 258 optimal weight: 8.9990 chunk 301 optimal weight: 6.9990 chunk 123 optimal weight: 8.9990 chunk 98 optimal weight: 3.9990 chunk 166 optimal weight: 5.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 121 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 = 0.3403 r_free = 0.3403 target = 0.043210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.031756 restraints weight = 213003.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.032556 restraints weight = 116206.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.033085 restraints weight = 79585.580| |-----------------------------------------------------------------------------| r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.3111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 25299 Z= 0.169 Angle : 0.552 8.688 34540 Z= 0.283 Chirality : 0.043 0.256 4081 Planarity : 0.004 0.041 4350 Dihedral : 5.689 56.852 4549 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.00 % Favored : 95.93 % Rotamer: Outliers : 1.43 % Allowed : 8.57 % Favored : 90.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.15), residues: 2999 helix: 1.87 (0.20), residues: 700 sheet: -0.10 (0.19), residues: 640 loop : -0.82 (0.15), residues: 1659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 64 HIS 0.004 0.001 HIS A1064 PHE 0.016 0.001 PHE B 392 TYR 0.021 0.001 TYR C1067 ARG 0.003 0.000 ARG A 454 Details of bonding type rmsd link_NAG-ASN : bond 0.00262 ( 47) link_NAG-ASN : angle 1.82480 ( 141) link_BETA1-4 : bond 0.00299 ( 14) link_BETA1-4 : angle 1.30143 ( 42) hydrogen bonds : bond 0.04014 ( 1021) hydrogen bonds : angle 5.35881 ( 2781) SS BOND : bond 0.00341 ( 39) SS BOND : angle 0.95511 ( 78) covalent geometry : bond 0.00382 (25199) covalent geometry : angle 0.53750 (34279) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5998 Ramachandran restraints generated. 2999 Oldfield, 0 Emsley, 2999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5998 Ramachandran restraints generated. 2999 Oldfield, 0 Emsley, 2999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 27 time to evaluate : 2.640 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 461 LEU cc_start: 0.8070 (OUTLIER) cc_final: 0.7772 (mm) REVERT: A 657 ASN cc_start: 0.8677 (OUTLIER) cc_final: 0.8419 (m-40) REVERT: B 1116 THR cc_start: 0.9355 (OUTLIER) cc_final: 0.9144 (p) REVERT: C 224 GLU cc_start: 0.8599 (OUTLIER) cc_final: 0.8306 (pm20) REVERT: C 329 PHE cc_start: 0.8233 (OUTLIER) cc_final: 0.8022 (t80) REVERT: C 646 ARG cc_start: 0.7866 (OUTLIER) cc_final: 0.7338 (tpm170) REVERT: C 740 MET cc_start: 0.8504 (tpt) cc_final: 0.8076 (tpt) outliers start: 38 outliers final: 27 residues processed: 63 average time/residue: 0.3081 time to fit residues: 36.0664 Evaluate side-chains 59 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 26 time to evaluate : 2.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 GLN Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 657 ASN Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 604 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 896 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 49 optimal weight: 8.9990 chunk 265 optimal weight: 10.0000 chunk 223 optimal weight: 6.9990 chunk 224 optimal weight: 0.8980 chunk 200 optimal weight: 7.9990 chunk 84 optimal weight: 5.9990 chunk 249 optimal weight: 0.9990 chunk 208 optimal weight: 30.0000 chunk 205 optimal weight: 8.9990 chunk 53 optimal weight: 2.9990 chunk 267 optimal weight: 0.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.043458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.032100 restraints weight = 214345.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.032923 restraints weight = 115746.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.033442 restraints weight = 78939.347| |-----------------------------------------------------------------------------| r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.3208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 25299 Z= 0.121 Angle : 0.519 8.688 34540 Z= 0.268 Chirality : 0.043 0.254 4081 Planarity : 0.003 0.042 4350 Dihedral : 5.487 56.793 4549 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.60 % Favored : 96.30 % Rotamer: Outliers : 1.20 % Allowed : 8.98 % Favored : 89.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.15), residues: 2999 helix: 1.94 (0.20), residues: 706 sheet: -0.02 (0.19), residues: 645 loop : -0.76 (0.15), residues: 1648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 64 HIS 0.003 0.001 HIS C1048 PHE 0.014 0.001 PHE B 456 TYR 0.020 0.001 TYR C1067 ARG 0.003 0.000 ARG C 466 Details of bonding type rmsd link_NAG-ASN : bond 0.00172 ( 47) link_NAG-ASN : angle 1.69421 ( 141) link_BETA1-4 : bond 0.00345 ( 14) link_BETA1-4 : angle 1.22535 ( 42) hydrogen bonds : bond 0.03816 ( 1021) hydrogen bonds : angle 5.22703 ( 2781) SS BOND : bond 0.00336 ( 39) SS BOND : angle 0.91279 ( 78) covalent geometry : bond 0.00270 (25199) covalent geometry : angle 0.50599 (34279) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5998 Ramachandran restraints generated. 2999 Oldfield, 0 Emsley, 2999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5998 Ramachandran restraints generated. 2999 Oldfield, 0 Emsley, 2999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 28 time to evaluate : 2.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 461 LEU cc_start: 0.8098 (OUTLIER) cc_final: 0.7812 (mm) REVERT: A 657 ASN cc_start: 0.8661 (OUTLIER) cc_final: 0.8410 (m-40) REVERT: A 869 MET cc_start: 0.8694 (mtt) cc_final: 0.8010 (mtm) REVERT: B 1116 THR cc_start: 0.9352 (OUTLIER) cc_final: 0.9135 (p) REVERT: C 224 GLU cc_start: 0.8622 (OUTLIER) cc_final: 0.8358 (pm20) REVERT: C 329 PHE cc_start: 0.8185 (OUTLIER) cc_final: 0.7969 (t80) REVERT: C 646 ARG cc_start: 0.7878 (OUTLIER) cc_final: 0.7331 (tpm170) REVERT: C 740 MET cc_start: 0.8473 (tpt) cc_final: 0.8036 (tpt) outliers start: 32 outliers final: 25 residues processed: 59 average time/residue: 0.3355 time to fit residues: 36.6929 Evaluate side-chains 57 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 26 time to evaluate : 2.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 GLN Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 657 ASN Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 604 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 646 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 256 optimal weight: 0.9980 chunk 240 optimal weight: 0.0980 chunk 35 optimal weight: 2.9990 chunk 43 optimal weight: 10.0000 chunk 269 optimal weight: 6.9990 chunk 243 optimal weight: 50.0000 chunk 268 optimal weight: 0.9980 chunk 263 optimal weight: 3.9990 chunk 231 optimal weight: 10.0000 chunk 185 optimal weight: 10.0000 chunk 50 optimal weight: 8.9990 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 762 GLN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 121 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.043609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.032337 restraints weight = 212474.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.033154 restraints weight = 114389.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.033681 restraints weight = 78127.704| |-----------------------------------------------------------------------------| r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.3312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.084 25299 Z= 0.110 Angle : 0.514 8.711 34540 Z= 0.266 Chirality : 0.042 0.261 4081 Planarity : 0.003 0.043 4350 Dihedral : 5.255 56.433 4548 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.47 % Favored : 96.43 % Rotamer: Outliers : 1.05 % Allowed : 9.13 % Favored : 89.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.15), residues: 2999 helix: 1.99 (0.20), residues: 704 sheet: 0.09 (0.19), residues: 642 loop : -0.72 (0.15), residues: 1653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 64 HIS 0.003 0.001 HIS C1048 PHE 0.022 0.001 PHE A 759 TYR 0.020 0.001 TYR C1067 ARG 0.003 0.000 ARG A1039 Details of bonding type rmsd link_NAG-ASN : bond 0.00150 ( 47) link_NAG-ASN : angle 1.61716 ( 141) link_BETA1-4 : bond 0.00346 ( 14) link_BETA1-4 : angle 1.19798 ( 42) hydrogen bonds : bond 0.03730 ( 1021) hydrogen bonds : angle 5.13238 ( 2781) SS BOND : bond 0.00342 ( 39) SS BOND : angle 1.33297 ( 78) covalent geometry : bond 0.00247 (25199) covalent geometry : angle 0.50002 (34279) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5998 Ramachandran restraints generated. 2999 Oldfield, 0 Emsley, 2999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5998 Ramachandran restraints generated. 2999 Oldfield, 0 Emsley, 2999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 27 time to evaluate : 3.010 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 461 LEU cc_start: 0.8224 (OUTLIER) cc_final: 0.7941 (mm) REVERT: A 657 ASN cc_start: 0.8667 (OUTLIER) cc_final: 0.8430 (m-40) REVERT: A 869 MET cc_start: 0.8619 (mtt) cc_final: 0.8334 (mtt) REVERT: B 1116 THR cc_start: 0.9353 (OUTLIER) cc_final: 0.9129 (p) REVERT: C 224 GLU cc_start: 0.8637 (OUTLIER) cc_final: 0.8405 (pm20) REVERT: C 329 PHE cc_start: 0.8109 (OUTLIER) cc_final: 0.7894 (t80) REVERT: C 646 ARG cc_start: 0.7871 (OUTLIER) cc_final: 0.7292 (tpm170) REVERT: C 740 MET cc_start: 0.8472 (tpt) cc_final: 0.8038 (tpt) outliers start: 28 outliers final: 18 residues processed: 54 average time/residue: 0.3315 time to fit residues: 33.6980 Evaluate side-chains 50 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 26 time to evaluate : 2.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 GLN Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 657 ASN Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 604 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 646 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 240 optimal weight: 40.0000 chunk 39 optimal weight: 40.0000 chunk 57 optimal weight: 0.0370 chunk 258 optimal weight: 6.9990 chunk 79 optimal weight: 0.9980 chunk 115 optimal weight: 2.9990 chunk 222 optimal weight: 7.9990 chunk 248 optimal weight: 10.0000 chunk 148 optimal weight: 0.0060 chunk 46 optimal weight: 20.0000 chunk 29 optimal weight: 0.6980 overall best weight: 0.9476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 777 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.044013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.032899 restraints weight = 213198.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.033721 restraints weight = 116167.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.034257 restraints weight = 79569.747| |-----------------------------------------------------------------------------| r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.3497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.076 25299 Z= 0.090 Angle : 0.495 9.357 34540 Z= 0.256 Chirality : 0.042 0.245 4081 Planarity : 0.003 0.043 4350 Dihedral : 4.911 55.862 4548 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.13 % Favored : 96.73 % Rotamer: Outliers : 0.83 % Allowed : 9.36 % Favored : 89.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.15), residues: 2999 helix: 2.11 (0.21), residues: 706 sheet: 0.27 (0.19), residues: 640 loop : -0.65 (0.15), residues: 1653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 64 HIS 0.004 0.001 HIS C1048 PHE 0.016 0.001 PHE B 456 TYR 0.020 0.001 TYR C1067 ARG 0.003 0.000 ARG A1039 Details of bonding type rmsd link_NAG-ASN : bond 0.00172 ( 47) link_NAG-ASN : angle 1.51514 ( 141) link_BETA1-4 : bond 0.00416 ( 14) link_BETA1-4 : angle 1.13951 ( 42) hydrogen bonds : bond 0.03374 ( 1021) hydrogen bonds : angle 4.96020 ( 2781) SS BOND : bond 0.00305 ( 39) SS BOND : angle 1.39953 ( 78) covalent geometry : bond 0.00195 (25199) covalent geometry : angle 0.48068 (34279) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6650.69 seconds wall clock time: 117 minutes 2.12 seconds (7022.12 seconds total)