Starting phenix.real_space_refine on Sun Jul 5 02:05:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7tp2_26046/07_2026/7tp2_26046.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tp2_26046/07_2026/7tp2_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_26046/07_2026/7tp2_26046.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tp2_26046/07_2026/7tp2_26046.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7tp2_26046/07_2026/7tp2_26046.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7tp2_26046/07_2026/7tp2_26046.cif" model { file = "/net/cci-nas-00/data/ceres_data/7tp2_26046/07_2026/7tp2_26046.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tp2_26046/07_2026/7tp2_26046.cif" } resolution = 3.72 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.003 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 chiralities: 11 Time building chain proxies: 5.25, per 1000 atoms: 0.21 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: 2.20 Conformation dependent library (CDL) restraints added in 895.4 milliseconds 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: 0.79 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: 6.06 Time building geometry restraints manager: 2.92 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: 13340 17.72 - 35.44: 936 35.44 - 53.16: 146 53.16 - 70.88: 56 70.88 - 88.60: 32 Dihedral angle restraints: 14510 sinusoidal: 5645 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 14507 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 1311)) selection = (chain 'B' and (resid 27 through 623 or resid 633 through 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: 1.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 23.810 Find NCS groups from input model: 0.740 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 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 : 13.758 88.601 8683 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -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 ARG 0.021 0.001 ARG C 466 TYR 0.190 0.021 TYR B 707 PHE 0.068 0.012 PHE C 497 TRP 0.116 0.019 TRP C 436 HIS 0.009 0.002 HIS C1048 Details of bonding type rmsd/Z covalent geometry : bond 0.01351 / 0.76 (25199) covalent geometry : angle 1.76337 / 1.17 (34279) SS BOND : bond 0.01209 / 0.71 ( 39) SS BOND : angle 1.88200 / 1.24 ( 78) hydrogen bonds : bond 0.16621 / 10.96 ( 1021) hydrogen bonds : angle 8.39642 / 5.77 ( 2781) link_BETA1-4 : bond 0.02366 / 1.42 ( 14) link_BETA1-4 : angle 4.70816 / 3.05 ( 42) link_NAG-ASN : bond 0.00880 / 0.57 ( 47) link_NAG-ASN : angle 4.50047 / 3.00 ( 141) *********************** 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 : 0.810 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: 0.8678 (mtt) cc_final: 0.8352 (mtm) REVERT: B 1029 MET cc_start: 0.9456 (tpp) cc_final: 0.9186 (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: 0.1670 time to fit residues: 20.8532 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 : 0.927 ------------------------------------------------------------------------------- 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 197 optimal weight: 2.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 7.9990 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 0.0040 chunk 183 optimal weight: 0.9980 chunk 298 optimal weight: 2.9990 overall best weight: 1.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 81 ASN A 641 ASN A 675 GLN A1048 HIS A1083 HIS C 207 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.044356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.033072 restraints weight = 213375.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.033910 restraints weight = 115056.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.034455 restraints weight = 78167.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.034801 restraints weight = 61336.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.035009 restraints weight = 52706.817| |-----------------------------------------------------------------------------| r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.1584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 25299 Z= 0.145 Angle : 0.704 11.147 34540 Z= 0.363 Chirality : 0.046 0.323 4081 Planarity : 0.004 0.050 4350 Dihedral : 6.990 51.606 3281 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.23 % Allowed : 3.03 % Favored : 96.73 % Rotamer: Outliers : 1.05 % Allowed : 5.07 % Favored : 93.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.15), residues: 2999 helix: 1.10 (0.19), residues: 689 sheet: -0.09 (0.19), residues: 639 loop : -0.89 (0.15), residues: 1671 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A1039 TYR 0.017 0.002 TYR C1067 PHE 0.023 0.002 PHE C 392 TRP 0.024 0.002 TRP A 64 HIS 0.006 0.001 HIS C1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 (25199) covalent geometry : angle 0.66652 / 0.35 (34279) SS BOND : bond 0.00627 / 0.42 ( 39) SS BOND : angle 1.64928 / 1.01 ( 78) hydrogen bonds : bond 0.05368 / 3.38 ( 1021) hydrogen bonds : angle 6.24728 / 4.33 ( 2781) link_BETA1-4 : bond 0.00362 / 0.20 ( 14) link_BETA1-4 : angle 1.81984 / 1.13 ( 42) link_NAG-ASN : bond 0.00339 / 0.20 ( 47) link_NAG-ASN : angle 3.30740 / 2.12 ( 141) *********************** 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 57 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 29 time to evaluate : 0.894 Fit side-chains revert: symmetry clash REVERT: A 461 LEU cc_start: 0.8088 (OUTLIER) cc_final: 0.7685 (mm) REVERT: C 646 ARG cc_start: 0.7691 (OUTLIER) cc_final: 0.7200 (tpm170) outliers start: 28 outliers final: 11 residues processed: 57 average time/residue: 0.1527 time to fit residues: 15.1468 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 : 0.898 ------------------------------------------------------------------------------- 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 83 optimal weight: 8.9990 chunk 221 optimal weight: 20.0000 chunk 172 optimal weight: 0.9980 chunk 254 optimal weight: 6.9990 chunk 37 optimal weight: 9.9990 chunk 3 optimal weight: 0.9990 chunk 234 optimal weight: 1.9990 chunk 43 optimal weight: 30.0000 chunk 107 optimal weight: 50.0000 chunk 291 optimal weight: 0.5980 chunk 157 optimal weight: 9.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.044085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.032741 restraints weight = 213748.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.033584 restraints weight = 114318.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.034122 restraints weight = 77455.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.034433 restraints weight = 60740.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.034652 restraints weight = 52646.544| |-----------------------------------------------------------------------------| r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.2110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 25299 Z= 0.126 Angle : 0.594 9.829 34540 Z= 0.307 Chirality : 0.044 0.262 4081 Planarity : 0.004 0.044 4350 Dihedral : 5.920 54.937 3271 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.63 % Favored : 96.20 % Rotamer: Outliers : 1.16 % Allowed : 5.41 % Favored : 93.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.15), residues: 2999 helix: 1.74 (0.20), residues: 688 sheet: -0.04 (0.19), residues: 623 loop : -0.79 (0.15), residues: 1688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1039 TYR 0.021 0.001 TYR C1067 PHE 0.018 0.001 PHE A 329 TRP 0.016 0.001 TRP A 64 HIS 0.003 0.001 HIS A 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.13 (25199) covalent geometry : angle 0.57155 / 0.30 (34279) SS BOND : bond 0.00886 / 0.40 ( 39) SS BOND : angle 1.34858 / 0.82 ( 78) hydrogen bonds : bond 0.04431 / 2.81 ( 1021) hydrogen bonds : angle 5.70311 / 3.94 ( 2781) link_BETA1-4 : bond 0.00372 / 0.22 ( 14) link_BETA1-4 : angle 1.41437 / 0.88 ( 42) link_NAG-ASN : bond 0.00227 / 0.13 ( 47) link_NAG-ASN : angle 2.33724 / 1.50 ( 141) *********************** 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 60 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 29 time to evaluate : 0.921 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 461 LEU cc_start: 0.8122 (OUTLIER) cc_final: 0.7736 (mm) REVERT: A 869 MET cc_start: 0.8695 (mtt) cc_final: 0.7904 (mtm) REVERT: C 329 PHE cc_start: 0.7907 (OUTLIER) cc_final: 0.7696 (t80) REVERT: C 646 ARG cc_start: 0.7691 (OUTLIER) cc_final: 0.7217 (tpm170) REVERT: C 740 MET cc_start: 0.8455 (tpt) cc_final: 0.8137 (tpt) outliers start: 31 outliers final: 13 residues processed: 58 average time/residue: 0.1443 time to fit residues: 15.0059 Evaluate side-chains 43 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 27 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 318 PHE 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 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 390 LEU Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 329 PHE 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 124 optimal weight: 0.6980 chunk 238 optimal weight: 5.9990 chunk 185 optimal weight: 10.0000 chunk 149 optimal weight: 10.0000 chunk 294 optimal weight: 9.9990 chunk 302 optimal weight: 8.9990 chunk 222 optimal weight: 6.9990 chunk 141 optimal weight: 30.0000 chunk 13 optimal weight: 10.0000 chunk 269 optimal weight: 8.9990 chunk 113 optimal weight: 20.0000 overall best weight: 6.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 115 GLN B 655 HIS C 955 ASN C1135 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.042925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.031763 restraints weight = 213908.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.032317 restraints weight = 117657.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.032795 restraints weight = 79001.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.032840 restraints weight = 76895.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.032835 restraints weight = 62802.223| |-----------------------------------------------------------------------------| r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.2482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 25299 Z= 0.275 Angle : 0.700 12.621 34540 Z= 0.353 Chirality : 0.046 0.245 4081 Planarity : 0.004 0.040 4350 Dihedral : 5.972 57.222 3269 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.37 % Favored : 95.53 % Rotamer: Outliers : 1.77 % Allowed : 5.94 % Favored : 92.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.15), residues: 2999 helix: 1.39 (0.20), residues: 689 sheet: -0.29 (0.19), residues: 621 loop : -0.91 (0.14), residues: 1689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 466 TYR 0.025 0.002 TYR C1067 PHE 0.020 0.002 PHE C1089 TRP 0.012 0.002 TRP A 64 HIS 0.006 0.001 HIS C1058 Details of bonding type rmsd/Z covalent geometry : bond 0.00624 / 0.27 (25199) covalent geometry : angle 0.67986 / 0.35 (34279) SS BOND : bond 0.00504 / 0.30 ( 39) SS BOND : angle 1.26965 / 0.79 ( 78) hydrogen bonds : bond 0.04904 / 3.14 ( 1021) hydrogen bonds : angle 5.87885 / 4.07 ( 2781) link_BETA1-4 : bond 0.00273 / 0.16 ( 14) link_BETA1-4 : angle 1.50898 / 0.97 ( 42) link_NAG-ASN : bond 0.00571 / 0.34 ( 47) link_NAG-ASN : angle 2.44363 / 1.55 ( 141) *********************** 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 74 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 27 time to evaluate : 0.826 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 108 THR cc_start: 0.8907 (OUTLIER) cc_final: 0.8690 (p) REVERT: A 461 LEU cc_start: 0.8094 (OUTLIER) cc_final: 0.7773 (mm) REVERT: B 697 MET cc_start: 0.9114 (OUTLIER) cc_final: 0.8736 (ttm) REVERT: C 329 PHE cc_start: 0.8258 (OUTLIER) cc_final: 0.8049 (t80) REVERT: C 646 ARG cc_start: 0.7787 (OUTLIER) cc_final: 0.7351 (tpm170) outliers start: 47 outliers final: 23 residues processed: 72 average time/residue: 0.1414 time to fit residues: 17.4600 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 : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR 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 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 916 LEU 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 697 MET Chi-restraints excluded: chain B residue 705 VAL 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 523 THR 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 62 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 294 optimal weight: 2.9990 chunk 186 optimal weight: 7.9990 chunk 51 optimal weight: 5.9990 chunk 213 optimal weight: 30.0000 chunk 68 optimal weight: 4.9990 chunk 255 optimal weight: 8.9990 chunk 30 optimal weight: 10.0000 chunk 261 optimal weight: 0.9980 chunk 97 optimal weight: 7.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3411 r_free = 0.3411 target = 0.043394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.031965 restraints weight = 214286.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.032788 restraints weight = 116040.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.033325 restraints weight = 79154.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.033649 restraints weight = 62263.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.033860 restraints weight = 53878.020| |-----------------------------------------------------------------------------| r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.2647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 25299 Z= 0.146 Angle : 0.571 9.044 34540 Z= 0.293 Chirality : 0.043 0.220 4081 Planarity : 0.004 0.045 4350 Dihedral : 5.610 55.942 3269 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.70 % Favored : 96.23 % Rotamer: Outliers : 1.32 % Allowed : 7.37 % Favored : 91.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.15), residues: 2999 helix: 1.71 (0.20), residues: 699 sheet: -0.11 (0.19), residues: 620 loop : -0.83 (0.15), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 457 TYR 0.035 0.001 TYR B 473 PHE 0.015 0.001 PHE B 456 TRP 0.015 0.001 TRP A 64 HIS 0.003 0.001 HIS C1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.15 (25199) covalent geometry : angle 0.55166 / 0.29 (34279) SS BOND : bond 0.00355 / 0.21 ( 39) SS BOND : angle 1.42897 / 0.90 ( 78) hydrogen bonds : bond 0.04228 / 2.68 ( 1021) hydrogen bonds : angle 5.54869 / 3.84 ( 2781) link_BETA1-4 : bond 0.00303 / 0.18 ( 14) link_BETA1-4 : angle 1.26135 / 0.78 ( 42) link_NAG-ASN : bond 0.00211 / 0.13 ( 47) link_NAG-ASN : angle 2.09682 / 1.32 ( 141) *********************** 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 64 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 29 time to evaluate : 0.934 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 461 LEU cc_start: 0.8054 (OUTLIER) cc_final: 0.7641 (tp) REVERT: B 697 MET cc_start: 0.9059 (OUTLIER) cc_final: 0.8747 (ttm) REVERT: C 646 ARG cc_start: 0.7796 (OUTLIER) cc_final: 0.7337 (tpm170) REVERT: C 740 MET cc_start: 0.8501 (tpt) cc_final: 0.8126 (tpt) outliers start: 35 outliers final: 23 residues processed: 61 average time/residue: 0.1227 time to fit residues: 13.7977 Evaluate side-chains 52 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 26 time to evaluate : 0.678 ------------------------------------------------------------------------------- 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 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 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 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 604 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 638 THR 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 121 optimal weight: 0.9980 chunk 154 optimal weight: 10.0000 chunk 209 optimal weight: 30.0000 chunk 203 optimal weight: 8.9990 chunk 188 optimal weight: 10.0000 chunk 278 optimal weight: 8.9990 chunk 186 optimal weight: 8.9990 chunk 75 optimal weight: 5.9990 chunk 58 optimal weight: 0.9980 chunk 174 optimal weight: 5.9990 chunk 11 optimal weight: 0.1980 overall best weight: 2.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1106 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 = 0.3413 r_free = 0.3413 target = 0.043414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.032000 restraints weight = 213806.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.032824 restraints weight = 115657.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.033358 restraints weight = 78875.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.033681 restraints weight = 62251.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.033895 restraints weight = 53805.918| |-----------------------------------------------------------------------------| r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.2818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 25299 Z= 0.139 Angle : 0.550 8.664 34540 Z= 0.282 Chirality : 0.043 0.216 4081 Planarity : 0.003 0.041 4350 Dihedral : 5.408 55.668 3269 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.60 % Favored : 96.33 % Rotamer: Outliers : 1.13 % Allowed : 8.42 % Favored : 90.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.15), residues: 2999 helix: 1.80 (0.20), residues: 706 sheet: -0.04 (0.19), residues: 622 loop : -0.79 (0.15), residues: 1671 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 403 TYR 0.021 0.001 TYR C1067 PHE 0.019 0.001 PHE C 329 TRP 0.015 0.001 TRP A 64 HIS 0.003 0.001 HIS C1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 (25199) covalent geometry : angle 0.53410 / 0.28 (34279) SS BOND : bond 0.00342 / 0.21 ( 39) SS BOND : angle 1.07672 / 0.67 ( 78) hydrogen bonds : bond 0.04019 / 2.56 ( 1021) hydrogen bonds : angle 5.40417 / 3.74 ( 2781) link_BETA1-4 : bond 0.00284 / 0.17 ( 14) link_BETA1-4 : angle 1.21789 / 0.76 ( 42) link_NAG-ASN : bond 0.00209 / 0.12 ( 47) link_NAG-ASN : angle 1.93429 / 1.25 ( 141) *********************** 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 57 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 27 time to evaluate : 0.965 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 461 LEU cc_start: 0.8171 (OUTLIER) cc_final: 0.7779 (tp) REVERT: A 869 MET cc_start: 0.8729 (mtt) cc_final: 0.8420 (mtt) REVERT: A 1050 MET cc_start: 0.7816 (ptm) cc_final: 0.7589 (ptm) REVERT: B 697 MET cc_start: 0.9040 (OUTLIER) cc_final: 0.8767 (ttm) REVERT: C 646 ARG cc_start: 0.7871 (OUTLIER) cc_final: 0.7335 (tpm170) REVERT: C 740 MET cc_start: 0.8493 (tpt) cc_final: 0.8111 (tpt) outliers start: 30 outliers final: 22 residues processed: 56 average time/residue: 0.1377 time to fit residues: 14.1721 Evaluate side-chains 51 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 26 time to evaluate : 0.696 ------------------------------------------------------------------------------- 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 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 65 optimal weight: 2.9990 chunk 226 optimal weight: 30.0000 chunk 235 optimal weight: 5.9990 chunk 39 optimal weight: 50.0000 chunk 24 optimal weight: 10.0000 chunk 61 optimal weight: 2.9990 chunk 141 optimal weight: 9.9990 chunk 35 optimal weight: 6.9990 chunk 105 optimal weight: 0.3980 chunk 166 optimal weight: 5.9990 chunk 298 optimal weight: 4.9990 overall best weight: 3.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN C 121 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.043287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.031878 restraints weight = 214037.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.032691 restraints weight = 116094.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.033221 restraints weight = 79388.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.033535 restraints weight = 62672.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.033749 restraints weight = 54363.039| |-----------------------------------------------------------------------------| r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.3028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 25299 Z= 0.158 Angle : 0.552 8.611 34540 Z= 0.283 Chirality : 0.043 0.203 4081 Planarity : 0.004 0.043 4350 Dihedral : 5.265 54.745 3268 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.87 % Favored : 96.07 % Rotamer: Outliers : 1.20 % Allowed : 9.02 % Favored : 89.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.00 (0.15), residues: 2999 helix: 1.83 (0.20), residues: 706 sheet: -0.07 (0.19), residues: 637 loop : -0.79 (0.15), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1039 TYR 0.020 0.001 TYR C1067 PHE 0.016 0.001 PHE C 329 TRP 0.015 0.001 TRP A 64 HIS 0.004 0.001 HIS C1058 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.16 (25199) covalent geometry : angle 0.53801 / 0.28 (34279) SS BOND : bond 0.00377 / 0.23 ( 39) SS BOND : angle 1.02288 / 0.64 ( 78) hydrogen bonds : bond 0.03978 / 2.54 ( 1021) hydrogen bonds : angle 5.35944 / 3.70 ( 2781) link_BETA1-4 : bond 0.00296 / 0.18 ( 14) link_BETA1-4 : angle 1.21823 / 0.76 ( 42) link_NAG-ASN : bond 0.00253 / 0.15 ( 47) link_NAG-ASN : angle 1.81886 / 1.18 ( 141) *********************** 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 59 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 27 time to evaluate : 0.733 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 461 LEU cc_start: 0.8175 (OUTLIER) cc_final: 0.7820 (tp) REVERT: A 1050 MET cc_start: 0.8096 (ptm) cc_final: 0.7895 (ptm) REVERT: C 224 GLU cc_start: 0.8533 (OUTLIER) cc_final: 0.8276 (pm20) REVERT: C 646 ARG cc_start: 0.7872 (OUTLIER) cc_final: 0.7309 (tpm170) outliers start: 32 outliers final: 24 residues processed: 57 average time/residue: 0.1243 time to fit residues: 13.0267 Evaluate side-chains 54 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 27 time to evaluate : 0.848 ------------------------------------------------------------------------------- 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 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 367 VAL Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 312 ILE 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 252 optimal weight: 9.9990 chunk 57 optimal weight: 2.9990 chunk 125 optimal weight: 4.9990 chunk 17 optimal weight: 10.0000 chunk 106 optimal weight: 0.0970 chunk 246 optimal weight: 9.9990 chunk 164 optimal weight: 5.9990 chunk 278 optimal weight: 0.9980 chunk 206 optimal weight: 6.9990 chunk 51 optimal weight: 10.0000 chunk 188 optimal weight: 0.8980 overall best weight: 1.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3420 r_free = 0.3420 target = 0.043587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.032229 restraints weight = 213794.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.033063 restraints weight = 115174.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.033593 restraints weight = 78328.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.033940 restraints weight = 61974.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.034147 restraints weight = 53246.145| |-----------------------------------------------------------------------------| r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.3140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 25299 Z= 0.111 Angle : 0.510 8.438 34540 Z= 0.263 Chirality : 0.042 0.259 4081 Planarity : 0.003 0.042 4350 Dihedral : 5.092 54.171 3268 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.33 % Favored : 96.60 % Rotamer: Outliers : 1.05 % Allowed : 9.09 % Favored : 89.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.15), residues: 2999 helix: 1.99 (0.20), residues: 708 sheet: -0.00 (0.19), residues: 642 loop : -0.72 (0.15), residues: 1649 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 466 TYR 0.020 0.001 TYR C1067 PHE 0.017 0.001 PHE B 392 TRP 0.016 0.001 TRP A 64 HIS 0.003 0.001 HIS C1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 (25199) covalent geometry : angle 0.49762 / 0.26 (34279) SS BOND : bond 0.00322 / 0.20 ( 39) SS BOND : angle 0.87980 / 0.55 ( 78) hydrogen bonds : bond 0.03707 / 2.36 ( 1021) hydrogen bonds : angle 5.19915 / 3.59 ( 2781) link_BETA1-4 : bond 0.00334 / 0.20 ( 14) link_BETA1-4 : angle 1.14663 / 0.71 ( 42) link_NAG-ASN : bond 0.00152 / 0.09 ( 47) link_NAG-ASN : angle 1.66350 / 1.09 ( 141) *********************** 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 56 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 28 time to evaluate : 0.876 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 461 LEU cc_start: 0.8224 (OUTLIER) cc_final: 0.7849 (tp) REVERT: A 869 MET cc_start: 0.8645 (mtt) cc_final: 0.7927 (mtm) REVERT: B 1116 THR cc_start: 0.9348 (OUTLIER) cc_final: 0.9110 (p) REVERT: C 224 GLU cc_start: 0.8525 (OUTLIER) cc_final: 0.8289 (pm20) REVERT: C 646 ARG cc_start: 0.7856 (OUTLIER) cc_final: 0.7293 (tpm170) REVERT: C 740 MET cc_start: 0.8437 (tpt) cc_final: 0.8093 (tpt) outliers start: 28 outliers final: 22 residues processed: 56 average time/residue: 0.1362 time to fit residues: 13.6595 Evaluate side-chains 53 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 27 time to evaluate : 0.696 ------------------------------------------------------------------------------- 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 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 367 VAL Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 461 LEU 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 224 GLU Chi-restraints excluded: chain C residue 312 ILE 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 1 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 139 optimal weight: 50.0000 chunk 300 optimal weight: 0.8980 chunk 6 optimal weight: 20.0000 chunk 284 optimal weight: 8.9990 chunk 134 optimal weight: 7.9990 chunk 80 optimal weight: 1.9990 chunk 175 optimal weight: 6.9990 chunk 220 optimal weight: 8.9990 chunk 292 optimal weight: 3.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3416 r_free = 0.3416 target = 0.043454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.032076 restraints weight = 213893.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.032895 restraints weight = 115600.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.033428 restraints weight = 78876.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.033744 restraints weight = 62268.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.033955 restraints weight = 53936.326| |-----------------------------------------------------------------------------| r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.3204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 25299 Z= 0.142 Angle : 0.531 9.305 34540 Z= 0.273 Chirality : 0.042 0.265 4081 Planarity : 0.003 0.042 4350 Dihedral : 5.007 54.661 3267 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.70 % Favored : 96.20 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.15), residues: 2999 helix: 1.91 (0.20), residues: 710 sheet: 0.02 (0.19), residues: 644 loop : -0.72 (0.15), residues: 1645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 466 TYR 0.020 0.001 TYR C1067 PHE 0.015 0.001 PHE B 456 TRP 0.016 0.001 TRP A 64 HIS 0.003 0.001 HIS C1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 (25199) covalent geometry : angle 0.51566 / 0.27 (34279) SS BOND : bond 0.00354 / 0.23 ( 39) SS BOND : angle 1.41820 / 0.79 ( 78) hydrogen bonds : bond 0.03829 / 2.48 ( 1021) hydrogen bonds : angle 5.20311 / 3.59 ( 2781) link_BETA1-4 : bond 0.00306 / 0.19 ( 14) link_BETA1-4 : angle 1.17189 / 0.73 ( 42) link_NAG-ASN : bond 0.00200 / 0.12 ( 47) link_NAG-ASN : angle 1.68536 / 1.11 ( 141) *********************** 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 55 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 27 time to evaluate : 0.720 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 461 LEU cc_start: 0.8219 (OUTLIER) cc_final: 0.7854 (tp) REVERT: A 869 MET cc_start: 0.8635 (mtt) cc_final: 0.8320 (mtt) REVERT: B 1116 THR cc_start: 0.9349 (OUTLIER) cc_final: 0.9117 (p) REVERT: C 224 GLU cc_start: 0.8581 (OUTLIER) cc_final: 0.8315 (pm20) REVERT: C 646 ARG cc_start: 0.7862 (OUTLIER) cc_final: 0.7277 (tpm170) REVERT: C 740 MET cc_start: 0.8460 (tpt) cc_final: 0.8124 (tpt) outliers start: 28 outliers final: 24 residues processed: 55 average time/residue: 0.1308 time to fit residues: 13.1647 Evaluate side-chains 54 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 26 time to evaluate : 0.845 ------------------------------------------------------------------------------- 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 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 367 VAL Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 461 LEU 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 224 GLU Chi-restraints excluded: chain C residue 312 ILE 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 638 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 38 optimal weight: 30.0000 chunk 82 optimal weight: 7.9990 chunk 118 optimal weight: 5.9990 chunk 26 optimal weight: 20.0000 chunk 203 optimal weight: 9.9990 chunk 251 optimal weight: 4.9990 chunk 231 optimal weight: 8.9990 chunk 37 optimal weight: 20.0000 chunk 296 optimal weight: 4.9990 chunk 255 optimal weight: 9.9990 chunk 7 optimal weight: 7.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1135 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 = 0.3386 r_free = 0.3386 target = 0.042716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.031431 restraints weight = 215448.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.032383 restraints weight = 119364.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.032788 restraints weight = 69777.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.032859 restraints weight = 64421.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.032867 restraints weight = 57534.545| |-----------------------------------------------------------------------------| r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.3259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 25299 Z= 0.270 Angle : 0.653 9.950 34540 Z= 0.331 Chirality : 0.045 0.270 4081 Planarity : 0.004 0.040 4350 Dihedral : 5.378 56.744 3267 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.90 % Favored : 95.00 % Rotamer: Outliers : 1.24 % Allowed : 9.24 % Favored : 89.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.15), residues: 2999 helix: 1.53 (0.20), residues: 701 sheet: -0.24 (0.18), residues: 640 loop : -0.85 (0.15), residues: 1658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 454 TYR 0.021 0.002 TYR C1067 PHE 0.017 0.002 PHE A1052 TRP 0.013 0.001 TRP A 64 HIS 0.005 0.001 HIS C1058 Details of bonding type rmsd/Z covalent geometry : bond 0.00612 / 0.27 (25199) covalent geometry : angle 0.63617 / 0.33 (34279) SS BOND : bond 0.00437 / 0.28 ( 39) SS BOND : angle 1.53917 / 0.90 ( 78) hydrogen bonds : bond 0.04608 / 2.99 ( 1021) hydrogen bonds : angle 5.59761 / 3.87 ( 2781) link_BETA1-4 : bond 0.00243 / 0.14 ( 14) link_BETA1-4 : angle 1.34288 / 0.86 ( 42) link_NAG-ASN : bond 0.00509 / 0.31 ( 47) link_NAG-ASN : angle 2.01428 / 1.30 ( 141) ********************** 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 60 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 27 time to evaluate : 0.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 ILE cc_start: 0.9277 (mm) cc_final: 0.9001 (mt) REVERT: A 461 LEU cc_start: 0.8077 (OUTLIER) cc_final: 0.7770 (mm) REVERT: C 224 GLU cc_start: 0.8629 (OUTLIER) cc_final: 0.8283 (pm20) REVERT: C 646 ARG cc_start: 0.7878 (OUTLIER) cc_final: 0.7318 (tpm170) outliers start: 33 outliers final: 26 residues processed: 60 average time/residue: 0.1121 time to fit residues: 12.2492 Evaluate side-chains 56 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 27 time to evaluate : 0.739 ------------------------------------------------------------------------------- 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 752 LEU Chi-restraints excluded: chain A residue 886 TRP 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 705 VAL Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 443 SER 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 638 THR Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 896 ILE Chi-restraints excluded: chain C residue 1094 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 63 optimal weight: 10.0000 chunk 138 optimal weight: 0.4980 chunk 299 optimal weight: 5.9990 chunk 111 optimal weight: 20.0000 chunk 172 optimal weight: 0.5980 chunk 261 optimal weight: 6.9990 chunk 202 optimal weight: 20.0000 chunk 119 optimal weight: 5.9990 chunk 120 optimal weight: 3.9990 chunk 152 optimal weight: 0.8980 chunk 290 optimal weight: 2.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3412 r_free = 0.3412 target = 0.043400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.031996 restraints weight = 212823.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.032828 restraints weight = 114942.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.033357 restraints weight = 78126.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.033688 restraints weight = 61516.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.033865 restraints weight = 53205.305| |-----------------------------------------------------------------------------| r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.3337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 25299 Z= 0.115 Angle : 0.525 8.417 34540 Z= 0.271 Chirality : 0.043 0.256 4081 Planarity : 0.003 0.041 4350 Dihedral : 5.046 56.307 3267 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.40 % Favored : 96.50 % Rotamer: Outliers : 0.98 % Allowed : 9.55 % Favored : 89.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.15), residues: 2999 helix: 1.93 (0.20), residues: 705 sheet: -0.04 (0.19), residues: 644 loop : -0.75 (0.15), residues: 1650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 466 TYR 0.021 0.001 TYR C1067 PHE 0.016 0.001 PHE B 456 TRP 0.017 0.001 TRP A 64 HIS 0.003 0.001 HIS C1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 (25199) covalent geometry : angle 0.51204 / 0.27 (34279) SS BOND : bond 0.00351 / 0.22 ( 39) SS BOND : angle 1.22780 / 0.70 ( 78) hydrogen bonds : bond 0.03903 / 2.52 ( 1021) hydrogen bonds : angle 5.23568 / 3.62 ( 2781) link_BETA1-4 : bond 0.00384 / 0.23 ( 14) link_BETA1-4 : angle 1.13784 / 0.70 ( 42) link_NAG-ASN : bond 0.00158 / 0.09 ( 47) link_NAG-ASN : angle 1.63334 / 1.08 ( 141) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3397.72 seconds wall clock time: 60 minutes 0.47 seconds (3600.47 seconds total)