Starting phenix.real_space_refine on Fri Mar 6 04:22:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7n0h_24106/03_2026/7n0h_24106_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7n0h_24106/03_2026/7n0h_24106.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7n0h_24106/03_2026/7n0h_24106_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7n0h_24106/03_2026/7n0h_24106_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7n0h_24106/03_2026/7n0h_24106.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7n0h_24106/03_2026/7n0h_24106.map" } resolution = 3.34 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= -0.001 sd= 0.018 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 122 5.16 5 C 17757 2.51 5 N 4607 2.21 5 O 5488 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 33 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 27974 Number of models: 1 Model: "" Number of chains: 25 Chain: "A" Number of atoms: 8395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1076, 8395 Classifications: {'peptide': 1076} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 57, 'TRANS': 1018} Chain breaks: 3 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "B" Number of atoms: 8395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1076, 8395 Classifications: {'peptide': 1076} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 57, 'TRANS': 1018} Chain breaks: 3 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "C" Number of atoms: 8384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1075, 8384 Classifications: {'peptide': 1075} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 57, 'TRANS': 1017} Chain breaks: 3 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 952 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 117} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "Z" Number of atoms: 952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 952 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 117} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Time building chain proxies: 6.23, per 1000 atoms: 0.22 Number of scatterers: 27974 At special positions: 0 Unit cell: (159.904, 160.956, 212.504, 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 122 16.00 O 5488 8.00 N 4607 7.00 C 17757 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=41, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.04 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.02 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS X 22 " - pdb=" SG CYS X 96 " distance=2.04 Simple disulfide: pdb=" SG CYS Z 22 " - pdb=" SG CYS Z 96 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG 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 S 1 " - " NAG S 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " NAG-ASN " NAG A1301 " - " ASN A 603 " " NAG A1302 " - " ASN A 61 " " NAG A1303 " - " ASN A 616 " " NAG A1304 " - " ASN A 149 " " NAG A1305 " - " ASN A 165 " " NAG A1306 " - " ASN A 657 " " NAG A1307 " - " ASN A 709 " " NAG A1308 " - " ASN A1134 " " NAG B1301 " - " ASN B 603 " " NAG B1302 " - " ASN B 61 " " NAG B1303 " - " ASN B 616 " " NAG B1304 " - " ASN B 149 " " NAG B1305 " - " ASN B 165 " " NAG B1306 " - " ASN B 657 " " NAG B1307 " - " ASN B 282 " " NAG B1308 " - " ASN B 709 " " NAG B1309 " - " ASN B1134 " " NAG B1310 " - " ASN C 282 " " NAG C1301 " - " ASN A 282 " " NAG C1302 " - " ASN C 331 " " NAG C1303 " - " ASN C 61 " " NAG C1304 " - " ASN C 343 " " NAG C1305 " - " ASN C 149 " " NAG C1306 " - " ASN C 165 " " NAG C1307 " - " ASN C 603 " " NAG C1308 " - " ASN C 616 " " NAG C1309 " - " ASN C 657 " " NAG C1310 " - " ASN C 709 " " NAG C1311 " - " ASN C1098 " " NAG C1312 " - " ASN C1134 " " NAG D 1 " - " ASN A 331 " " NAG E 1 " - " ASN A 343 " " NAG F 1 " - " ASN A 717 " " NAG G 1 " - " ASN A 801 " " NAG H 1 " - " ASN A1074 " " NAG I 1 " - " ASN A1098 " " NAG J 1 " - " ASN B 801 " " NAG K 1 " - " ASN B1074 " " NAG L 1 " - " ASN C 717 " " NAG M 1 " - " ASN C 801 " " NAG N 1 " - " ASN C1074 " " NAG O 1 " - " ASN A 17 " " NAG P 1 " - " ASN A 122 " " NAG Q 1 " - " ASN A 234 " " NAG S 1 " - " ASN B 137 " " NAG U 1 " - " ASN C 17 " " NAG V 1 " - " ASN C 122 " Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.32 Conformation dependent library (CDL) restraints added in 1.5 seconds 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6470 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 58 sheets defined 22.6% alpha, 30.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.14 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 365 through 372 removed outlier: 4.302A pdb=" N ALA A 372 " --> pdb=" O LEU A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 389 removed outlier: 3.777A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.110A 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 502 through 505 Processing helix chain 'A' and resid 737 through 742 Processing helix chain 'A' and resid 747 through 755 removed outlier: 3.650A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.579A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.556A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.251A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.658A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.669A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.626A 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: 3.666A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1032 removed outlier: 5.393A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 342 removed outlier: 4.285A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 372 removed outlier: 3.888A pdb=" N ALA B 372 " --> pdb=" O LEU B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 390 Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 747 through 755 removed outlier: 3.647A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.559A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.558A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.533A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.210A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.722A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.664A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) 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 977 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 5.063A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1146 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.910A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 371 Processing helix chain 'C' and resid 383 through 389 removed outlier: 4.519A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.445A 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 438 through 443 removed outlier: 3.758A pdb=" N SER C 443 " --> pdb=" O ASN C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.508A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) 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: 3.572A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.787A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 913 through 919 Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.843A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.711A 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 983 removed outlier: 3.856A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1032 removed outlier: 5.126A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 removed outlier: 4.114A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ASP C1146 " --> pdb=" O GLN C1142 " (cutoff:3.500A) Processing helix chain 'X' and resid 87 through 91 Processing helix chain 'Z' and resid 87 through 91 removed outlier: 3.546A pdb=" N THR Z 91 " --> pdb=" O PRO Z 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 4.130A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 8.148A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 8.988A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 27 through 30 removed outlier: 4.130A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 4.096A 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: 3.574A pdb=" N ARG A 246 " --> pdb=" O VAL A 143 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 7.041A pdb=" N ARG A 237 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N PHE A 106 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N GLN A 239 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N TRP A 104 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N LEU A 241 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 6.836A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.410A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N THR A 572 " --> pdb=" O ASP A 568 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (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 391 through 392 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 473 through 474 removed outlier: 4.005A pdb=" N TYR A 473 " --> pdb=" O TYR A 489 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.990A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.366A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 715 Processing sheet with id=AB6, first strand: chain 'A' and resid 718 through 728 removed outlier: 7.012A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 733 through 735 removed outlier: 4.398A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 787 through 790 Processing sheet with id=AB9, first strand: chain 'A' and resid 1120 through 1122 removed outlier: 3.733A pdb=" N VAL A1133 " --> pdb=" O ALA A1080 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AC2, first strand: chain 'B' and resid 27 through 30 removed outlier: 4.261A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 27 through 30 removed outlier: 4.261A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 8.681A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.112A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 84 through 85 removed outlier: 12.925A pdb=" N PHE B 238 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 12.052A pdb=" N ASN B 137 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 10.767A pdb=" N THR B 240 " --> pdb=" O ASN B 137 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N LEU B 242 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ARG B 246 " --> pdb=" O VAL B 143 " (cutoff:3.500A) removed outlier: 10.562A pdb=" N ASP B 138 " --> pdb=" O TYR B 160 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N TYR B 160 " --> pdb=" O ASP B 138 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.904A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.895A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 325 through 328 removed outlier: 3.593A pdb=" N ARG B 328 " --> pdb=" O ASN B 542 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N THR B 573 " --> pdb=" O ASP B 568 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N ASP B 568 " --> pdb=" O THR B 573 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AD1, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.225A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD3, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.888A pdb=" N TYR B 473 " --> pdb=" O TYR B 489 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'B' and resid 654 through 655 Processing sheet with id=AD5, first strand: chain 'B' and resid 701 through 702 removed outlier: 6.535A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.590A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 718 through 728 removed outlier: 7.018A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.348A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 1120 through 1122 removed outlier: 3.748A pdb=" N VAL B1133 " --> pdb=" O ALA B1080 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 27 through 30 removed outlier: 4.618A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N LYS C 187 " --> pdb=" O ILE C 210 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.203A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.182A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 27 through 30 removed outlier: 4.618A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 47 through 55 removed outlier: 4.024A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 84 through 85 removed outlier: 13.123A pdb=" N PHE C 238 " --> pdb=" O PHE C 135 " (cutoff:3.500A) removed outlier: 12.648A pdb=" N ASN C 137 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 10.604A pdb=" N THR C 240 " --> pdb=" O ASN C 137 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N LEU C 242 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 10.509A pdb=" N ASP C 138 " --> pdb=" O TYR C 160 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N TYR C 160 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N TYR C 144 " --> pdb=" O GLU C 154 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N GLU C 154 " --> pdb=" O TYR C 144 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N HIS C 146 " --> pdb=" O TRP C 152 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N TRP C 152 " --> pdb=" O HIS C 146 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 84 through 85 removed outlier: 7.001A pdb=" N ARG C 237 " --> pdb=" O PHE C 106 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N PHE C 106 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N GLN C 239 " --> pdb=" O TRP C 104 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N TRP C 104 " --> pdb=" O GLN C 239 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N LEU C 241 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.530A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 325 through 328 removed outlier: 6.859A pdb=" N ILE C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AE9, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.899A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AF2, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.938A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.737A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.206A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.279A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.316A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AF7, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AF8, first strand: chain 'X' and resid 3 through 7 Processing sheet with id=AF9, first strand: chain 'X' and resid 10 through 13 removed outlier: 6.108A pdb=" N GLY X 10 " --> pdb=" O THR X 118 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N SER X 120 " --> pdb=" O GLY X 10 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N VAL X 12 " --> pdb=" O SER X 120 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N LYS X 99 " --> pdb=" O ARG X 33 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N ARG X 33 " --> pdb=" O LYS X 99 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N ARG X 38 " --> pdb=" O TRP X 47 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N TRP X 47 " --> pdb=" O ARG X 38 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'X' and resid 10 through 13 removed outlier: 6.108A pdb=" N GLY X 10 " --> pdb=" O THR X 118 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N SER X 120 " --> pdb=" O GLY X 10 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N VAL X 12 " --> pdb=" O SER X 120 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'Z' and resid 3 through 8 Processing sheet with id=AG3, first strand: chain 'Z' and resid 10 through 13 removed outlier: 6.222A pdb=" N GLY Z 10 " --> pdb=" O THR Z 118 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N SER Z 120 " --> pdb=" O GLY Z 10 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N VAL Z 12 " --> pdb=" O SER Z 120 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N LYS Z 99 " --> pdb=" O ARG Z 33 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ARG Z 33 " --> pdb=" O LYS Z 99 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ARG Z 38 " --> pdb=" O TRP Z 47 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N TRP Z 47 " --> pdb=" O ARG Z 38 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'Z' and resid 10 through 13 removed outlier: 6.222A pdb=" N GLY Z 10 " --> pdb=" O THR Z 118 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N SER Z 120 " --> pdb=" O GLY Z 10 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N VAL Z 12 " --> pdb=" O SER Z 120 " (cutoff:3.500A) 1130 hydrogen bonds defined for protein. 3057 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: 6.72 Time building geometry restraints manager: 2.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8936 1.34 - 1.46: 7036 1.46 - 1.58: 12486 1.58 - 1.70: 0 1.70 - 1.82: 156 Bond restraints: 28614 Sorted by residual: bond pdb=" C1 NAG C1306 " pdb=" O5 NAG C1306 " ideal model delta sigma weight residual 1.406 1.505 -0.099 2.00e-02 2.50e+03 2.43e+01 bond pdb=" C1 NAG L 1 " pdb=" O5 NAG L 1 " ideal model delta sigma weight residual 1.406 1.482 -0.076 2.00e-02 2.50e+03 1.46e+01 bond pdb=" C1 NAG A1305 " pdb=" O5 NAG A1305 " ideal model delta sigma weight residual 1.406 1.479 -0.073 2.00e-02 2.50e+03 1.32e+01 bond pdb=" C1 NAG B1301 " pdb=" O5 NAG B1301 " ideal model delta sigma weight residual 1.406 1.478 -0.072 2.00e-02 2.50e+03 1.30e+01 bond pdb=" C1 NAG C1303 " pdb=" O5 NAG C1303 " ideal model delta sigma weight residual 1.406 1.475 -0.069 2.00e-02 2.50e+03 1.19e+01 ... (remaining 28609 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.66: 37790 1.66 - 3.33: 1036 3.33 - 4.99: 104 4.99 - 6.65: 20 6.65 - 8.31: 7 Bond angle restraints: 38957 Sorted by residual: angle pdb=" C GLU C 96 " pdb=" N LYS C 97 " pdb=" CA LYS C 97 " ideal model delta sigma weight residual 121.98 129.50 -7.52 1.53e+00 4.27e-01 2.41e+01 angle pdb=" N GLY B 648 " pdb=" CA GLY B 648 " pdb=" C GLY B 648 " ideal model delta sigma weight residual 111.21 115.67 -4.46 1.04e+00 9.25e-01 1.84e+01 angle pdb=" N VAL C1128 " pdb=" CA VAL C1128 " pdb=" C VAL C1128 " ideal model delta sigma weight residual 113.53 109.37 4.16 9.80e-01 1.04e+00 1.80e+01 angle pdb=" C LYS B1073 " pdb=" N ASN B1074 " pdb=" CA ASN B1074 " ideal model delta sigma weight residual 122.93 117.55 5.38 1.45e+00 4.76e-01 1.37e+01 angle pdb=" CB LYS C 97 " pdb=" CG LYS C 97 " pdb=" CD LYS C 97 " ideal model delta sigma weight residual 111.30 102.99 8.31 2.30e+00 1.89e-01 1.31e+01 ... (remaining 38952 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.08: 16810 25.08 - 50.17: 740 50.17 - 75.25: 143 75.25 - 100.33: 97 100.33 - 125.41: 65 Dihedral angle restraints: 17855 sinusoidal: 7770 harmonic: 10085 Sorted by residual: dihedral pdb=" CB CYS C 738 " pdb=" SG CYS C 738 " pdb=" SG CYS C 760 " pdb=" CB CYS C 760 " ideal model delta sinusoidal sigma weight residual 93.00 10.34 82.66 1 1.00e+01 1.00e-02 8.37e+01 dihedral pdb=" CB CYS B 743 " pdb=" SG CYS B 743 " pdb=" SG CYS B 749 " pdb=" CB CYS B 749 " ideal model delta sinusoidal sigma weight residual 93.00 167.82 -74.82 1 1.00e+01 1.00e-02 7.09e+01 dihedral pdb=" CB CYS B 538 " pdb=" SG CYS B 538 " pdb=" SG CYS B 590 " pdb=" CB CYS B 590 " ideal model delta sinusoidal sigma weight residual -86.00 -14.76 -71.24 1 1.00e+01 1.00e-02 6.51e+01 ... (remaining 17852 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.144: 4529 0.144 - 0.288: 30 0.288 - 0.432: 4 0.432 - 0.576: 1 0.576 - 0.719: 1 Chirality restraints: 4565 Sorted by residual: chirality pdb=" C1 NAG B1302 " pdb=" ND2 ASN B 61 " pdb=" C2 NAG B1302 " pdb=" O5 NAG B1302 " both_signs ideal model delta sigma weight residual False -2.40 -1.68 -0.72 2.00e-01 2.50e+01 1.29e+01 chirality pdb=" C1 NAG C1308 " pdb=" ND2 ASN C 616 " pdb=" C2 NAG C1308 " pdb=" O5 NAG C1308 " both_signs ideal model delta sigma weight residual False -2.40 -1.93 -0.47 2.00e-01 2.50e+01 5.64e+00 chirality pdb=" C1 NAG S 1 " pdb=" ND2 ASN B 137 " pdb=" C2 NAG S 1 " pdb=" O5 NAG S 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.98 -0.42 2.00e-01 2.50e+01 4.42e+00 ... (remaining 4562 not shown) Planarity restraints: 5029 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 61 " -0.003 2.00e-02 2.50e+03 3.56e-02 1.58e+01 pdb=" CG ASN C 61 " 0.049 2.00e-02 2.50e+03 pdb=" OD1 ASN C 61 " -0.043 2.00e-02 2.50e+03 pdb=" ND2 ASN C 61 " 0.030 2.00e-02 2.50e+03 pdb=" C1 NAG C1303 " -0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 603 " -0.036 2.00e-02 2.50e+03 3.28e-02 1.35e+01 pdb=" CG ASN B 603 " 0.041 2.00e-02 2.50e+03 pdb=" OD1 ASN B 603 " -0.003 2.00e-02 2.50e+03 pdb=" ND2 ASN B 603 " 0.034 2.00e-02 2.50e+03 pdb=" C1 NAG B1301 " -0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 801 " -0.023 2.00e-02 2.50e+03 2.29e-02 6.55e+00 pdb=" CG ASN B 801 " 0.041 2.00e-02 2.50e+03 pdb=" OD1 ASN B 801 " -0.011 2.00e-02 2.50e+03 pdb=" ND2 ASN B 801 " 0.009 2.00e-02 2.50e+03 pdb=" C1 NAG J 1 " -0.016 2.00e-02 2.50e+03 ... (remaining 5026 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.70: 883 2.70 - 3.25: 27464 3.25 - 3.80: 44027 3.80 - 4.35: 54325 4.35 - 4.90: 93107 Nonbonded interactions: 219806 Sorted by model distance: nonbonded pdb=" OG1 THR B 618 " pdb=" OE1 GLU B 619 " model vdw 2.156 3.040 nonbonded pdb=" OG1 THR C1116 " pdb=" OD1 ASP C1118 " model vdw 2.180 3.040 nonbonded pdb=" O PHE A 329 " pdb=" NE2 GLN A 580 " model vdw 2.201 3.120 nonbonded pdb=" OG1 THR C 323 " pdb=" OE1 GLU C 324 " model vdw 2.201 3.040 nonbonded pdb=" O THR A 393 " pdb=" OG1 THR A 523 " model vdw 2.214 3.040 ... (remaining 219801 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 14 through 331 or (resid 332 through 333 and (name N or na \ me CA or name C or name O or name CB )) or resid 334 through 620 or resid 641 th \ rough 1308)) selection = (chain 'B' and (resid 14 through 331 or (resid 332 through 333 and (name N or na \ me CA or name C or name O or name CB )) or resid 334 through 620 or resid 641 th \ rough 1308)) selection = (chain 'C' and resid 14 through 1308) } 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' selection = chain 'S' selection = chain 'U' selection = chain 'V' } ncs_group { reference = chain 'X' selection = chain 'Z' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.460 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 27.370 Find NCS groups from input model: 0.940 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 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 : 0.005 0.099 28721 Z= 0.226 Angle : 0.706 22.429 39231 Z= 0.345 Chirality : 0.050 0.719 4565 Planarity : 0.004 0.059 4982 Dihedral : 17.695 125.413 11262 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % 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: 0.29 (0.14), residues: 3441 helix: 2.26 (0.21), residues: 643 sheet: 0.17 (0.17), residues: 877 loop : -0.49 (0.14), residues: 1921 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 995 TYR 0.032 0.001 TYR A 904 PHE 0.026 0.001 PHE A 906 TRP 0.013 0.001 TRP C 152 HIS 0.003 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00486 (28614) covalent geometry : angle 0.63335 (38957) SS BOND : bond 0.00246 ( 41) SS BOND : angle 1.55180 ( 82) hydrogen bonds : bond 0.10695 ( 1107) hydrogen bonds : angle 6.35829 ( 3057) Misc. bond : bond 0.00013 ( 2) link_BETA1-4 : bond 0.00667 ( 17) link_BETA1-4 : angle 1.74540 ( 51) link_NAG-ASN : bond 0.00607 ( 47) link_NAG-ASN : angle 5.04260 ( 141) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 3019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 1.011 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 515 PHE cc_start: 0.8117 (m-80) cc_final: 0.7859 (m-80) REVERT: Z 34 MET cc_start: 0.5226 (mpp) cc_final: 0.4685 (mpp) outliers start: 0 outliers final: 0 residues processed: 103 average time/residue: 0.1703 time to fit residues: 29.8423 Evaluate side-chains 75 residues out of total 3019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 30.0000 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 3.9990 chunk 298 optimal weight: 0.7980 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN A 564 GLN A 658 ASN ** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 564 GLN C 99 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.116746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.066100 restraints weight = 87306.074| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 5.27 r_work: 0.2874 rms_B_bonded: 5.06 restraints_weight: 2.0000 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.0803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 28721 Z= 0.220 Angle : 0.678 22.174 39231 Z= 0.317 Chirality : 0.048 0.368 4565 Planarity : 0.004 0.045 4982 Dihedral : 14.821 122.340 5083 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 0.27 % Allowed : 5.05 % Favored : 94.68 % 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: 0.29 (0.14), residues: 3441 helix: 2.18 (0.21), residues: 656 sheet: 0.25 (0.17), residues: 872 loop : -0.52 (0.14), residues: 1913 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG C 403 TYR 0.019 0.001 TYR C1067 PHE 0.019 0.001 PHE A 906 TRP 0.009 0.001 TRP A 436 HIS 0.004 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00506 (28614) covalent geometry : angle 0.62837 (38957) SS BOND : bond 0.00262 ( 41) SS BOND : angle 1.35209 ( 82) hydrogen bonds : bond 0.04085 ( 1107) hydrogen bonds : angle 5.51303 ( 3057) Misc. bond : bond 0.00153 ( 2) link_BETA1-4 : bond 0.00471 ( 17) link_BETA1-4 : angle 2.22057 ( 51) link_NAG-ASN : bond 0.00576 ( 47) link_NAG-ASN : angle 4.00346 ( 141) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 3019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 78 time to evaluate : 0.976 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1010 GLN cc_start: 0.8703 (OUTLIER) cc_final: 0.8296 (mp10) REVERT: B 191 GLU cc_start: 0.9267 (mt-10) cc_final: 0.8307 (mp0) REVERT: B 740 MET cc_start: 0.9344 (mmm) cc_final: 0.8650 (tpp) REVERT: B 950 ASP cc_start: 0.9168 (t0) cc_final: 0.8946 (t0) REVERT: Z 52 TYR cc_start: 0.6753 (m-10) cc_final: 0.5641 (m-10) REVERT: Z 83 MET cc_start: 0.2943 (mpp) cc_final: 0.2201 (mmp) outliers start: 8 outliers final: 2 residues processed: 84 average time/residue: 0.1735 time to fit residues: 25.1191 Evaluate side-chains 70 residues out of total 3019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 67 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain Z residue 51 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 268 optimal weight: 2.9990 chunk 311 optimal weight: 0.9990 chunk 30 optimal weight: 0.0970 chunk 194 optimal weight: 2.9990 chunk 200 optimal weight: 0.9990 chunk 205 optimal weight: 0.8980 chunk 293 optimal weight: 0.7980 chunk 270 optimal weight: 0.0370 chunk 88 optimal weight: 1.9990 chunk 340 optimal weight: 6.9990 chunk 185 optimal weight: 7.9990 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 ASN ** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.117906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.068481 restraints weight = 87749.003| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 4.99 r_work: 0.2933 rms_B_bonded: 4.95 restraints_weight: 0.5000 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.1064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 28721 Z= 0.106 Angle : 0.608 21.858 39231 Z= 0.280 Chirality : 0.046 0.346 4565 Planarity : 0.004 0.046 4982 Dihedral : 12.083 121.626 5083 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.47 % Allowed : 7.11 % Favored : 92.42 % 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: 0.38 (0.14), residues: 3441 helix: 2.28 (0.21), residues: 653 sheet: 0.33 (0.17), residues: 882 loop : -0.49 (0.14), residues: 1906 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 995 TYR 0.017 0.001 TYR Z 105 PHE 0.013 0.001 PHE C 392 TRP 0.010 0.001 TRP B 104 HIS 0.003 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00234 (28614) covalent geometry : angle 0.56227 (38957) SS BOND : bond 0.00231 ( 41) SS BOND : angle 0.95986 ( 82) hydrogen bonds : bond 0.03471 ( 1107) hydrogen bonds : angle 5.22521 ( 3057) Misc. bond : bond 0.00086 ( 2) link_BETA1-4 : bond 0.00466 ( 17) link_BETA1-4 : angle 2.34021 ( 51) link_NAG-ASN : bond 0.00570 ( 47) link_NAG-ASN : angle 3.61067 ( 141) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 3019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 89 time to evaluate : 0.996 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.7221 (ppp) cc_final: 0.6947 (ppp) REVERT: A 571 ASP cc_start: 0.9097 (m-30) cc_final: 0.8715 (p0) REVERT: A 1010 GLN cc_start: 0.8626 (OUTLIER) cc_final: 0.8230 (mp10) REVERT: B 740 MET cc_start: 0.9341 (mmm) cc_final: 0.8565 (tpp) REVERT: C 492 LEU cc_start: 0.8341 (mp) cc_final: 0.7883 (tp) REVERT: C 515 PHE cc_start: 0.7894 (m-80) cc_final: 0.7488 (m-80) REVERT: C 661 GLU cc_start: 0.8325 (tm-30) cc_final: 0.8120 (tm-30) outliers start: 14 outliers final: 4 residues processed: 100 average time/residue: 0.1743 time to fit residues: 29.1359 Evaluate side-chains 79 residues out of total 3019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 74 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain Z residue 51 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 18 optimal weight: 1.9990 chunk 306 optimal weight: 3.9990 chunk 150 optimal weight: 40.0000 chunk 202 optimal weight: 0.5980 chunk 158 optimal weight: 1.9990 chunk 191 optimal weight: 2.9990 chunk 225 optimal weight: 9.9990 chunk 280 optimal weight: 3.9990 chunk 219 optimal weight: 10.0000 chunk 271 optimal weight: 0.9980 chunk 11 optimal weight: 9.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.116474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.065708 restraints weight = 87077.585| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 5.04 r_work: 0.2877 rms_B_bonded: 5.01 restraints_weight: 2.0000 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.1311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 28721 Z= 0.188 Angle : 0.631 21.091 39231 Z= 0.292 Chirality : 0.046 0.357 4565 Planarity : 0.003 0.037 4982 Dihedral : 10.824 120.683 5083 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 0.83 % Allowed : 8.81 % Favored : 90.36 % 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: 0.38 (0.14), residues: 3441 helix: 2.13 (0.21), residues: 666 sheet: 0.33 (0.17), residues: 886 loop : -0.45 (0.14), residues: 1889 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 815 TYR 0.036 0.001 TYR A 904 PHE 0.014 0.001 PHE B 898 TRP 0.012 0.001 TRP B 152 HIS 0.003 0.001 HIS A1083 Details of bonding type rmsd covalent geometry : bond 0.00432 (28614) covalent geometry : angle 0.58894 (38957) SS BOND : bond 0.00227 ( 41) SS BOND : angle 1.08549 ( 82) hydrogen bonds : bond 0.03690 ( 1107) hydrogen bonds : angle 5.21150 ( 3057) Misc. bond : bond 0.00034 ( 2) link_BETA1-4 : bond 0.00389 ( 17) link_BETA1-4 : angle 2.46350 ( 51) link_NAG-ASN : bond 0.00544 ( 47) link_NAG-ASN : angle 3.46723 ( 141) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 3019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 75 time to evaluate : 0.851 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.7212 (ppp) cc_final: 0.6701 (ppp) REVERT: A 571 ASP cc_start: 0.9133 (m-30) cc_final: 0.8771 (p0) REVERT: A 1010 GLN cc_start: 0.8752 (OUTLIER) cc_final: 0.8328 (mp10) REVERT: B 740 MET cc_start: 0.9404 (mmm) cc_final: 0.8671 (tpp) REVERT: C 324 GLU cc_start: 0.9147 (OUTLIER) cc_final: 0.8567 (pm20) REVERT: C 492 LEU cc_start: 0.8554 (mp) cc_final: 0.8133 (tp) outliers start: 25 outliers final: 9 residues processed: 98 average time/residue: 0.1718 time to fit residues: 28.4350 Evaluate side-chains 75 residues out of total 3019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 64 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain Z residue 51 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 18 optimal weight: 4.9990 chunk 280 optimal weight: 0.0010 chunk 143 optimal weight: 7.9990 chunk 177 optimal weight: 0.6980 chunk 293 optimal weight: 0.0060 chunk 229 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 85 optimal weight: 0.8980 chunk 223 optimal weight: 10.0000 chunk 123 optimal weight: 0.0020 chunk 46 optimal weight: 30.0000 overall best weight: 0.3210 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 ASN C 99 ASN C 207 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.118676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.071679 restraints weight = 88880.810| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 4.21 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.1474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.065 28721 Z= 0.095 Angle : 0.583 21.256 39231 Z= 0.268 Chirality : 0.045 0.334 4565 Planarity : 0.003 0.038 4982 Dihedral : 10.083 120.059 5083 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 0.80 % Allowed : 9.70 % Favored : 89.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.42 (0.14), residues: 3441 helix: 2.26 (0.21), residues: 653 sheet: 0.35 (0.17), residues: 904 loop : -0.44 (0.14), residues: 1884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 995 TYR 0.020 0.001 TYR Z 105 PHE 0.010 0.001 PHE A 133 TRP 0.008 0.001 TRP B 104 HIS 0.005 0.000 HIS Z 104 Details of bonding type rmsd covalent geometry : bond 0.00207 (28614) covalent geometry : angle 0.53741 (38957) SS BOND : bond 0.00315 ( 41) SS BOND : angle 1.46469 ( 82) hydrogen bonds : bond 0.03237 ( 1107) hydrogen bonds : angle 5.04054 ( 3057) Misc. bond : bond 0.00042 ( 2) link_BETA1-4 : bond 0.00481 ( 17) link_BETA1-4 : angle 2.57492 ( 51) link_NAG-ASN : bond 0.00537 ( 47) link_NAG-ASN : angle 3.35399 ( 141) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 3019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 75 time to evaluate : 0.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.6422 (ppp) cc_final: 0.5666 (ppp) REVERT: A 571 ASP cc_start: 0.9007 (m-30) cc_final: 0.8669 (p0) REVERT: A 1010 GLN cc_start: 0.8380 (OUTLIER) cc_final: 0.7915 (mp10) REVERT: B 740 MET cc_start: 0.9007 (mmm) cc_final: 0.8269 (tpp) REVERT: C 324 GLU cc_start: 0.9096 (OUTLIER) cc_final: 0.8572 (pm20) REVERT: C 505 TYR cc_start: 0.8237 (OUTLIER) cc_final: 0.7326 (m-80) REVERT: Z 83 MET cc_start: 0.1661 (mpp) cc_final: 0.0853 (mmp) outliers start: 24 outliers final: 10 residues processed: 96 average time/residue: 0.1551 time to fit residues: 25.8699 Evaluate side-chains 77 residues out of total 3019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 64 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain Z residue 51 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 260 optimal weight: 8.9990 chunk 58 optimal weight: 1.9990 chunk 152 optimal weight: 0.3980 chunk 187 optimal weight: 1.9990 chunk 22 optimal weight: 4.9990 chunk 62 optimal weight: 4.9990 chunk 219 optimal weight: 9.9990 chunk 324 optimal weight: 3.9990 chunk 130 optimal weight: 0.0270 chunk 205 optimal weight: 0.9980 chunk 335 optimal weight: 7.9990 overall best weight: 1.0842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 148 ASN C 207 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.116535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.067013 restraints weight = 87495.907| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 4.83 r_work: 0.2901 rms_B_bonded: 4.91 restraints_weight: 0.5000 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.1588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 28721 Z= 0.133 Angle : 0.594 20.780 39231 Z= 0.272 Chirality : 0.045 0.329 4565 Planarity : 0.003 0.038 4982 Dihedral : 9.443 119.729 5083 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 0.96 % Allowed : 9.77 % Favored : 89.27 % 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: 0.48 (0.15), residues: 3441 helix: 2.30 (0.21), residues: 654 sheet: 0.37 (0.17), residues: 897 loop : -0.39 (0.14), residues: 1890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 995 TYR 0.015 0.001 TYR A1067 PHE 0.014 0.001 PHE B 898 TRP 0.008 0.001 TRP A 436 HIS 0.002 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00305 (28614) covalent geometry : angle 0.54803 (38957) SS BOND : bond 0.00300 ( 41) SS BOND : angle 1.35728 ( 82) hydrogen bonds : bond 0.03384 ( 1107) hydrogen bonds : angle 5.00911 ( 3057) Misc. bond : bond 0.00017 ( 2) link_BETA1-4 : bond 0.00405 ( 17) link_BETA1-4 : angle 2.63514 ( 51) link_NAG-ASN : bond 0.00502 ( 47) link_NAG-ASN : angle 3.40360 ( 141) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 3019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 72 time to evaluate : 1.049 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.6875 (ppp) cc_final: 0.6114 (ppp) REVERT: A 571 ASP cc_start: 0.9125 (m-30) cc_final: 0.8756 (p0) REVERT: A 1010 GLN cc_start: 0.8758 (OUTLIER) cc_final: 0.8294 (mp10) REVERT: B 102 ARG cc_start: 0.7537 (mmt90) cc_final: 0.7276 (mmm160) REVERT: B 740 MET cc_start: 0.9400 (mmm) cc_final: 0.8665 (tpp) REVERT: C 505 TYR cc_start: 0.8885 (OUTLIER) cc_final: 0.8137 (m-80) REVERT: C 740 MET cc_start: 0.8967 (OUTLIER) cc_final: 0.8121 (tmm) outliers start: 29 outliers final: 12 residues processed: 98 average time/residue: 0.1653 time to fit residues: 27.7851 Evaluate side-chains 84 residues out of total 3019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 69 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 749 CYS Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain Z residue 51 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 214 optimal weight: 20.0000 chunk 287 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 255 optimal weight: 9.9990 chunk 306 optimal weight: 0.9980 chunk 204 optimal weight: 3.9990 chunk 332 optimal weight: 50.0000 chunk 27 optimal weight: 1.9990 chunk 223 optimal weight: 9.9990 chunk 35 optimal weight: 2.9990 chunk 310 optimal weight: 1.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 ASN C 164 ASN C 207 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.117231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.067507 restraints weight = 88536.349| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 5.24 r_work: 0.2926 rms_B_bonded: 4.91 restraints_weight: 0.5000 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.1873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 28721 Z= 0.223 Angle : 0.652 20.516 39231 Z= 0.304 Chirality : 0.046 0.323 4565 Planarity : 0.003 0.037 4982 Dihedral : 8.984 119.806 5083 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 1.10 % Allowed : 10.30 % Favored : 88.60 % 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: 0.41 (0.14), residues: 3441 helix: 2.28 (0.21), residues: 644 sheet: 0.34 (0.17), residues: 869 loop : -0.43 (0.14), residues: 1928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 577 TYR 0.020 0.001 TYR C 873 PHE 0.014 0.001 PHE B 898 TRP 0.012 0.001 TRP A 436 HIS 0.004 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00514 (28614) covalent geometry : angle 0.60909 (38957) SS BOND : bond 0.00280 ( 41) SS BOND : angle 1.46712 ( 82) hydrogen bonds : bond 0.03870 ( 1107) hydrogen bonds : angle 5.16742 ( 3057) Misc. bond : bond 0.00021 ( 2) link_BETA1-4 : bond 0.00388 ( 17) link_BETA1-4 : angle 2.72306 ( 51) link_NAG-ASN : bond 0.00540 ( 47) link_NAG-ASN : angle 3.45018 ( 141) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 3019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 69 time to evaluate : 0.845 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.6932 (ppp) cc_final: 0.6081 (ppp) REVERT: A 571 ASP cc_start: 0.9032 (m-30) cc_final: 0.8742 (p0) REVERT: A 1010 GLN cc_start: 0.8697 (OUTLIER) cc_final: 0.8293 (mp10) REVERT: B 102 ARG cc_start: 0.7303 (mmt90) cc_final: 0.7027 (mmm160) REVERT: C 505 TYR cc_start: 0.8893 (OUTLIER) cc_final: 0.8122 (m-80) REVERT: C 740 MET cc_start: 0.9100 (OUTLIER) cc_final: 0.8253 (tmm) REVERT: C 1050 MET cc_start: 0.8904 (ptp) cc_final: 0.8678 (ptp) outliers start: 33 outliers final: 17 residues processed: 99 average time/residue: 0.1722 time to fit residues: 29.0114 Evaluate side-chains 86 residues out of total 3019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 66 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 749 CYS Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain Z residue 51 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 106 optimal weight: 4.9990 chunk 263 optimal weight: 9.9990 chunk 153 optimal weight: 0.6980 chunk 183 optimal weight: 2.9990 chunk 71 optimal weight: 0.7980 chunk 81 optimal weight: 0.5980 chunk 270 optimal weight: 0.3980 chunk 244 optimal weight: 2.9990 chunk 226 optimal weight: 6.9990 chunk 108 optimal weight: 7.9990 chunk 15 optimal weight: 5.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.118843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.072089 restraints weight = 88781.273| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 4.00 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 28721 Z= 0.131 Angle : 0.599 20.746 39231 Z= 0.276 Chirality : 0.045 0.331 4565 Planarity : 0.003 0.038 4982 Dihedral : 8.577 118.627 5083 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 0.96 % Allowed : 10.83 % Favored : 88.20 % 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: 0.44 (0.14), residues: 3441 helix: 2.40 (0.21), residues: 640 sheet: 0.31 (0.17), residues: 877 loop : -0.42 (0.14), residues: 1924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 214 TYR 0.016 0.001 TYR A1067 PHE 0.011 0.001 PHE B 898 TRP 0.008 0.001 TRP A 436 HIS 0.002 0.000 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00301 (28614) covalent geometry : angle 0.55364 (38957) SS BOND : bond 0.00260 ( 41) SS BOND : angle 1.45637 ( 82) hydrogen bonds : bond 0.03492 ( 1107) hydrogen bonds : angle 5.02336 ( 3057) Misc. bond : bond 0.00012 ( 2) link_BETA1-4 : bond 0.00462 ( 17) link_BETA1-4 : angle 2.74961 ( 51) link_NAG-ASN : bond 0.00481 ( 47) link_NAG-ASN : angle 3.35048 ( 141) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 3019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 69 time to evaluate : 1.034 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.6298 (ppp) cc_final: 0.5325 (ppp) REVERT: A 1010 GLN cc_start: 0.8237 (OUTLIER) cc_final: 0.7807 (mp10) REVERT: C 324 GLU cc_start: 0.8917 (OUTLIER) cc_final: 0.8477 (pm20) REVERT: C 505 TYR cc_start: 0.8055 (OUTLIER) cc_final: 0.7096 (m-80) REVERT: C 740 MET cc_start: 0.8942 (OUTLIER) cc_final: 0.8064 (tmm) REVERT: Z 83 MET cc_start: 0.1749 (mpp) cc_final: 0.0864 (mmp) outliers start: 29 outliers final: 18 residues processed: 95 average time/residue: 0.1725 time to fit residues: 27.8563 Evaluate side-chains 87 residues out of total 3019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 65 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 749 CYS Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain Z residue 51 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 322 optimal weight: 0.8980 chunk 201 optimal weight: 0.7980 chunk 3 optimal weight: 6.9990 chunk 227 optimal weight: 7.9990 chunk 190 optimal weight: 0.6980 chunk 42 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 chunk 149 optimal weight: 1.9990 chunk 150 optimal weight: 30.0000 chunk 143 optimal weight: 8.9990 chunk 323 optimal weight: 30.0000 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.118379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.071317 restraints weight = 89051.023| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 4.04 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.2073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 28721 Z= 0.162 Angle : 0.612 20.552 39231 Z= 0.283 Chirality : 0.045 0.344 4565 Planarity : 0.003 0.038 4982 Dihedral : 8.175 118.120 5083 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 0.96 % Allowed : 10.97 % Favored : 88.07 % 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: 0.45 (0.14), residues: 3441 helix: 2.34 (0.21), residues: 646 sheet: 0.32 (0.17), residues: 892 loop : -0.40 (0.14), residues: 1903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 214 TYR 0.017 0.001 TYR C 873 PHE 0.012 0.001 PHE B 898 TRP 0.009 0.001 TRP A 436 HIS 0.002 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00373 (28614) covalent geometry : angle 0.56689 (38957) SS BOND : bond 0.00265 ( 41) SS BOND : angle 1.42844 ( 82) hydrogen bonds : bond 0.03549 ( 1107) hydrogen bonds : angle 5.02703 ( 3057) Misc. bond : bond 0.00017 ( 2) link_BETA1-4 : bond 0.00418 ( 17) link_BETA1-4 : angle 2.81363 ( 51) link_NAG-ASN : bond 0.00490 ( 47) link_NAG-ASN : angle 3.38747 ( 141) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 3019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 68 time to evaluate : 0.856 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.6286 (ppp) cc_final: 0.5346 (ppp) REVERT: A 1010 GLN cc_start: 0.8262 (OUTLIER) cc_final: 0.7835 (mp10) REVERT: A 1050 MET cc_start: 0.8430 (ptt) cc_final: 0.8216 (ptt) REVERT: B 102 ARG cc_start: 0.6594 (mmm160) cc_final: 0.6373 (mmm160) REVERT: C 324 GLU cc_start: 0.8958 (OUTLIER) cc_final: 0.8416 (pm20) REVERT: C 505 TYR cc_start: 0.8080 (OUTLIER) cc_final: 0.7110 (m-80) outliers start: 29 outliers final: 18 residues processed: 93 average time/residue: 0.1580 time to fit residues: 25.3632 Evaluate side-chains 87 residues out of total 3019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 66 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 749 CYS Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain Z residue 51 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 298 optimal weight: 0.7980 chunk 31 optimal weight: 5.9990 chunk 280 optimal weight: 0.8980 chunk 295 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 chunk 341 optimal weight: 4.9990 chunk 7 optimal weight: 0.9990 chunk 82 optimal weight: 0.5980 chunk 303 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 388 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.119217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.072404 restraints weight = 88323.338| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 4.07 r_work: 0.2987 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.2147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 28721 Z= 0.114 Angle : 0.587 20.668 39231 Z= 0.270 Chirality : 0.045 0.370 4565 Planarity : 0.003 0.038 4982 Dihedral : 7.822 117.030 5083 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 0.76 % Allowed : 11.07 % Favored : 88.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.47 (0.15), residues: 3441 helix: 2.43 (0.21), residues: 641 sheet: 0.25 (0.17), residues: 907 loop : -0.36 (0.14), residues: 1893 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 214 TYR 0.016 0.001 TYR A1067 PHE 0.009 0.001 PHE A1121 TRP 0.017 0.001 TRP B 152 HIS 0.002 0.000 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00259 (28614) covalent geometry : angle 0.54121 (38957) SS BOND : bond 0.00250 ( 41) SS BOND : angle 1.26142 ( 82) hydrogen bonds : bond 0.03311 ( 1107) hydrogen bonds : angle 4.92975 ( 3057) Misc. bond : bond 0.00018 ( 2) link_BETA1-4 : bond 0.00488 ( 17) link_BETA1-4 : angle 2.84373 ( 51) link_NAG-ASN : bond 0.00484 ( 47) link_NAG-ASN : angle 3.34279 ( 141) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 3019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 67 time to evaluate : 1.106 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.6667 (ppp) cc_final: 0.5713 (ppp) REVERT: A 396 TYR cc_start: 0.6614 (m-10) cc_final: 0.6407 (m-10) REVERT: A 1010 GLN cc_start: 0.8648 (OUTLIER) cc_final: 0.8236 (mp10) REVERT: C 324 GLU cc_start: 0.9121 (OUTLIER) cc_final: 0.8601 (pm20) REVERT: C 505 TYR cc_start: 0.8772 (OUTLIER) cc_final: 0.7935 (m-80) REVERT: Z 83 MET cc_start: 0.2801 (mpp) cc_final: 0.2105 (mmp) outliers start: 23 outliers final: 16 residues processed: 89 average time/residue: 0.1754 time to fit residues: 26.3720 Evaluate side-chains 84 residues out of total 3019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 65 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 749 CYS Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain Z residue 51 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 196 optimal weight: 3.9990 chunk 114 optimal weight: 0.7980 chunk 262 optimal weight: 10.0000 chunk 315 optimal weight: 2.9990 chunk 221 optimal weight: 9.9990 chunk 82 optimal weight: 1.9990 chunk 320 optimal weight: 0.8980 chunk 23 optimal weight: 0.5980 chunk 177 optimal weight: 0.9990 chunk 15 optimal weight: 4.9990 chunk 283 optimal weight: 4.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.123181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.073841 restraints weight = 80765.678| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 4.66 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.2204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 28721 Z= 0.130 Angle : 0.593 20.454 39231 Z= 0.274 Chirality : 0.045 0.384 4565 Planarity : 0.003 0.038 4982 Dihedral : 7.622 116.717 5083 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 0.80 % Allowed : 11.13 % Favored : 88.07 % 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: 0.48 (0.15), residues: 3441 helix: 2.45 (0.21), residues: 640 sheet: 0.26 (0.17), residues: 900 loop : -0.36 (0.14), residues: 1901 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 102 TYR 0.015 0.001 TYR A1067 PHE 0.015 0.001 PHE C 515 TRP 0.008 0.001 TRP A 436 HIS 0.002 0.000 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00298 (28614) covalent geometry : angle 0.54744 (38957) SS BOND : bond 0.00245 ( 41) SS BOND : angle 1.27396 ( 82) hydrogen bonds : bond 0.03381 ( 1107) hydrogen bonds : angle 4.91213 ( 3057) Misc. bond : bond 0.00011 ( 2) link_BETA1-4 : bond 0.00448 ( 17) link_BETA1-4 : angle 2.83181 ( 51) link_NAG-ASN : bond 0.00479 ( 47) link_NAG-ASN : angle 3.35375 ( 141) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8176.26 seconds wall clock time: 140 minutes 11.00 seconds (8411.00 seconds total)