Starting phenix.real_space_refine on Tue Apr 7 05:52:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dlt_27515/04_2026/8dlt_27515.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dlt_27515/04_2026/8dlt_27515.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8dlt_27515/04_2026/8dlt_27515.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dlt_27515/04_2026/8dlt_27515.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8dlt_27515/04_2026/8dlt_27515.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dlt_27515/04_2026/8dlt_27515.map" } resolution = 2.4 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= 0.038 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 111 5.16 5 C 16059 2.51 5 N 4137 2.21 5 O 4938 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25245 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 8135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1040, 8135 Classifications: {'peptide': 1040} Link IDs: {'PTRANS': 56, 'TRANS': 983} Chain breaks: 7 Chain: "B" Number of atoms: 8135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1040, 8135 Classifications: {'peptide': 1040} Link IDs: {'PTRANS': 56, 'TRANS': 983} Chain breaks: 7 Chain: "C" Number of atoms: 8135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1040, 8135 Classifications: {'peptide': 1040} Link IDs: {'PTRANS': 56, 'TRANS': 983} Chain breaks: 7 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: "R" 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: "T" 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: "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: 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: "C" 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 Time building chain proxies: 5.53, per 1000 atoms: 0.22 Number of scatterers: 25245 At special positions: 0 Unit cell: (140, 146, 197, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 111 16.00 O 4938 8.00 N 4137 7.00 C 16059 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS 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 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 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 131 " - pdb=" SG CYS C 166 " 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=2.04 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 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 165 " " NAG A1304 " - " ASN A 234 " " NAG A1305 " - " ASN A 282 " " NAG A1306 " - " ASN A 331 " " NAG A1307 " - " ASN A 343 " " NAG A1308 " - " ASN A 709 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 165 " " NAG B1304 " - " ASN B 234 " " NAG B1305 " - " ASN B 282 " " NAG B1306 " - " ASN B 331 " " NAG B1307 " - " ASN B 343 " " NAG B1308 " - " ASN B 709 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 122 " " NAG C1303 " - " ASN C 165 " " NAG C1304 " - " ASN C 234 " " NAG C1305 " - " ASN C 282 " " NAG C1306 " - " ASN C 331 " " NAG C1307 " - " ASN C 343 " " NAG C1308 " - " ASN C 709 " " NAG D 1 " - " ASN A 17 " " NAG E 1 " - " ASN A 717 " " NAG F 1 " - " ASN A 801 " " NAG G 1 " - " ASN A1074 " " NAG H 1 " - " ASN A1098 " " NAG I 1 " - " ASN A1134 " " NAG J 1 " - " ASN B 17 " " NAG K 1 " - " ASN B 717 " " NAG L 1 " - " ASN B 801 " " NAG M 1 " - " ASN B1074 " " NAG N 1 " - " ASN B1098 " " NAG O 1 " - " ASN B1134 " " NAG P 1 " - " ASN C 17 " " NAG Q 1 " - " ASN C 717 " " NAG R 1 " - " ASN C 801 " " NAG S 1 " - " ASN C1074 " " NAG T 1 " - " ASN C1098 " " NAG U 1 " - " ASN C1134 " Time building additional restraints: 2.29 Conformation dependent library (CDL) restraints added in 1.1 seconds 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5844 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 42 sheets defined 25.1% alpha, 25.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.06 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.599A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 370 removed outlier: 3.815A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 387 removed outlier: 3.643A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 616 through 620 removed outlier: 4.015A pdb=" N VAL A 620 " --> pdb=" O CYS A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.571A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (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 Processing helix chain 'A' and resid 912 through 918 removed outlier: 4.035A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 940 Processing helix chain 'A' and resid 945 through 965 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 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.999A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1147 removed outlier: 3.556A pdb=" N LEU A1145 " --> pdb=" O LEU A1141 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASP A1146 " --> pdb=" O GLN A1142 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N SER A1147 " --> pdb=" O PRO A1143 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1141 through 1147' Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 removed outlier: 4.153A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 386 through 389 Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.083A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'B' and resid 616 through 620 removed outlier: 3.817A pdb=" N VAL B 620 " --> pdb=" O CYS B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.544A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 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 Processing helix chain 'B' and resid 912 through 918 removed outlier: 3.997A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 3.736A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1147 removed outlier: 3.612A pdb=" N LEU B1145 " --> pdb=" O LEU B1141 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.805A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 383 through 390 removed outlier: 3.658A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 409 removed outlier: 3.701A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 616 through 620 removed outlier: 3.973A pdb=" N VAL C 620 " --> pdb=" O CYS C 617 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.602A 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 890 Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.103A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.062A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1147 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 8.212A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR A 95 " --> pdb=" O ALA A 264 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ASN A 188 " --> pdb=" O GLU A 96 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU A 191 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS A 206 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.088A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 4.081A 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 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 84 through 85 current: chain 'A' and resid 116 through 121 removed outlier: 3.668A pdb=" N VAL A 126 " --> pdb=" O SER A 172 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 10.030A pdb=" N GLN A 134 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 9.235A pdb=" N ASN A 164 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 8.344A pdb=" N CYS A 136 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 10.445A pdb=" N SER A 162 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 11.077A pdb=" N ASP A 138 " --> pdb=" O TYR A 160 " (cutoff:3.500A) removed outlier: 8.471A pdb=" N TYR A 160 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLU A 156 " --> pdb=" O GLY A 142 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 318 removed outlier: 6.968A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.285A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.933A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 391 through 392 Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.098A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.513A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 701 through 703 removed outlier: 6.611A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 711 through 728 current: chain 'A' and resid 1059 through 1078 removed outlier: 3.756A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.197A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 787 through 790 removed outlier: 3.581A pdb=" N LYS A 790 " --> pdb=" O ASN C 703 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB8, first strand: chain 'B' and resid 27 through 30 removed outlier: 8.635A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASN B 188 " --> pdb=" O GLU B 96 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLU B 191 " --> pdb=" O LYS B 206 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS B 206 " --> pdb=" O GLU B 191 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 48 through 55 removed outlier: 4.119A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 84 through 85 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 84 through 85 current: chain 'B' and resid 116 through 121 removed outlier: 3.929A pdb=" N VAL B 126 " --> pdb=" O SER B 172 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER B 172 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N GLU B 132 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N CYS B 166 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 9.683A pdb=" N GLN B 134 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 8.712A pdb=" N ASN B 164 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 8.358A pdb=" N CYS B 136 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 10.544A pdb=" N SER B 162 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 10.150A pdb=" N ASP B 138 " --> pdb=" O TYR B 160 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N TYR B 160 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG B 158 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLU B 156 " --> pdb=" O GLY B 142 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N TYR B 144 " --> pdb=" O GLU B 154 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N GLU B 154 " --> pdb=" O TYR B 144 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 154 through 172 current: chain 'B' and resid 259 through 260 Processing sheet with id=AC2, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.212A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.009A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.540A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N VAL B 433 " --> pdb=" O LYS B 378 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N LYS B 378 " --> pdb=" O VAL B 433 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.885A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC7, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.768A pdb=" N TYR B 473 " --> pdb=" O TYR B 489 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.100A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.799A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 701 through 704 removed outlier: 6.484A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N LYS C 790 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N ASN B 703 " --> pdb=" O LYS C 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 728 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 711 through 728 current: chain 'B' and resid 1059 through 1078 removed outlier: 3.791A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.232A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD4, first strand: chain 'C' and resid 27 through 30 removed outlier: 3.734A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 78 through 79 current: chain 'C' and resid 189 through 197 removed outlier: 6.377A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.944A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 84 through 85 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 84 through 85 current: chain 'C' and resid 116 through 121 removed outlier: 3.622A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N GLU C 132 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N CYS C 166 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 9.689A pdb=" N GLN C 134 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 8.801A pdb=" N ASN C 164 " --> pdb=" O GLN C 134 " (cutoff:3.500A) removed outlier: 8.217A pdb=" N CYS C 136 " --> pdb=" O SER C 162 " (cutoff:3.500A) removed outlier: 10.258A pdb=" N SER C 162 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 10.844A pdb=" N ASP C 138 " --> pdb=" O TYR C 160 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N TYR C 160 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ARG C 158 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N TYR C 144 " --> pdb=" O GLU C 154 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N GLU C 154 " --> pdb=" O TYR C 144 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.220A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.876A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 361 through 362 removed outlier: 7.101A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE2, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.579A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.168A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.554A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 711 through 728 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 711 through 728 current: chain 'C' and resid 1059 through 1078 removed outlier: 3.777A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.137A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 1120 through 1122 917 hydrogen bonds defined for protein. 2526 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: 5.79 Time building geometry restraints manager: 3.10 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: 7985 1.34 - 1.47: 6384 1.47 - 1.59: 11305 1.59 - 1.71: 0 1.71 - 1.83: 138 Bond restraints: 25812 Sorted by residual: bond pdb=" CG LEU A 916 " pdb=" CD1 LEU A 916 " ideal model delta sigma weight residual 1.521 1.416 0.105 3.30e-02 9.18e+02 1.02e+01 bond pdb=" CG LEU B 916 " pdb=" CD1 LEU B 916 " ideal model delta sigma weight residual 1.521 1.429 0.092 3.30e-02 9.18e+02 7.80e+00 bond pdb=" CG LEU C 916 " pdb=" CD1 LEU C 916 " ideal model delta sigma weight residual 1.521 1.434 0.087 3.30e-02 9.18e+02 6.92e+00 bond pdb=" C1 NAG J 1 " pdb=" O5 NAG J 1 " ideal model delta sigma weight residual 1.406 1.454 -0.048 2.00e-02 2.50e+03 5.69e+00 bond pdb=" C1 NAG P 1 " pdb=" O5 NAG P 1 " ideal model delta sigma weight residual 1.406 1.454 -0.048 2.00e-02 2.50e+03 5.66e+00 ... (remaining 25807 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.27: 34320 2.27 - 4.54: 733 4.54 - 6.81: 60 6.81 - 9.09: 17 9.09 - 11.36: 3 Bond angle restraints: 35133 Sorted by residual: angle pdb=" N PRO B 986 " pdb=" CA PRO B 986 " pdb=" C PRO B 986 " ideal model delta sigma weight residual 110.70 116.57 -5.87 1.22e+00 6.72e-01 2.32e+01 angle pdb=" N PRO C 986 " pdb=" CA PRO C 986 " pdb=" C PRO C 986 " ideal model delta sigma weight residual 110.70 115.78 -5.08 1.22e+00 6.72e-01 1.73e+01 angle pdb=" N PRO A 986 " pdb=" CA PRO A 986 " pdb=" C PRO A 986 " ideal model delta sigma weight residual 110.70 115.63 -4.93 1.22e+00 6.72e-01 1.64e+01 angle pdb=" CA PRO B 986 " pdb=" C PRO B 986 " pdb=" N PRO B 987 " ideal model delta sigma weight residual 117.93 122.59 -4.66 1.20e+00 6.94e-01 1.51e+01 angle pdb=" CA PRO C 986 " pdb=" C PRO C 986 " pdb=" N PRO C 987 " ideal model delta sigma weight residual 117.93 122.18 -4.25 1.20e+00 6.94e-01 1.25e+01 ... (remaining 35128 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 14921 17.89 - 35.78: 990 35.78 - 53.67: 185 53.67 - 71.57: 53 71.57 - 89.46: 30 Dihedral angle restraints: 16179 sinusoidal: 7101 harmonic: 9078 Sorted by residual: dihedral pdb=" CA CYS B 379 " pdb=" C CYS B 379 " pdb=" N TYR B 380 " pdb=" CA TYR B 380 " ideal model delta harmonic sigma weight residual -180.00 -155.00 -25.00 0 5.00e+00 4.00e-02 2.50e+01 dihedral pdb=" CA PHE C 392 " pdb=" C PHE C 392 " pdb=" N THR C 393 " pdb=" CA THR C 393 " ideal model delta harmonic sigma weight residual 180.00 156.16 23.84 0 5.00e+00 4.00e-02 2.27e+01 dihedral pdb=" CA THR B 599 " pdb=" C THR B 599 " pdb=" N PRO B 600 " pdb=" CA PRO B 600 " ideal model delta harmonic sigma weight residual 180.00 158.75 21.25 0 5.00e+00 4.00e-02 1.81e+01 ... (remaining 16176 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 3519 0.078 - 0.156: 596 0.156 - 0.234: 35 0.234 - 0.312: 3 0.312 - 0.391: 2 Chirality restraints: 4155 Sorted by residual: chirality pdb=" C1 NAG P 1 " pdb=" ND2 ASN C 17 " pdb=" C2 NAG P 1 " pdb=" O5 NAG P 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.01 -0.39 2.00e-01 2.50e+01 3.81e+00 chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN A 17 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.08 -0.32 2.00e-01 2.50e+01 2.49e+00 chirality pdb=" CG LEU C 277 " pdb=" CB LEU C 277 " pdb=" CD1 LEU C 277 " pdb=" CD2 LEU C 277 " both_signs ideal model delta sigma weight residual False -2.59 -2.29 -0.30 2.00e-01 2.50e+01 2.24e+00 ... (remaining 4152 not shown) Planarity restraints: 4521 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 906 " 0.020 2.00e-02 2.50e+03 2.25e-02 8.87e+00 pdb=" CG PHE A 906 " -0.052 2.00e-02 2.50e+03 pdb=" CD1 PHE A 906 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 PHE A 906 " 0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE A 906 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 906 " 0.008 2.00e-02 2.50e+03 pdb=" CZ PHE A 906 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET B1029 " 0.014 2.00e-02 2.50e+03 2.80e-02 7.84e+00 pdb=" C MET B1029 " -0.048 2.00e-02 2.50e+03 pdb=" O MET B1029 " 0.018 2.00e-02 2.50e+03 pdb=" N SER B1030 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET C1029 " -0.013 2.00e-02 2.50e+03 2.64e-02 6.99e+00 pdb=" C MET C1029 " 0.046 2.00e-02 2.50e+03 pdb=" O MET C1029 " -0.017 2.00e-02 2.50e+03 pdb=" N SER C1030 " -0.015 2.00e-02 2.50e+03 ... (remaining 4518 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 2407 2.76 - 3.29: 23171 3.29 - 3.83: 42958 3.83 - 4.36: 50127 4.36 - 4.90: 86249 Nonbonded interactions: 204912 Sorted by model distance: nonbonded pdb=" OG1 THR C 323 " pdb=" OE1 GLU C 324 " model vdw 2.220 3.040 nonbonded pdb=" OE1 GLN B 115 " pdb=" OG1 THR B 167 " model vdw 2.263 3.040 nonbonded pdb=" OG1 THR C 109 " pdb=" OD1 ASP C 111 " model vdw 2.283 3.040 nonbonded pdb=" OG1 THR C 618 " pdb=" OE1 GLU C 619 " model vdw 2.290 3.040 nonbonded pdb=" O PRO C 85 " pdb=" OH TYR C 269 " model vdw 2.298 3.040 ... (remaining 204907 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' } 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.620 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: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 23.670 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.070 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:9.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 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 0.105 25914 Z= 0.237 Angle : 0.791 15.189 35397 Z= 0.407 Chirality : 0.055 0.391 4155 Planarity : 0.005 0.059 4479 Dihedral : 12.931 89.456 10209 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.21 (0.15), residues: 3072 helix: 1.57 (0.20), residues: 663 sheet: 0.59 (0.20), residues: 634 loop : -0.59 (0.14), residues: 1775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 983 TYR 0.021 0.002 TYR A 200 PHE 0.052 0.002 PHE A 906 TRP 0.034 0.002 TRP C 886 HIS 0.006 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00510 (25812) covalent geometry : angle 0.76479 (35133) SS BOND : bond 0.00295 ( 42) SS BOND : angle 1.12690 ( 84) hydrogen bonds : bond 0.19326 ( 917) hydrogen bonds : angle 8.09866 ( 2526) link_BETA1-4 : bond 0.00709 ( 18) link_BETA1-4 : angle 1.31271 ( 54) link_NAG-ASN : bond 0.00833 ( 42) link_NAG-ASN : angle 3.36388 ( 126) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 190 time to evaluate : 0.872 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 85 PRO cc_start: 0.8548 (Cg_exo) cc_final: 0.8055 (Cg_endo) REVERT: B 229 LEU cc_start: 0.8127 (mm) cc_final: 0.7899 (mt) REVERT: B 237 ARG cc_start: 0.8461 (mmt90) cc_final: 0.8151 (mmm-85) REVERT: B 238 PHE cc_start: 0.7233 (p90) cc_final: 0.6764 (p90) REVERT: B 394 ASN cc_start: 0.6626 (m-40) cc_final: 0.6189 (p0) REVERT: B 565 PHE cc_start: 0.8374 (p90) cc_final: 0.7880 (p90) REVERT: B 985 ASP cc_start: 0.8127 (p0) cc_final: 0.7611 (p0) REVERT: C 189 LEU cc_start: 0.8183 (tp) cc_final: 0.7931 (tp) REVERT: C 351 TYR cc_start: 0.8938 (p90) cc_final: 0.8015 (p90) REVERT: C 453 TYR cc_start: 0.8521 (p90) cc_final: 0.8038 (p90) REVERT: C 697 MET cc_start: 0.8818 (ptm) cc_final: 0.8615 (ptm) REVERT: C 1145 LEU cc_start: 0.7401 (pt) cc_final: 0.6914 (tm) outliers start: 0 outliers final: 1 residues processed: 190 average time/residue: 0.6066 time to fit residues: 134.1185 Evaluate side-chains 110 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 109 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 569 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 197 optimal weight: 0.0070 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 9.9990 chunk 183 optimal weight: 0.9990 chunk 298 optimal weight: 0.6980 overall best weight: 0.9402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 ASN A 901 GLN A1002 GLN B 955 ASN ** B1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN ** C 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.112518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.067661 restraints weight = 64353.040| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 3.50 r_work: 0.3016 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2898 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.1189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 25914 Z= 0.136 Angle : 0.573 16.284 35397 Z= 0.281 Chirality : 0.045 0.289 4155 Planarity : 0.004 0.048 4479 Dihedral : 6.766 53.607 4607 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 0.73 % Allowed : 4.68 % Favored : 94.58 % 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: 0.46 (0.15), residues: 3072 helix: 2.14 (0.20), residues: 647 sheet: 0.49 (0.20), residues: 667 loop : -0.46 (0.14), residues: 1758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 403 TYR 0.016 0.001 TYR B 265 PHE 0.023 0.001 PHE A 906 TRP 0.011 0.001 TRP A 64 HIS 0.005 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00301 (25812) covalent geometry : angle 0.53991 (35133) SS BOND : bond 0.00161 ( 42) SS BOND : angle 0.63048 ( 84) hydrogen bonds : bond 0.04403 ( 917) hydrogen bonds : angle 6.15517 ( 2526) link_BETA1-4 : bond 0.00299 ( 18) link_BETA1-4 : angle 1.10718 ( 54) link_NAG-ASN : bond 0.00606 ( 42) link_NAG-ASN : angle 3.17035 ( 126) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 119 time to evaluate : 0.903 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 TRP cc_start: 0.7516 (t60) cc_final: 0.7289 (t60) REVERT: B 237 ARG cc_start: 0.8522 (mmt90) cc_final: 0.8242 (mmm-85) REVERT: B 238 PHE cc_start: 0.6879 (p90) cc_final: 0.6410 (p90) REVERT: B 421 TYR cc_start: 0.8400 (m-80) cc_final: 0.7918 (m-80) REVERT: B 456 PHE cc_start: 0.6629 (m-80) cc_final: 0.6340 (m-80) REVERT: B 985 ASP cc_start: 0.8585 (p0) cc_final: 0.8052 (p0) REVERT: B 990 GLU cc_start: 0.8483 (tm-30) cc_final: 0.8254 (tm-30) REVERT: B 1029 MET cc_start: 0.9545 (tpp) cc_final: 0.9245 (tpp) REVERT: C 189 LEU cc_start: 0.8216 (tp) cc_final: 0.7840 (tp) REVERT: C 237 ARG cc_start: 0.7346 (OUTLIER) cc_final: 0.6923 (ttp-170) REVERT: C 351 TYR cc_start: 0.9156 (p90) cc_final: 0.8327 (p90) REVERT: C 378 LYS cc_start: 0.8739 (mtpt) cc_final: 0.8328 (mmtp) REVERT: C 452 ARG cc_start: 0.8447 (OUTLIER) cc_final: 0.7879 (mtm-85) REVERT: C 453 TYR cc_start: 0.8243 (p90) cc_final: 0.8020 (p90) REVERT: C 456 PHE cc_start: 0.8591 (m-80) cc_final: 0.8269 (m-80) outliers start: 20 outliers final: 7 residues processed: 132 average time/residue: 0.5761 time to fit residues: 89.1882 Evaluate side-chains 117 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 108 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 237 ARG Chi-restraints excluded: chain C residue 452 ARG Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 1010 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 305 optimal weight: 0.9980 chunk 91 optimal weight: 3.9990 chunk 234 optimal weight: 0.0980 chunk 273 optimal weight: 0.9980 chunk 187 optimal weight: 8.9990 chunk 111 optimal weight: 9.9990 chunk 216 optimal weight: 0.9980 chunk 175 optimal weight: 0.7980 chunk 205 optimal weight: 2.9990 chunk 103 optimal weight: 4.9990 chunk 155 optimal weight: 6.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 GLN B 87 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.112540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.067927 restraints weight = 64364.994| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 3.30 r_work: 0.3017 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2900 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.1425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 25914 Z= 0.116 Angle : 0.519 10.985 35397 Z= 0.256 Chirality : 0.044 0.288 4155 Planarity : 0.003 0.039 4479 Dihedral : 5.953 55.199 4605 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 0.88 % Allowed : 5.56 % Favored : 93.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.61 (0.15), residues: 3072 helix: 2.31 (0.20), residues: 659 sheet: 0.52 (0.19), residues: 706 loop : -0.39 (0.14), residues: 1707 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 567 TYR 0.016 0.001 TYR C 505 PHE 0.024 0.001 PHE C 168 TRP 0.006 0.001 TRP C 886 HIS 0.003 0.000 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00256 (25812) covalent geometry : angle 0.49354 (35133) SS BOND : bond 0.00157 ( 42) SS BOND : angle 0.58381 ( 84) hydrogen bonds : bond 0.04070 ( 917) hydrogen bonds : angle 5.68944 ( 2526) link_BETA1-4 : bond 0.00332 ( 18) link_BETA1-4 : angle 1.05088 ( 54) link_NAG-ASN : bond 0.00574 ( 42) link_NAG-ASN : angle 2.63614 ( 126) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 122 time to evaluate : 0.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 TRP cc_start: 0.7479 (t60) cc_final: 0.7117 (t60) REVERT: A 990 GLU cc_start: 0.8807 (tt0) cc_final: 0.8473 (mt-10) REVERT: B 153 MET cc_start: 0.4931 (ppp) cc_final: 0.4651 (ppp) REVERT: B 237 ARG cc_start: 0.8509 (mmt90) cc_final: 0.8244 (mmm-85) REVERT: B 238 PHE cc_start: 0.6901 (p90) cc_final: 0.6391 (p90) REVERT: B 421 TYR cc_start: 0.8394 (m-80) cc_final: 0.7906 (m-80) REVERT: B 456 PHE cc_start: 0.6717 (m-10) cc_final: 0.6458 (m-80) REVERT: B 985 ASP cc_start: 0.8553 (p0) cc_final: 0.8221 (p0) REVERT: C 83 VAL cc_start: 0.7384 (OUTLIER) cc_final: 0.7124 (p) REVERT: C 189 LEU cc_start: 0.8325 (tp) cc_final: 0.7840 (tp) REVERT: C 237 ARG cc_start: 0.7384 (OUTLIER) cc_final: 0.7037 (ttp-170) REVERT: C 351 TYR cc_start: 0.9177 (p90) cc_final: 0.8498 (p90) REVERT: C 378 LYS cc_start: 0.8708 (mtpt) cc_final: 0.8320 (mmtp) REVERT: C 453 TYR cc_start: 0.8204 (p90) cc_final: 0.7973 (p90) REVERT: C 456 PHE cc_start: 0.8663 (m-80) cc_final: 0.8347 (m-80) outliers start: 24 outliers final: 8 residues processed: 136 average time/residue: 0.5405 time to fit residues: 87.2545 Evaluate side-chains 114 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 104 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 237 ARG Chi-restraints excluded: chain C residue 452 ARG Chi-restraints excluded: chain C residue 1010 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 214 optimal weight: 8.9990 chunk 47 optimal weight: 20.0000 chunk 53 optimal weight: 10.0000 chunk 153 optimal weight: 3.9990 chunk 38 optimal weight: 9.9990 chunk 243 optimal weight: 5.9990 chunk 144 optimal weight: 10.0000 chunk 270 optimal weight: 1.9990 chunk 192 optimal weight: 0.8980 chunk 147 optimal weight: 7.9990 chunk 107 optimal weight: 4.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 ASN A 824 ASN ** B 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 121 ASN B 755 GLN B1011 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.108962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.063718 restraints weight = 64209.933| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 3.25 r_work: 0.2911 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2803 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.2074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.092 25914 Z= 0.363 Angle : 0.694 15.463 35397 Z= 0.340 Chirality : 0.049 0.308 4155 Planarity : 0.004 0.039 4479 Dihedral : 6.343 59.772 4605 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.21 % Allowed : 7.35 % Favored : 91.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.15 (0.15), residues: 3072 helix: 1.76 (0.20), residues: 679 sheet: 0.08 (0.19), residues: 704 loop : -0.55 (0.14), residues: 1689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 567 TYR 0.019 0.002 TYR B1067 PHE 0.026 0.002 PHE A 906 TRP 0.022 0.002 TRP C 886 HIS 0.005 0.001 HIS C1058 Details of bonding type rmsd covalent geometry : bond 0.00832 (25812) covalent geometry : angle 0.66725 (35133) SS BOND : bond 0.00314 ( 42) SS BOND : angle 0.77311 ( 84) hydrogen bonds : bond 0.05278 ( 917) hydrogen bonds : angle 5.96595 ( 2526) link_BETA1-4 : bond 0.00270 ( 18) link_BETA1-4 : angle 1.34772 ( 54) link_NAG-ASN : bond 0.00832 ( 42) link_NAG-ASN : angle 3.17045 ( 126) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 107 time to evaluate : 0.906 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.6095 (t70) cc_final: 0.5871 (t70) REVERT: B 53 ASP cc_start: 0.8458 (OUTLIER) cc_final: 0.8008 (t70) REVERT: B 153 MET cc_start: 0.4913 (ppp) cc_final: 0.4646 (ppp) REVERT: B 229 LEU cc_start: 0.7950 (mm) cc_final: 0.7727 (mp) REVERT: B 237 ARG cc_start: 0.8655 (mmt90) cc_final: 0.8287 (mmm-85) REVERT: B 238 PHE cc_start: 0.7220 (p90) cc_final: 0.6458 (p90) REVERT: B 269 TYR cc_start: 0.8229 (m-80) cc_final: 0.7808 (m-80) REVERT: B 380 TYR cc_start: 0.8925 (m-80) cc_final: 0.8676 (m-80) REVERT: B 421 TYR cc_start: 0.8408 (m-10) cc_final: 0.8113 (m-80) REVERT: B 456 PHE cc_start: 0.6629 (OUTLIER) cc_final: 0.6353 (m-80) REVERT: C 83 VAL cc_start: 0.7572 (OUTLIER) cc_final: 0.7338 (p) REVERT: C 189 LEU cc_start: 0.8338 (tp) cc_final: 0.8029 (tp) REVERT: C 351 TYR cc_start: 0.9174 (p90) cc_final: 0.8213 (p90) REVERT: C 378 LYS cc_start: 0.8686 (mtpt) cc_final: 0.8324 (mmtp) REVERT: C 452 ARG cc_start: 0.8391 (OUTLIER) cc_final: 0.7922 (mtp-110) REVERT: C 453 TYR cc_start: 0.8110 (p90) cc_final: 0.7802 (p90) REVERT: C 456 PHE cc_start: 0.8663 (m-80) cc_final: 0.8424 (m-80) REVERT: C 490 PHE cc_start: 0.7773 (t80) cc_final: 0.7573 (t80) outliers start: 33 outliers final: 14 residues processed: 128 average time/residue: 0.4901 time to fit residues: 75.5506 Evaluate side-chains 120 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 102 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 452 ARG Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 1010 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 295 optimal weight: 0.9980 chunk 97 optimal weight: 3.9990 chunk 279 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 246 optimal weight: 0.0470 chunk 83 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 190 optimal weight: 0.8980 chunk 33 optimal weight: 9.9990 chunk 141 optimal weight: 9.9990 chunk 254 optimal weight: 3.9990 overall best weight: 0.9480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 69 HIS B 121 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.110862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.066327 restraints weight = 63695.582| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 3.21 r_work: 0.2975 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2855 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.1995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 25914 Z= 0.130 Angle : 0.535 10.989 35397 Z= 0.262 Chirality : 0.044 0.285 4155 Planarity : 0.003 0.040 4479 Dihedral : 5.746 52.896 4605 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 0.91 % Allowed : 8.16 % Favored : 90.93 % 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 (0.15), residues: 3072 helix: 2.15 (0.20), residues: 666 sheet: 0.13 (0.19), residues: 719 loop : -0.40 (0.14), residues: 1687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 567 TYR 0.016 0.001 TYR B1067 PHE 0.026 0.001 PHE C 168 TRP 0.017 0.001 TRP A 64 HIS 0.002 0.000 HIS B 66 Details of bonding type rmsd covalent geometry : bond 0.00290 (25812) covalent geometry : angle 0.50791 (35133) SS BOND : bond 0.00206 ( 42) SS BOND : angle 0.63893 ( 84) hydrogen bonds : bond 0.04132 ( 917) hydrogen bonds : angle 5.58904 ( 2526) link_BETA1-4 : bond 0.00358 ( 18) link_BETA1-4 : angle 0.96967 ( 54) link_NAG-ASN : bond 0.00561 ( 42) link_NAG-ASN : angle 2.76674 ( 126) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 109 time to evaluate : 0.940 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.6062 (t70) cc_final: 0.5790 (t70) REVERT: A 990 GLU cc_start: 0.8882 (tt0) cc_final: 0.8571 (mt-10) REVERT: B 53 ASP cc_start: 0.8434 (OUTLIER) cc_final: 0.7992 (t70) REVERT: B 153 MET cc_start: 0.5027 (ppp) cc_final: 0.4733 (ppp) REVERT: B 237 ARG cc_start: 0.8567 (mmt90) cc_final: 0.8179 (mmm-85) REVERT: B 238 PHE cc_start: 0.7248 (p90) cc_final: 0.6476 (p90) REVERT: B 269 TYR cc_start: 0.8350 (m-80) cc_final: 0.7981 (m-80) REVERT: B 421 TYR cc_start: 0.8323 (m-10) cc_final: 0.7835 (m-80) REVERT: B 985 ASP cc_start: 0.8680 (p0) cc_final: 0.8430 (p0) REVERT: C 83 VAL cc_start: 0.7550 (OUTLIER) cc_final: 0.7321 (p) REVERT: C 351 TYR cc_start: 0.9151 (p90) cc_final: 0.8556 (p90) REVERT: C 378 LYS cc_start: 0.8797 (mtpt) cc_final: 0.8443 (mmtp) REVERT: C 453 TYR cc_start: 0.8275 (p90) cc_final: 0.7978 (p90) REVERT: C 456 PHE cc_start: 0.8731 (m-80) cc_final: 0.8434 (m-80) outliers start: 25 outliers final: 12 residues processed: 126 average time/residue: 0.4725 time to fit residues: 72.2672 Evaluate side-chains 112 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 98 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 452 ARG Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1010 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 292 optimal weight: 3.9990 chunk 91 optimal weight: 0.7980 chunk 214 optimal weight: 2.9990 chunk 269 optimal weight: 0.9990 chunk 201 optimal weight: 3.9990 chunk 7 optimal weight: 6.9990 chunk 255 optimal weight: 0.9980 chunk 99 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 257 optimal weight: 0.9990 chunk 4 optimal weight: 4.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1010 GLN B1011 GLN C 437 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.110986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.065904 restraints weight = 64159.763| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 3.47 r_work: 0.2978 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2862 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.2086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 25914 Z= 0.130 Angle : 0.524 11.252 35397 Z= 0.256 Chirality : 0.045 0.479 4155 Planarity : 0.003 0.040 4479 Dihedral : 5.338 52.890 4605 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 0.99 % Allowed : 8.78 % Favored : 90.23 % 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: 0.51 (0.15), residues: 3072 helix: 2.26 (0.20), residues: 667 sheet: 0.17 (0.19), residues: 708 loop : -0.33 (0.14), residues: 1697 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 567 TYR 0.015 0.001 TYR B1067 PHE 0.024 0.001 PHE A 168 TRP 0.011 0.001 TRP A 64 HIS 0.002 0.000 HIS B 66 Details of bonding type rmsd covalent geometry : bond 0.00293 (25812) covalent geometry : angle 0.50004 (35133) SS BOND : bond 0.00204 ( 42) SS BOND : angle 0.65376 ( 84) hydrogen bonds : bond 0.03939 ( 917) hydrogen bonds : angle 5.43260 ( 2526) link_BETA1-4 : bond 0.00286 ( 18) link_BETA1-4 : angle 0.98323 ( 54) link_NAG-ASN : bond 0.00526 ( 42) link_NAG-ASN : angle 2.57019 ( 126) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 106 time to evaluate : 0.723 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 TRP cc_start: 0.7705 (t60) cc_final: 0.7229 (t60) REVERT: A 66 HIS cc_start: 0.5910 (t70) cc_final: 0.5644 (t70) REVERT: A 990 GLU cc_start: 0.8869 (tt0) cc_final: 0.8562 (mt-10) REVERT: B 53 ASP cc_start: 0.8437 (OUTLIER) cc_final: 0.8015 (t70) REVERT: B 153 MET cc_start: 0.5000 (ppp) cc_final: 0.4741 (ppp) REVERT: B 191 GLU cc_start: 0.8559 (OUTLIER) cc_final: 0.8059 (mp0) REVERT: B 237 ARG cc_start: 0.8504 (mmt90) cc_final: 0.8109 (mmm-85) REVERT: B 238 PHE cc_start: 0.7133 (p90) cc_final: 0.6411 (p90) REVERT: B 269 TYR cc_start: 0.8268 (m-80) cc_final: 0.7947 (m-80) REVERT: B 421 TYR cc_start: 0.8331 (m-10) cc_final: 0.8054 (m-80) REVERT: B 456 PHE cc_start: 0.7022 (m-80) cc_final: 0.6732 (m-80) REVERT: B 985 ASP cc_start: 0.8681 (p0) cc_final: 0.8273 (p0) REVERT: B 987 PRO cc_start: 0.8782 (Cg_exo) cc_final: 0.8351 (Cg_endo) REVERT: C 83 VAL cc_start: 0.7424 (OUTLIER) cc_final: 0.7191 (p) REVERT: C 378 LYS cc_start: 0.8797 (mtpt) cc_final: 0.8461 (mmtp) REVERT: C 453 TYR cc_start: 0.8093 (p90) cc_final: 0.7741 (p90) REVERT: C 456 PHE cc_start: 0.8778 (m-80) cc_final: 0.8532 (m-80) outliers start: 27 outliers final: 10 residues processed: 126 average time/residue: 0.5029 time to fit residues: 76.2119 Evaluate side-chains 112 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 99 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 1010 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 29 optimal weight: 10.0000 chunk 9 optimal weight: 9.9990 chunk 249 optimal weight: 8.9990 chunk 160 optimal weight: 0.7980 chunk 230 optimal weight: 8.9990 chunk 89 optimal weight: 2.9990 chunk 271 optimal weight: 1.9990 chunk 247 optimal weight: 20.0000 chunk 10 optimal weight: 0.8980 chunk 284 optimal weight: 0.9980 chunk 133 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1011 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.110608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.065659 restraints weight = 63989.346| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 3.27 r_work: 0.2966 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2849 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.2235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 25914 Z= 0.160 Angle : 0.561 21.819 35397 Z= 0.269 Chirality : 0.045 0.385 4155 Planarity : 0.003 0.039 4479 Dihedral : 5.141 58.203 4605 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 0.88 % Allowed : 9.37 % Favored : 89.75 % 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: 0.51 (0.15), residues: 3072 helix: 2.28 (0.21), residues: 667 sheet: 0.14 (0.19), residues: 700 loop : -0.33 (0.14), residues: 1705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 567 TYR 0.015 0.001 TYR B1067 PHE 0.025 0.001 PHE C 168 TRP 0.012 0.001 TRP A 64 HIS 0.002 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00361 (25812) covalent geometry : angle 0.52038 (35133) SS BOND : bond 0.00280 ( 42) SS BOND : angle 0.71041 ( 84) hydrogen bonds : bond 0.04045 ( 917) hydrogen bonds : angle 5.39619 ( 2526) link_BETA1-4 : bond 0.00240 ( 18) link_BETA1-4 : angle 1.01699 ( 54) link_NAG-ASN : bond 0.00608 ( 42) link_NAG-ASN : angle 3.49718 ( 126) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 105 time to evaluate : 0.845 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 ASP cc_start: 0.8991 (t0) cc_final: 0.8642 (t70) REVERT: A 66 HIS cc_start: 0.5914 (t70) cc_final: 0.5683 (t70) REVERT: A 990 GLU cc_start: 0.8876 (tt0) cc_final: 0.8580 (mt-10) REVERT: B 53 ASP cc_start: 0.8444 (OUTLIER) cc_final: 0.8014 (t70) REVERT: B 191 GLU cc_start: 0.8624 (OUTLIER) cc_final: 0.7628 (mp0) REVERT: B 237 ARG cc_start: 0.8591 (mmt90) cc_final: 0.8177 (mmm-85) REVERT: B 238 PHE cc_start: 0.7225 (p90) cc_final: 0.6485 (p90) REVERT: B 269 TYR cc_start: 0.8282 (m-80) cc_final: 0.7997 (m-80) REVERT: B 421 TYR cc_start: 0.8313 (m-10) cc_final: 0.8023 (m-80) REVERT: B 456 PHE cc_start: 0.6981 (m-80) cc_final: 0.6660 (m-80) REVERT: B 985 ASP cc_start: 0.8666 (p0) cc_final: 0.8264 (p0) REVERT: B 987 PRO cc_start: 0.8715 (Cg_exo) cc_final: 0.8297 (Cg_endo) REVERT: C 237 ARG cc_start: 0.7595 (OUTLIER) cc_final: 0.7345 (ttp-170) REVERT: C 378 LYS cc_start: 0.8831 (mtpt) cc_final: 0.8477 (mmtp) REVERT: C 453 TYR cc_start: 0.8092 (p90) cc_final: 0.7782 (p90) REVERT: C 456 PHE cc_start: 0.8784 (m-80) cc_final: 0.8524 (m-80) outliers start: 24 outliers final: 11 residues processed: 122 average time/residue: 0.5019 time to fit residues: 73.8538 Evaluate side-chains 117 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 103 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain C residue 237 ARG Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1010 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 116 optimal weight: 9.9990 chunk 243 optimal weight: 5.9990 chunk 188 optimal weight: 0.9980 chunk 96 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 259 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 12 optimal weight: 9.9990 chunk 151 optimal weight: 0.8980 chunk 258 optimal weight: 0.8980 chunk 120 optimal weight: 5.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 437 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.110418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.065787 restraints weight = 64161.898| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 3.28 r_work: 0.2958 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2844 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.2339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 25914 Z= 0.177 Angle : 0.556 17.695 35397 Z= 0.269 Chirality : 0.045 0.381 4155 Planarity : 0.003 0.039 4479 Dihedral : 5.014 52.238 4605 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.99 % Allowed : 9.37 % Favored : 89.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.50 (0.15), residues: 3072 helix: 2.26 (0.21), residues: 668 sheet: 0.15 (0.19), residues: 702 loop : -0.34 (0.15), residues: 1702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 567 TYR 0.015 0.001 TYR B1067 PHE 0.020 0.001 PHE A 168 TRP 0.015 0.001 TRP A 64 HIS 0.002 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00404 (25812) covalent geometry : angle 0.52537 (35133) SS BOND : bond 0.00207 ( 42) SS BOND : angle 0.78819 ( 84) hydrogen bonds : bond 0.04089 ( 917) hydrogen bonds : angle 5.39682 ( 2526) link_BETA1-4 : bond 0.00255 ( 18) link_BETA1-4 : angle 1.01961 ( 54) link_NAG-ASN : bond 0.00582 ( 42) link_NAG-ASN : angle 3.00901 ( 126) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 102 time to evaluate : 0.700 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 ASP cc_start: 0.8979 (t0) cc_final: 0.8616 (t70) REVERT: A 64 TRP cc_start: 0.7690 (t60) cc_final: 0.7230 (t60) REVERT: A 66 HIS cc_start: 0.5931 (t70) cc_final: 0.5694 (t70) REVERT: A 990 GLU cc_start: 0.8869 (tt0) cc_final: 0.8563 (mt-10) REVERT: B 53 ASP cc_start: 0.8422 (OUTLIER) cc_final: 0.8020 (t70) REVERT: B 191 GLU cc_start: 0.8606 (OUTLIER) cc_final: 0.8044 (mp0) REVERT: B 237 ARG cc_start: 0.8642 (mmt90) cc_final: 0.8218 (mmm-85) REVERT: B 238 PHE cc_start: 0.7139 (p90) cc_final: 0.6410 (p90) REVERT: B 269 TYR cc_start: 0.8188 (m-10) cc_final: 0.7960 (m-80) REVERT: B 421 TYR cc_start: 0.8332 (m-10) cc_final: 0.8043 (m-80) REVERT: B 456 PHE cc_start: 0.6982 (m-80) cc_final: 0.6656 (m-80) REVERT: B 985 ASP cc_start: 0.8664 (p0) cc_final: 0.8270 (p0) REVERT: B 987 PRO cc_start: 0.8750 (Cg_exo) cc_final: 0.8316 (Cg_endo) REVERT: C 378 LYS cc_start: 0.8834 (mtpt) cc_final: 0.8497 (mmtp) REVERT: C 453 TYR cc_start: 0.8093 (p90) cc_final: 0.7774 (p90) REVERT: C 456 PHE cc_start: 0.8789 (m-80) cc_final: 0.8555 (m-80) REVERT: C 531 THR cc_start: 0.8939 (OUTLIER) cc_final: 0.8654 (p) outliers start: 27 outliers final: 16 residues processed: 122 average time/residue: 0.4798 time to fit residues: 71.2969 Evaluate side-chains 119 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 100 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1010 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 254 optimal weight: 10.0000 chunk 311 optimal weight: 2.9990 chunk 212 optimal weight: 1.9990 chunk 267 optimal weight: 0.7980 chunk 292 optimal weight: 3.9990 chunk 100 optimal weight: 0.9990 chunk 270 optimal weight: 0.7980 chunk 84 optimal weight: 2.9990 chunk 242 optimal weight: 0.7980 chunk 121 optimal weight: 1.9990 chunk 195 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.110872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.065911 restraints weight = 63820.672| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 3.51 r_work: 0.2973 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2854 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.2387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 25914 Z= 0.135 Angle : 0.535 15.399 35397 Z= 0.260 Chirality : 0.044 0.366 4155 Planarity : 0.003 0.039 4479 Dihedral : 4.824 52.668 4605 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 0.77 % Allowed : 9.88 % Favored : 89.35 % 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: 0.56 (0.15), residues: 3072 helix: 2.33 (0.21), residues: 668 sheet: 0.19 (0.19), residues: 701 loop : -0.31 (0.15), residues: 1703 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 567 TYR 0.015 0.001 TYR B1067 PHE 0.023 0.001 PHE C 168 TRP 0.013 0.001 TRP A 64 HIS 0.002 0.001 HIS B 66 Details of bonding type rmsd covalent geometry : bond 0.00307 (25812) covalent geometry : angle 0.50747 (35133) SS BOND : bond 0.00190 ( 42) SS BOND : angle 0.70570 ( 84) hydrogen bonds : bond 0.03878 ( 917) hydrogen bonds : angle 5.30418 ( 2526) link_BETA1-4 : bond 0.00286 ( 18) link_BETA1-4 : angle 0.96618 ( 54) link_NAG-ASN : bond 0.00538 ( 42) link_NAG-ASN : angle 2.81764 ( 126) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 104 time to evaluate : 0.798 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 ASP cc_start: 0.8979 (t0) cc_final: 0.8626 (t70) REVERT: A 66 HIS cc_start: 0.6019 (t70) cc_final: 0.5788 (t70) REVERT: A 990 GLU cc_start: 0.8892 (tt0) cc_final: 0.8595 (mt-10) REVERT: B 53 ASP cc_start: 0.8427 (OUTLIER) cc_final: 0.8021 (t70) REVERT: B 191 GLU cc_start: 0.8659 (OUTLIER) cc_final: 0.8074 (mp0) REVERT: B 237 ARG cc_start: 0.8638 (mmt90) cc_final: 0.8203 (mmm-85) REVERT: B 238 PHE cc_start: 0.7251 (p90) cc_final: 0.6497 (p90) REVERT: B 269 TYR cc_start: 0.8277 (m-10) cc_final: 0.7981 (m-80) REVERT: B 421 TYR cc_start: 0.8318 (m-10) cc_final: 0.8030 (m-80) REVERT: B 456 PHE cc_start: 0.7013 (m-80) cc_final: 0.6686 (m-80) REVERT: B 985 ASP cc_start: 0.8658 (p0) cc_final: 0.8284 (p0) REVERT: B 987 PRO cc_start: 0.8744 (Cg_exo) cc_final: 0.8320 (Cg_endo) REVERT: C 378 LYS cc_start: 0.8925 (mtpt) cc_final: 0.8590 (mmtp) REVERT: C 453 TYR cc_start: 0.8098 (p90) cc_final: 0.7779 (p90) REVERT: C 456 PHE cc_start: 0.8742 (m-80) cc_final: 0.8487 (m-80) REVERT: C 531 THR cc_start: 0.8973 (OUTLIER) cc_final: 0.8703 (p) outliers start: 21 outliers final: 14 residues processed: 119 average time/residue: 0.5120 time to fit residues: 73.7577 Evaluate side-chains 118 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 101 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1010 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 159 optimal weight: 5.9990 chunk 22 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 38 optimal weight: 0.2980 chunk 157 optimal weight: 0.7980 chunk 46 optimal weight: 8.9990 chunk 213 optimal weight: 10.0000 chunk 60 optimal weight: 0.9990 chunk 108 optimal weight: 4.9990 chunk 239 optimal weight: 9.9990 chunk 222 optimal weight: 0.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.110895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.066307 restraints weight = 63711.461| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 3.30 r_work: 0.2978 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2862 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.2452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 25914 Z= 0.134 Angle : 0.540 14.932 35397 Z= 0.262 Chirality : 0.044 0.359 4155 Planarity : 0.003 0.039 4479 Dihedral : 4.726 52.655 4605 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 0.59 % Allowed : 10.17 % Favored : 89.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.58 (0.15), residues: 3072 helix: 2.35 (0.21), residues: 668 sheet: 0.21 (0.19), residues: 701 loop : -0.30 (0.15), residues: 1703 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 567 TYR 0.014 0.001 TYR B1067 PHE 0.014 0.001 PHE A 898 TRP 0.017 0.001 TRP A 64 HIS 0.002 0.000 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00305 (25812) covalent geometry : angle 0.51380 (35133) SS BOND : bond 0.00190 ( 42) SS BOND : angle 0.70598 ( 84) hydrogen bonds : bond 0.03848 ( 917) hydrogen bonds : angle 5.27282 ( 2526) link_BETA1-4 : bond 0.00266 ( 18) link_BETA1-4 : angle 0.98180 ( 54) link_NAG-ASN : bond 0.00547 ( 42) link_NAG-ASN : angle 2.76569 ( 126) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 105 time to evaluate : 0.740 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 ASP cc_start: 0.8964 (t0) cc_final: 0.8610 (t70) REVERT: A 66 HIS cc_start: 0.5971 (t70) cc_final: 0.5747 (t70) REVERT: A 226 LEU cc_start: 0.8904 (mt) cc_final: 0.8620 (mp) REVERT: A 990 GLU cc_start: 0.8878 (tt0) cc_final: 0.8581 (mt-10) REVERT: B 53 ASP cc_start: 0.8367 (OUTLIER) cc_final: 0.7982 (t70) REVERT: B 191 GLU cc_start: 0.8630 (OUTLIER) cc_final: 0.8063 (mp0) REVERT: B 237 ARG cc_start: 0.8617 (mmt90) cc_final: 0.8185 (mmm-85) REVERT: B 238 PHE cc_start: 0.7188 (p90) cc_final: 0.6460 (p90) REVERT: B 269 TYR cc_start: 0.8150 (m-10) cc_final: 0.7895 (m-80) REVERT: B 421 TYR cc_start: 0.8363 (m-10) cc_final: 0.8056 (m-80) REVERT: B 456 PHE cc_start: 0.6996 (m-80) cc_final: 0.6660 (m-80) REVERT: B 985 ASP cc_start: 0.8663 (p0) cc_final: 0.8290 (p0) REVERT: B 987 PRO cc_start: 0.8731 (Cg_exo) cc_final: 0.8295 (Cg_endo) REVERT: C 378 LYS cc_start: 0.8902 (mtpt) cc_final: 0.8567 (mmtp) REVERT: C 453 TYR cc_start: 0.8117 (p90) cc_final: 0.7795 (p90) REVERT: C 456 PHE cc_start: 0.8776 (m-80) cc_final: 0.8529 (m-80) REVERT: C 531 THR cc_start: 0.8967 (OUTLIER) cc_final: 0.8716 (p) outliers start: 16 outliers final: 12 residues processed: 117 average time/residue: 0.5152 time to fit residues: 72.8344 Evaluate side-chains 116 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 101 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1010 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 68 optimal weight: 3.9990 chunk 287 optimal weight: 0.9980 chunk 70 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 273 optimal weight: 0.9990 chunk 223 optimal weight: 4.9990 chunk 305 optimal weight: 0.8980 chunk 1 optimal weight: 6.9990 chunk 60 optimal weight: 3.9990 chunk 241 optimal weight: 0.3980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 370 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.111120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.066763 restraints weight = 63800.592| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 3.22 r_work: 0.2990 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2871 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.2498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 25914 Z= 0.120 Angle : 0.531 14.405 35397 Z= 0.257 Chirality : 0.044 0.350 4155 Planarity : 0.003 0.038 4479 Dihedral : 4.595 52.828 4605 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 0.62 % Allowed : 10.21 % Favored : 89.17 % 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: 0.64 (0.15), residues: 3072 helix: 2.45 (0.21), residues: 661 sheet: 0.26 (0.19), residues: 702 loop : -0.28 (0.15), residues: 1709 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 567 TYR 0.014 0.001 TYR B1067 PHE 0.026 0.001 PHE A 168 TRP 0.017 0.001 TRP A 64 HIS 0.002 0.000 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00274 (25812) covalent geometry : angle 0.50507 (35133) SS BOND : bond 0.00189 ( 42) SS BOND : angle 0.68615 ( 84) hydrogen bonds : bond 0.03735 ( 917) hydrogen bonds : angle 5.21085 ( 2526) link_BETA1-4 : bond 0.00301 ( 18) link_BETA1-4 : angle 0.96377 ( 54) link_NAG-ASN : bond 0.00545 ( 42) link_NAG-ASN : angle 2.70625 ( 126) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15768.13 seconds wall clock time: 267 minutes 21.79 seconds (16041.79 seconds total)