Starting phenix.real_space_refine on Sun Jul 5 04:08:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8dlt_27515/07_2026/8dlt_27515.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dlt_27515/07_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/8dlt_27515/07_2026/8dlt_27515.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8dlt_27515/07_2026/8dlt_27515.cif" model { file = "/net/cci-nas-00/data/ceres_data/8dlt_27515/07_2026/8dlt_27515.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dlt_27515/07_2026/8dlt_27515.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8dlt_27515/07_2026/8dlt_27515.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dlt_27515/07_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-dev-6108/lib/python3.11/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 chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "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 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 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 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 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 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 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 chiralities: 8 Time building chain proxies: 5.92, per 1000 atoms: 0.23 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: 2.46 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: 1.04 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: 6.19 Time building geometry restraints manager: 3.27 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: 13777 17.89 - 35.78: 935 35.78 - 53.67: 137 53.67 - 71.57: 40 71.57 - 89.46: 30 Dihedral angle restraints: 14919 sinusoidal: 5841 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 14916 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: 6.480 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: 0.030 Extract box with map and model: 0.510 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 26.350 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.090 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:8.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 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 : 12.960 89.456 8949 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/Z covalent geometry : bond 0.00510 / 0.24 (25812) covalent geometry : angle 0.76479 / 0.40 (35133) SS BOND : bond 0.00295 / 0.24 ( 42) SS BOND : angle 1.12690 / 0.79 ( 84) hydrogen bonds : bond 0.19326 / 12.68 ( 917) hydrogen bonds : angle 8.09866 / 5.62 ( 2526) link_BETA1-4 : bond 0.00709 / 0.46 ( 18) link_BETA1-4 : angle 1.31271 / 0.90 ( 54) link_NAG-ASN : bond 0.00833 / 0.42 ( 42) link_NAG-ASN : angle 3.36388 / 2.83 ( 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 : 0.855 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: 0.5792 time to fit residues: 128.7293 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 : 0.888 ------------------------------------------------------------------------------- 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... A 211 ASN A 901 GLN A1002 GLN B 755 GLN B 955 ASN B1011 GLN C 394 ASN ** C 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.112578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.068024 restraints weight = 64258.295| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 3.38 r_work: 0.3017 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2899 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.1124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 25914 Z= 0.134 Angle : 0.571 15.752 35397 Z= 0.282 Chirality : 0.044 0.274 4155 Planarity : 0.004 0.047 4479 Dihedral : 4.197 21.492 3347 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 0.77 % Allowed : 4.68 % Favored : 94.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.15), residues: 3072 helix: 2.14 (0.20), residues: 647 sheet: 0.46 (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 A 577 TYR 0.015 0.001 TYR B 265 PHE 0.023 0.001 PHE A 906 TRP 0.011 0.001 TRP C 886 HIS 0.004 0.001 HIS A 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (25812) covalent geometry : angle 0.54139 / 0.28 (35133) SS BOND : bond 0.00157 / 0.13 ( 42) SS BOND : angle 0.62652 / 0.44 ( 84) hydrogen bonds : bond 0.04607 / 3.07 ( 917) hydrogen bonds : angle 6.22969 / 4.33 ( 2526) link_BETA1-4 : bond 0.00352 / 0.24 ( 18) link_BETA1-4 : angle 1.02699 / 0.71 ( 54) link_NAG-ASN : bond 0.00612 / 0.32 ( 42) link_NAG-ASN : angle 3.04872 / 2.39 ( 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 140 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 119 time to evaluate : 0.962 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.6288 (t70) cc_final: 0.6063 (t70) REVERT: A 1050 MET cc_start: 0.9487 (ptm) cc_final: 0.9283 (ptm) REVERT: B 237 ARG cc_start: 0.8526 (mmt90) cc_final: 0.8255 (mmm-85) REVERT: B 238 PHE cc_start: 0.6886 (p90) cc_final: 0.6414 (p90) REVERT: B 421 TYR cc_start: 0.8391 (m-80) cc_final: 0.7902 (m-80) REVERT: B 456 PHE cc_start: 0.6646 (m-80) cc_final: 0.6357 (m-80) REVERT: B 985 ASP cc_start: 0.8564 (p0) cc_final: 0.8061 (p0) REVERT: C 189 LEU cc_start: 0.8260 (tp) cc_final: 0.7889 (tp) REVERT: C 237 ARG cc_start: 0.7310 (OUTLIER) cc_final: 0.7063 (ttp80) REVERT: C 351 TYR cc_start: 0.9139 (p90) cc_final: 0.8137 (p90) REVERT: C 378 LYS cc_start: 0.8712 (mtpt) cc_final: 0.8287 (mmtp) REVERT: C 452 ARG cc_start: 0.8417 (OUTLIER) cc_final: 0.7645 (ttp80) REVERT: C 453 TYR cc_start: 0.8239 (p90) cc_final: 0.7998 (p90) REVERT: C 456 PHE cc_start: 0.8579 (m-80) cc_final: 0.8273 (m-80) outliers start: 21 outliers final: 8 residues processed: 134 average time/residue: 0.5900 time to fit residues: 93.4669 Evaluate side-chains 115 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 105 time to evaluate : 0.917 ------------------------------------------------------------------------------- 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 571 ASP 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: 5.9990 chunk 91 optimal weight: 3.9990 chunk 234 optimal weight: 0.0070 chunk 273 optimal weight: 0.8980 chunk 187 optimal weight: 6.9990 chunk 111 optimal weight: 10.0000 chunk 216 optimal weight: 0.8980 chunk 175 optimal weight: 2.9990 chunk 205 optimal weight: 2.9990 chunk 103 optimal weight: 4.9990 chunk 155 optimal weight: 6.9990 overall best weight: 1.5602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 239 GLN A 388 ASN B 69 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.111397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.066218 restraints weight = 64326.541| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 3.46 r_work: 0.2981 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2862 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.1478 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= 0.180 Angle : 0.559 13.989 35397 Z= 0.275 Chirality : 0.045 0.281 4155 Planarity : 0.004 0.039 4479 Dihedral : 4.142 21.030 3345 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 0.95 % Allowed : 5.67 % Favored : 93.38 % 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: 0.49 (0.15), residues: 3072 helix: 2.21 (0.20), residues: 671 sheet: 0.43 (0.19), residues: 707 loop : -0.48 (0.14), residues: 1694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 567 TYR 0.015 0.001 TYR B1067 PHE 0.023 0.001 PHE C 168 TRP 0.012 0.001 TRP A 64 HIS 0.003 0.001 HIS B 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.18 (25812) covalent geometry : angle 0.53090 / 0.27 (35133) SS BOND : bond 0.00188 / 0.16 ( 42) SS BOND : angle 0.60815 / 0.42 ( 84) hydrogen bonds : bond 0.04419 / 2.97 ( 917) hydrogen bonds : angle 5.81099 / 4.03 ( 2526) link_BETA1-4 : bond 0.00280 / 0.19 ( 18) link_BETA1-4 : angle 1.03150 / 0.71 ( 54) link_NAG-ASN : bond 0.00594 / 0.32 ( 42) link_NAG-ASN : angle 2.92195 / 2.31 ( 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 140 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 114 time to evaluate : 0.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.6319 (t70) cc_final: 0.6071 (t70) REVERT: A 990 GLU cc_start: 0.8892 (tt0) cc_final: 0.8561 (mt-10) REVERT: B 153 MET cc_start: 0.4877 (ppp) cc_final: 0.4584 (ppp) REVERT: B 237 ARG cc_start: 0.8522 (mmt90) cc_final: 0.8256 (mmm-85) REVERT: B 238 PHE cc_start: 0.6997 (p90) cc_final: 0.6412 (p90) REVERT: B 421 TYR cc_start: 0.8334 (m-80) cc_final: 0.7853 (m-80) REVERT: B 456 PHE cc_start: 0.6644 (OUTLIER) cc_final: 0.6358 (m-80) REVERT: B 985 ASP cc_start: 0.8562 (p0) cc_final: 0.8226 (p0) REVERT: C 83 VAL cc_start: 0.7468 (OUTLIER) cc_final: 0.7206 (p) REVERT: C 189 LEU cc_start: 0.8316 (tp) cc_final: 0.7958 (tp) REVERT: C 237 ARG cc_start: 0.7418 (OUTLIER) cc_final: 0.7092 (ttp-170) REVERT: C 351 TYR cc_start: 0.9190 (p90) cc_final: 0.8142 (p90) REVERT: C 378 LYS cc_start: 0.8762 (mtpt) cc_final: 0.8344 (mmtp) REVERT: C 452 ARG cc_start: 0.8398 (OUTLIER) cc_final: 0.7961 (mtp-110) REVERT: C 453 TYR cc_start: 0.8212 (p90) cc_final: 0.7959 (p90) REVERT: C 456 PHE cc_start: 0.8632 (m-80) cc_final: 0.8307 (m-80) REVERT: C 490 PHE cc_start: 0.7714 (t80) cc_final: 0.7508 (t80) outliers start: 26 outliers final: 9 residues processed: 130 average time/residue: 0.5047 time to fit residues: 78.6102 Evaluate side-chains 117 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 104 time to evaluate : 0.701 ------------------------------------------------------------------------------- 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 456 PHE Chi-restraints excluded: chain B residue 571 ASP 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 214 optimal weight: 0.1980 chunk 47 optimal weight: 6.9990 chunk 53 optimal weight: 9.9990 chunk 153 optimal weight: 4.9990 chunk 38 optimal weight: 40.0000 chunk 243 optimal weight: 2.9990 chunk 144 optimal weight: 10.0000 chunk 270 optimal weight: 4.9990 chunk 192 optimal weight: 0.7980 chunk 147 optimal weight: 2.9990 chunk 107 optimal weight: 8.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 824 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.109736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.064618 restraints weight = 64009.939| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 3.34 r_work: 0.2935 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2819 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 moved from start: 0.2015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 25914 Z= 0.255 Angle : 0.604 14.789 35397 Z= 0.299 Chirality : 0.047 0.289 4155 Planarity : 0.004 0.039 4479 Dihedral : 4.363 22.830 3345 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.10 % Allowed : 7.28 % Favored : 91.62 % 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: 0.31 (0.15), residues: 3072 helix: 2.05 (0.20), residues: 661 sheet: 0.14 (0.20), residues: 681 loop : -0.47 (0.14), residues: 1730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 567 TYR 0.017 0.001 TYR B1067 PHE 0.022 0.002 PHE A 906 TRP 0.019 0.002 TRP B 886 HIS 0.004 0.001 HIS C1058 Details of bonding type rmsd/Z covalent geometry : bond 0.00583 / 0.25 (25812) covalent geometry : angle 0.57728 / 0.29 (35133) SS BOND : bond 0.00253 / 0.21 ( 42) SS BOND : angle 0.68444 / 0.46 ( 84) hydrogen bonds : bond 0.04756 / 3.20 ( 917) hydrogen bonds : angle 5.77242 / 4.01 ( 2526) link_BETA1-4 : bond 0.00213 / 0.14 ( 18) link_BETA1-4 : angle 1.07535 / 0.74 ( 54) link_NAG-ASN : bond 0.00745 / 0.40 ( 42) link_NAG-ASN : angle 2.94653 / 2.30 ( 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 138 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 108 time to evaluate : 0.958 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.6169 (t70) cc_final: 0.5869 (t70) REVERT: B 53 ASP cc_start: 0.8519 (OUTLIER) cc_final: 0.8060 (t70) REVERT: B 153 MET cc_start: 0.4989 (ppp) cc_final: 0.4694 (ppp) REVERT: B 229 LEU cc_start: 0.8140 (mm) cc_final: 0.7928 (mp) REVERT: B 237 ARG cc_start: 0.8557 (mmt90) cc_final: 0.8191 (mmm-85) REVERT: B 238 PHE cc_start: 0.7207 (p90) cc_final: 0.6481 (p90) REVERT: B 269 TYR cc_start: 0.8232 (m-80) cc_final: 0.7937 (m-80) REVERT: B 380 TYR cc_start: 0.8934 (m-80) cc_final: 0.8673 (m-80) REVERT: B 421 TYR cc_start: 0.8353 (m-10) cc_final: 0.7859 (m-80) REVERT: B 456 PHE cc_start: 0.6670 (OUTLIER) cc_final: 0.6384 (m-80) REVERT: B 1029 MET cc_start: 0.9591 (tpp) cc_final: 0.9273 (tpp) REVERT: C 83 VAL cc_start: 0.7514 (OUTLIER) cc_final: 0.7291 (p) REVERT: C 189 LEU cc_start: 0.8412 (tp) cc_final: 0.8076 (tp) REVERT: C 378 LYS cc_start: 0.8750 (mtpt) cc_final: 0.8381 (mmtp) REVERT: C 453 TYR cc_start: 0.8201 (p90) cc_final: 0.7799 (p90) REVERT: C 456 PHE cc_start: 0.8762 (m-80) cc_final: 0.8508 (m-80) outliers start: 30 outliers final: 12 residues processed: 128 average time/residue: 0.4802 time to fit residues: 74.5032 Evaluate side-chains 115 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 100 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 392 PHE 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 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: 0.9990 chunk 97 optimal weight: 2.9990 chunk 279 optimal weight: 1.9990 chunk 100 optimal weight: 0.5980 chunk 246 optimal weight: 4.9990 chunk 83 optimal weight: 0.8980 chunk 61 optimal weight: 3.9990 chunk 190 optimal weight: 0.9990 chunk 33 optimal weight: 10.0000 chunk 141 optimal weight: 9.9990 chunk 254 optimal weight: 5.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B1010 GLN B1011 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.110896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.066180 restraints weight = 63599.444| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 3.17 r_work: 0.2979 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2858 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.2033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 25914 Z= 0.137 Angle : 0.533 13.361 35397 Z= 0.260 Chirality : 0.045 0.438 4155 Planarity : 0.003 0.042 4479 Dihedral : 4.108 21.764 3345 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 0.91 % Allowed : 8.53 % Favored : 90.56 % 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: 0.47 (0.15), residues: 3072 helix: 2.23 (0.21), residues: 666 sheet: 0.14 (0.19), residues: 714 loop : -0.36 (0.14), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 567 TYR 0.015 0.001 TYR B1067 PHE 0.018 0.001 PHE B 565 TRP 0.011 0.001 TRP A 64 HIS 0.002 0.000 HIS B 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 (25812) covalent geometry : angle 0.50711 / 0.25 (35133) SS BOND : bond 0.00210 / 0.19 ( 42) SS BOND : angle 0.64669 / 0.45 ( 84) hydrogen bonds : bond 0.04071 / 2.73 ( 917) hydrogen bonds : angle 5.52556 / 3.85 ( 2526) link_BETA1-4 : bond 0.00321 / 0.21 ( 18) link_BETA1-4 : angle 0.85872 / 0.60 ( 54) link_NAG-ASN : bond 0.00612 / 0.32 ( 42) link_NAG-ASN : angle 2.75215 / 2.27 ( 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 130 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 105 time to evaluate : 0.913 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.6181 (t70) cc_final: 0.5922 (t70) REVERT: A 990 GLU cc_start: 0.8883 (tt0) cc_final: 0.8577 (mt-10) REVERT: B 53 ASP cc_start: 0.8456 (OUTLIER) cc_final: 0.8028 (t70) REVERT: B 153 MET cc_start: 0.5011 (ppp) cc_final: 0.4724 (ppp) REVERT: B 237 ARG cc_start: 0.8546 (mmt90) cc_final: 0.8156 (mmm-85) REVERT: B 238 PHE cc_start: 0.7210 (p90) cc_final: 0.6450 (p90) REVERT: B 269 TYR cc_start: 0.8361 (m-80) cc_final: 0.8048 (m-80) REVERT: B 421 TYR cc_start: 0.8284 (m-10) cc_final: 0.8015 (m-80) REVERT: B 456 PHE cc_start: 0.6760 (OUTLIER) cc_final: 0.6462 (m-80) REVERT: B 985 ASP cc_start: 0.8636 (p0) cc_final: 0.8356 (p0) REVERT: B 987 PRO cc_start: 0.8889 (Cg_exo) cc_final: 0.8519 (Cg_endo) REVERT: C 83 VAL cc_start: 0.7514 (OUTLIER) cc_final: 0.7297 (p) REVERT: C 189 LEU cc_start: 0.8433 (tp) cc_final: 0.8114 (tp) REVERT: C 378 LYS cc_start: 0.8796 (mtpt) cc_final: 0.8444 (mmtp) REVERT: C 453 TYR cc_start: 0.8101 (p90) cc_final: 0.7794 (p90) REVERT: C 456 PHE cc_start: 0.8774 (m-80) cc_final: 0.8534 (m-80) outliers start: 25 outliers final: 12 residues processed: 123 average time/residue: 0.5229 time to fit residues: 77.2920 Evaluate side-chains 117 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 102 time to evaluate : 0.825 ------------------------------------------------------------------------------- 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 226 LEU Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 456 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 505 TYR 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 292 optimal weight: 3.9990 chunk 91 optimal weight: 0.9980 chunk 214 optimal weight: 2.9990 chunk 269 optimal weight: 1.9990 chunk 201 optimal weight: 4.9990 chunk 7 optimal weight: 7.9990 chunk 255 optimal weight: 9.9990 chunk 99 optimal weight: 3.9990 chunk 1 optimal weight: 0.8980 chunk 257 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B1011 GLN C 437 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.109939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.065012 restraints weight = 64198.071| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 3.19 r_work: 0.2946 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2827 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.2209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 25914 Z= 0.214 Angle : 0.565 13.603 35397 Z= 0.277 Chirality : 0.046 0.399 4155 Planarity : 0.004 0.045 4479 Dihedral : 4.169 22.306 3345 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.02 % Allowed : 8.96 % Favored : 90.01 % 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: 0.40 (0.15), residues: 3072 helix: 2.16 (0.21), residues: 669 sheet: 0.09 (0.19), residues: 699 loop : -0.40 (0.14), residues: 1704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C 452 TYR 0.016 0.001 TYR C1067 PHE 0.022 0.001 PHE A 168 TRP 0.013 0.001 TRP A 64 HIS 0.003 0.001 HIS B 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00487 / 0.21 (25812) covalent geometry : angle 0.53971 / 0.27 (35133) SS BOND : bond 0.00230 / 0.20 ( 42) SS BOND : angle 0.68784 / 0.46 ( 84) hydrogen bonds : bond 0.04363 / 2.94 ( 917) hydrogen bonds : angle 5.57757 / 3.87 ( 2526) link_BETA1-4 : bond 0.00261 / 0.16 ( 18) link_BETA1-4 : angle 0.99397 / 0.69 ( 54) link_NAG-ASN : bond 0.00646 / 0.34 ( 42) link_NAG-ASN : angle 2.78031 / 2.25 ( 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: 28 poor density : 105 time to evaluate : 0.930 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 ASP cc_start: 0.8972 (t0) cc_final: 0.8610 (t70) REVERT: A 64 TRP cc_start: 0.7614 (t60) cc_final: 0.7195 (t60) REVERT: A 66 HIS cc_start: 0.6147 (t70) cc_final: 0.5884 (t70) REVERT: A 990 GLU cc_start: 0.8885 (tt0) cc_final: 0.8573 (mt-10) REVERT: B 53 ASP cc_start: 0.8426 (OUTLIER) cc_final: 0.7980 (t70) REVERT: B 153 MET cc_start: 0.4848 (ppp) cc_final: 0.4618 (ppp) REVERT: B 191 GLU cc_start: 0.8603 (OUTLIER) cc_final: 0.8030 (mp0) REVERT: B 237 ARG cc_start: 0.8660 (mmt90) cc_final: 0.8235 (mmm-85) REVERT: B 238 PHE cc_start: 0.7260 (p90) cc_final: 0.6484 (p90) REVERT: B 269 TYR cc_start: 0.8275 (m-80) cc_final: 0.8010 (m-80) REVERT: B 380 TYR cc_start: 0.8929 (m-80) cc_final: 0.8691 (m-80) REVERT: B 421 TYR cc_start: 0.8334 (m-10) cc_final: 0.8065 (m-80) REVERT: B 456 PHE cc_start: 0.6680 (OUTLIER) cc_final: 0.6385 (m-80) REVERT: B 985 ASP cc_start: 0.8684 (p0) cc_final: 0.8315 (p0) REVERT: B 987 PRO cc_start: 0.8895 (Cg_exo) cc_final: 0.8450 (Cg_endo) REVERT: B 1029 MET cc_start: 0.9569 (tpp) cc_final: 0.9193 (tpp) REVERT: C 189 LEU cc_start: 0.8396 (tp) cc_final: 0.8016 (tp) REVERT: C 378 LYS cc_start: 0.8837 (mtpt) cc_final: 0.8490 (mmtp) REVERT: C 453 TYR cc_start: 0.8149 (p90) cc_final: 0.7769 (p90) REVERT: C 456 PHE cc_start: 0.8733 (m-80) cc_final: 0.8481 (m-80) outliers start: 28 outliers final: 15 residues processed: 124 average time/residue: 0.4746 time to fit residues: 71.1177 Evaluate side-chains 115 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 97 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL 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 456 PHE Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 900 MET 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 582 LEU 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: 8.9990 chunk 9 optimal weight: 7.9990 chunk 249 optimal weight: 0.7980 chunk 160 optimal weight: 0.8980 chunk 230 optimal weight: 7.9990 chunk 89 optimal weight: 1.9990 chunk 271 optimal weight: 0.6980 chunk 247 optimal weight: 9.9990 chunk 10 optimal weight: 0.9990 chunk 284 optimal weight: 0.5980 chunk 133 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.111043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.066693 restraints weight = 63859.743| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 3.16 r_work: 0.2981 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2867 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.2231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 25914 Z= 0.119 Angle : 0.529 13.220 35397 Z= 0.257 Chirality : 0.044 0.381 4155 Planarity : 0.003 0.042 4479 Dihedral : 4.015 24.860 3345 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.70 % Allowed : 9.33 % Favored : 89.97 % 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: 0.54 (0.15), residues: 3072 helix: 2.32 (0.21), residues: 667 sheet: 0.19 (0.19), residues: 694 loop : -0.33 (0.15), residues: 1711 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 567 TYR 0.014 0.001 TYR C1067 PHE 0.021 0.001 PHE A 168 TRP 0.010 0.001 TRP A 64 HIS 0.002 0.000 HIS B 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (25812) covalent geometry : angle 0.50351 / 0.25 (35133) SS BOND : bond 0.00213 / 0.18 ( 42) SS BOND : angle 0.85109 / 0.58 ( 84) hydrogen bonds : bond 0.03856 / 2.59 ( 917) hydrogen bonds : angle 5.38367 / 3.74 ( 2526) link_BETA1-4 : bond 0.00313 / 0.21 ( 18) link_BETA1-4 : angle 0.84478 / 0.59 ( 54) link_NAG-ASN : bond 0.00594 / 0.31 ( 42) link_NAG-ASN : angle 2.65206 / 2.18 ( 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 128 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 109 time to evaluate : 0.932 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 ASP cc_start: 0.8975 (t0) cc_final: 0.8617 (t70) REVERT: A 66 HIS cc_start: 0.6120 (t70) cc_final: 0.5885 (t70) REVERT: A 990 GLU cc_start: 0.8856 (tt0) cc_final: 0.8558 (mt-10) REVERT: B 53 ASP cc_start: 0.8377 (OUTLIER) cc_final: 0.7984 (t70) REVERT: B 153 MET cc_start: 0.4621 (ppp) cc_final: 0.4405 (ppp) REVERT: B 191 GLU cc_start: 0.8635 (OUTLIER) cc_final: 0.8084 (mp0) REVERT: B 226 LEU cc_start: 0.7984 (OUTLIER) cc_final: 0.7782 (mt) REVERT: B 237 ARG cc_start: 0.8589 (mmt90) cc_final: 0.8168 (mmm-85) REVERT: B 238 PHE cc_start: 0.7115 (p90) cc_final: 0.6392 (p90) REVERT: B 269 TYR cc_start: 0.8204 (m-80) cc_final: 0.7927 (m-80) REVERT: B 421 TYR cc_start: 0.8311 (m-10) cc_final: 0.8040 (m-80) REVERT: B 456 PHE cc_start: 0.6760 (OUTLIER) cc_final: 0.6452 (m-80) REVERT: B 985 ASP cc_start: 0.8620 (p0) cc_final: 0.8232 (p0) REVERT: B 987 PRO cc_start: 0.8785 (Cg_exo) cc_final: 0.8357 (Cg_endo) REVERT: B 990 GLU cc_start: 0.8414 (tm-30) cc_final: 0.8164 (tm-30) REVERT: C 83 VAL cc_start: 0.7513 (OUTLIER) cc_final: 0.7289 (p) REVERT: C 378 LYS cc_start: 0.8859 (mtpt) cc_final: 0.8498 (mmtp) REVERT: C 453 TYR cc_start: 0.8141 (p90) cc_final: 0.7750 (p90) REVERT: C 456 PHE cc_start: 0.8764 (m-80) cc_final: 0.8501 (m-80) outliers start: 19 outliers final: 11 residues processed: 122 average time/residue: 0.4744 time to fit residues: 70.5343 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 : 0.931 ------------------------------------------------------------------------------- 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 456 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 582 LEU 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: 7.9990 chunk 243 optimal weight: 6.9990 chunk 188 optimal weight: 3.9990 chunk 96 optimal weight: 0.9980 chunk 85 optimal weight: 2.9990 chunk 259 optimal weight: 5.9990 chunk 0 optimal weight: 30.0000 chunk 12 optimal weight: 6.9990 chunk 151 optimal weight: 4.9990 chunk 258 optimal weight: 0.9980 chunk 120 optimal weight: 5.9990 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 207 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.109018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.064229 restraints weight = 64302.313| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 3.07 r_work: 0.2916 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2801 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.2486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.090 25914 Z= 0.289 Angle : 0.614 13.585 35397 Z= 0.301 Chirality : 0.047 0.382 4155 Planarity : 0.004 0.039 4479 Dihedral : 4.270 22.640 3345 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.02 % Allowed : 9.59 % Favored : 89.39 % 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: 0.33 (0.15), residues: 3072 helix: 2.08 (0.20), residues: 675 sheet: 0.03 (0.19), residues: 691 loop : -0.44 (0.14), residues: 1706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 567 TYR 0.016 0.001 TYR C1067 PHE 0.020 0.002 PHE A 898 TRP 0.017 0.001 TRP A 64 HIS 0.004 0.001 HIS B 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00668 / 0.29 (25812) covalent geometry : angle 0.58935 / 0.30 (35133) SS BOND : bond 0.00263 / 0.21 ( 42) SS BOND : angle 0.87472 / 0.59 ( 84) hydrogen bonds : bond 0.04646 / 3.12 ( 917) hydrogen bonds : angle 5.62733 / 3.90 ( 2526) link_BETA1-4 : bond 0.00249 / 0.17 ( 18) link_BETA1-4 : angle 1.07775 / 0.75 ( 54) link_NAG-ASN : bond 0.00719 / 0.39 ( 42) link_NAG-ASN : angle 2.80990 / 2.25 ( 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 131 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 103 time to evaluate : 0.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ASP cc_start: 0.9007 (t0) cc_final: 0.8615 (t70) REVERT: A 66 HIS cc_start: 0.6046 (t70) cc_final: 0.5794 (t70) REVERT: A 990 GLU cc_start: 0.8931 (tt0) cc_final: 0.8643 (mt-10) REVERT: B 53 ASP cc_start: 0.8437 (OUTLIER) cc_final: 0.8031 (t70) REVERT: B 191 GLU cc_start: 0.8612 (OUTLIER) cc_final: 0.7590 (mp0) REVERT: B 237 ARG cc_start: 0.8709 (mmt90) cc_final: 0.8276 (mmm-85) REVERT: B 238 PHE cc_start: 0.7283 (p90) cc_final: 0.6522 (p90) REVERT: B 335 LEU cc_start: 0.8598 (OUTLIER) cc_final: 0.8128 (tm) REVERT: B 421 TYR cc_start: 0.8310 (m-10) cc_final: 0.8067 (m-80) REVERT: B 456 PHE cc_start: 0.6671 (OUTLIER) cc_final: 0.6372 (m-80) REVERT: B 985 ASP cc_start: 0.8705 (p0) cc_final: 0.8323 (p0) REVERT: B 987 PRO cc_start: 0.8825 (Cg_exo) cc_final: 0.8360 (Cg_endo) REVERT: B 990 GLU cc_start: 0.8477 (tm-30) cc_final: 0.8265 (tm-30) REVERT: B 1029 MET cc_start: 0.9585 (tpp) cc_final: 0.9252 (tpp) REVERT: C 378 LYS cc_start: 0.8828 (mtpt) cc_final: 0.8529 (mmtp) REVERT: C 453 TYR cc_start: 0.8117 (p90) cc_final: 0.7740 (p90) REVERT: C 456 PHE cc_start: 0.8680 (m-80) cc_final: 0.8389 (m-80) REVERT: C 531 THR cc_start: 0.8923 (OUTLIER) cc_final: 0.8659 (p) outliers start: 28 outliers final: 14 residues processed: 124 average time/residue: 0.4945 time to fit residues: 74.8965 Evaluate side-chains 116 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 97 time to evaluate : 0.915 ------------------------------------------------------------------------------- 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 226 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 582 LEU 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: 0.0020 chunk 311 optimal weight: 0.9990 chunk 212 optimal weight: 4.9990 chunk 267 optimal weight: 0.7980 chunk 292 optimal weight: 1.9990 chunk 100 optimal weight: 0.7980 chunk 270 optimal weight: 0.6980 chunk 84 optimal weight: 0.9980 chunk 242 optimal weight: 1.9990 chunk 121 optimal weight: 8.9990 chunk 195 optimal weight: 0.6980 overall best weight: 0.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.110759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 97)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.065387 restraints weight = 63856.760| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 3.32 r_work: 0.2978 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2863 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.2450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 25914 Z= 0.110 Angle : 0.542 13.122 35397 Z= 0.265 Chirality : 0.044 0.369 4155 Planarity : 0.003 0.045 4479 Dihedral : 4.059 21.090 3345 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 0.73 % Allowed : 10.03 % 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: 0.50 (0.15), residues: 3072 helix: 2.28 (0.21), residues: 669 sheet: 0.07 (0.19), residues: 706 loop : -0.31 (0.15), residues: 1697 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 567 TYR 0.014 0.001 TYR B1067 PHE 0.020 0.001 PHE A 168 TRP 0.013 0.001 TRP A 64 HIS 0.003 0.000 HIS B 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 (25812) covalent geometry : angle 0.51886 / 0.26 (35133) SS BOND : bond 0.00188 / 0.16 ( 42) SS BOND : angle 0.69816 / 0.49 ( 84) hydrogen bonds : bond 0.03891 / 2.61 ( 917) hydrogen bonds : angle 5.38446 / 3.74 ( 2526) link_BETA1-4 : bond 0.00331 / 0.22 ( 18) link_BETA1-4 : angle 0.84555 / 0.59 ( 54) link_NAG-ASN : bond 0.00585 / 0.31 ( 42) link_NAG-ASN : angle 2.64137 / 2.17 ( 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 131 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 111 time to evaluate : 0.956 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 ASP cc_start: 0.8963 (t0) cc_final: 0.8598 (t70) REVERT: A 66 HIS cc_start: 0.6035 (t70) cc_final: 0.5795 (t70) REVERT: A 990 GLU cc_start: 0.8858 (tt0) cc_final: 0.8541 (mt-10) REVERT: B 53 ASP cc_start: 0.8364 (OUTLIER) cc_final: 0.7974 (t70) REVERT: B 191 GLU cc_start: 0.8642 (OUTLIER) cc_final: 0.8066 (mp0) REVERT: B 201 PHE cc_start: 0.8180 (t80) cc_final: 0.7871 (t80) REVERT: B 226 LEU cc_start: 0.7931 (OUTLIER) cc_final: 0.7727 (mt) REVERT: B 237 ARG cc_start: 0.8623 (mmt90) cc_final: 0.8172 (mmm-85) REVERT: B 238 PHE cc_start: 0.7207 (p90) cc_final: 0.6615 (p90) REVERT: B 269 TYR cc_start: 0.8014 (m-80) cc_final: 0.7802 (m-10) REVERT: B 421 TYR cc_start: 0.8306 (m-10) cc_final: 0.8011 (m-80) REVERT: B 456 PHE cc_start: 0.6789 (OUTLIER) cc_final: 0.6476 (m-80) REVERT: B 985 ASP cc_start: 0.8659 (p0) cc_final: 0.8285 (p0) REVERT: B 987 PRO cc_start: 0.8791 (Cg_exo) cc_final: 0.8364 (Cg_endo) REVERT: C 378 LYS cc_start: 0.8896 (mtpt) cc_final: 0.8574 (mmtp) REVERT: C 453 TYR cc_start: 0.8199 (p90) cc_final: 0.7811 (p90) REVERT: C 456 PHE cc_start: 0.8747 (m-80) cc_final: 0.8480 (m-80) REVERT: C 505 TYR cc_start: 0.9069 (m-80) cc_final: 0.8481 (t80) REVERT: C 531 THR cc_start: 0.8991 (OUTLIER) cc_final: 0.8727 (p) outliers start: 20 outliers final: 11 residues processed: 127 average time/residue: 0.5164 time to fit residues: 79.0925 Evaluate side-chains 119 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 103 time to evaluate : 1.202 ------------------------------------------------------------------------------- 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 277 LEU Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 990 GLU 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: 3.9990 chunk 22 optimal weight: 3.9990 chunk 93 optimal weight: 0.9990 chunk 38 optimal weight: 0.0670 chunk 157 optimal weight: 2.9990 chunk 46 optimal weight: 30.0000 chunk 213 optimal weight: 9.9990 chunk 60 optimal weight: 0.9980 chunk 108 optimal weight: 5.9990 chunk 239 optimal weight: 9.9990 chunk 222 optimal weight: 2.9990 overall best weight: 1.6124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 87 ASN B 207 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.109938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.065508 restraints weight = 63826.575| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 3.13 r_work: 0.2948 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2830 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.2552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 25914 Z= 0.183 Angle : 0.561 13.237 35397 Z= 0.274 Chirality : 0.045 0.364 4155 Planarity : 0.003 0.040 4479 Dihedral : 4.085 21.403 3345 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 0.73 % Allowed : 10.25 % Favored : 89.02 % 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: 2.27 (0.21), residues: 669 sheet: 0.12 (0.19), residues: 687 loop : -0.33 (0.15), residues: 1716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 567 TYR 0.015 0.001 TYR C1067 PHE 0.022 0.001 PHE C 168 TRP 0.017 0.001 TRP A 64 HIS 0.002 0.001 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.18 (25812) covalent geometry : angle 0.53756 / 0.27 (35133) SS BOND : bond 0.00162 / 0.13 ( 42) SS BOND : angle 0.69748 / 0.48 ( 84) hydrogen bonds : bond 0.04148 / 2.78 ( 917) hydrogen bonds : angle 5.41653 / 3.76 ( 2526) link_BETA1-4 : bond 0.00260 / 0.17 ( 18) link_BETA1-4 : angle 0.97178 / 0.68 ( 54) link_NAG-ASN : bond 0.00609 / 0.31 ( 42) link_NAG-ASN : angle 2.68082 / 2.18 ( 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 123 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 103 time to evaluate : 0.929 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 ASP cc_start: 0.8983 (t0) cc_final: 0.8607 (t70) REVERT: A 66 HIS cc_start: 0.6051 (t70) cc_final: 0.5821 (t70) REVERT: A 990 GLU cc_start: 0.8874 (tt0) cc_final: 0.8574 (mt-10) REVERT: B 53 ASP cc_start: 0.8435 (OUTLIER) cc_final: 0.8033 (t70) REVERT: B 191 GLU cc_start: 0.8595 (OUTLIER) cc_final: 0.8043 (mp0) REVERT: B 237 ARG cc_start: 0.8718 (mmt90) cc_final: 0.8275 (mmm-85) REVERT: B 238 PHE cc_start: 0.7216 (p90) cc_final: 0.6653 (p90) REVERT: B 378 LYS cc_start: 0.8577 (OUTLIER) cc_final: 0.8217 (tmmt) REVERT: B 421 TYR cc_start: 0.8293 (m-10) cc_final: 0.8008 (m-80) REVERT: B 456 PHE cc_start: 0.6755 (OUTLIER) cc_final: 0.6469 (m-80) REVERT: B 985 ASP cc_start: 0.8665 (p0) cc_final: 0.8345 (p0) REVERT: B 987 PRO cc_start: 0.8776 (Cg_exo) cc_final: 0.8362 (Cg_endo) REVERT: C 378 LYS cc_start: 0.8899 (mtpt) cc_final: 0.8578 (mmtp) REVERT: C 453 TYR cc_start: 0.8162 (p90) cc_final: 0.7790 (p90) REVERT: C 456 PHE cc_start: 0.8743 (m-80) cc_final: 0.8481 (m-80) REVERT: C 531 THR cc_start: 0.8938 (OUTLIER) cc_final: 0.8657 (p) outliers start: 20 outliers final: 12 residues processed: 118 average time/residue: 0.4665 time to fit residues: 66.9834 Evaluate side-chains 116 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 99 time to evaluate : 0.867 ------------------------------------------------------------------------------- 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 277 LEU Chi-restraints excluded: chain B residue 378 LYS Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 531 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 68 optimal weight: 2.9990 chunk 287 optimal weight: 0.5980 chunk 70 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 chunk 100 optimal weight: 1.9990 chunk 273 optimal weight: 1.9990 chunk 223 optimal weight: 6.9990 chunk 305 optimal weight: 0.7980 chunk 1 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 chunk 241 optimal weight: 0.8980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 207 HIS C 370 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.110333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 87)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.064986 restraints weight = 63845.247| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 3.49 r_work: 0.2961 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.2848 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.2597 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= 0.151 Angle : 0.547 13.095 35397 Z= 0.267 Chirality : 0.045 0.359 4155 Planarity : 0.003 0.041 4479 Dihedral : 4.022 20.407 3345 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 0.66 % Allowed : 10.43 % Favored : 88.91 % 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: 0.52 (0.15), residues: 3072 helix: 2.29 (0.20), residues: 669 sheet: 0.11 (0.19), residues: 701 loop : -0.31 (0.15), residues: 1702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 567 TYR 0.014 0.001 TYR B1067 PHE 0.015 0.001 PHE A 898 TRP 0.019 0.001 TRP A 64 HIS 0.002 0.001 HIS B 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 (25812) covalent geometry : angle 0.52347 / 0.26 (35133) SS BOND : bond 0.00161 / 0.13 ( 42) SS BOND : angle 0.67311 / 0.47 ( 84) hydrogen bonds : bond 0.03957 / 2.65 ( 917) hydrogen bonds : angle 5.35227 / 3.72 ( 2526) link_BETA1-4 : bond 0.00283 / 0.19 ( 18) link_BETA1-4 : angle 0.88362 / 0.62 ( 54) link_NAG-ASN : bond 0.00580 / 0.30 ( 42) link_NAG-ASN : angle 2.63921 / 2.16 ( 126) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15153.47 seconds wall clock time: 257 minutes 23.78 seconds (15443.78 seconds total)