Starting phenix.real_space_refine on Tue Aug 26 09:20:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dm7_27529/08_2025/8dm7_27529.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dm7_27529/08_2025/8dm7_27529.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8dm7_27529/08_2025/8dm7_27529.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dm7_27529/08_2025/8dm7_27529.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8dm7_27529/08_2025/8dm7_27529.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dm7_27529/08_2025/8dm7_27529.map" } resolution = 2.49 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= 0.022 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 175 5.16 5 C 22417 2.51 5 N 5791 2.21 5 O 6782 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 35165 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 8215 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1048, 8215 Classifications: {'peptide': 1048} Link IDs: {'PTRANS': 55, 'TRANS': 992} Chain breaks: 7 Chain: "B" Number of atoms: 8215 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1048, 8215 Classifications: {'peptide': 1048} Link IDs: {'PTRANS': 55, 'TRANS': 992} Chain breaks: 7 Chain: "C" Number of atoms: 8215 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1048, 8215 Classifications: {'peptide': 1048} Link IDs: {'PTRANS': 55, 'TRANS': 992} Chain breaks: 7 Chain: "D" Number of atoms: 4833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 593, 4833 Classifications: {'peptide': 593} Link IDs: {'PTRANS': 27, 'TRANS': 565} Chain: "E" Number of atoms: 4833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 593, 4833 Classifications: {'peptide': 593} Link IDs: {'PTRANS': 27, 'TRANS': 565} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "B" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "C" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 9.07, per 1000 atoms: 0.26 Number of scatterers: 35165 At special positions: 0 Unit cell: (136, 159, 237, 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 175 16.00 O 6782 8.00 N 5791 7.00 C 22417 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=46, 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=2.04 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.05 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.05 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=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.04 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=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 133 " - pdb=" SG CYS D 141 " distance=2.04 Simple disulfide: pdb=" SG CYS D 530 " - pdb=" SG CYS D 542 " distance=2.02 Simple disulfide: pdb=" SG CYS E 133 " - pdb=" SG CYS E 141 " distance=2.04 Simple disulfide: pdb=" SG CYS E 530 " - pdb=" SG CYS E 542 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG 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 V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 165 " " NAG A1303 " - " ASN A 234 " " NAG A1304 " - " ASN A 282 " " NAG A1305 " - " ASN A 331 " " NAG A1306 " - " ASN A 343 " " NAG A1307 " - " ASN A 709 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 165 " " NAG B1303 " - " ASN B 234 " " NAG B1304 " - " ASN B 282 " " NAG B1305 " - " ASN B 331 " " NAG B1306 " - " ASN B 343 " " NAG B1307 " - " ASN B 709 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 165 " " NAG C1303 " - " ASN C 234 " " NAG C1304 " - " ASN C 282 " " NAG C1305 " - " ASN C 331 " " NAG C1306 " - " ASN C 343 " " NAG C1307 " - " ASN C 709 " " NAG D 701 " - " ASN D 53 " " NAG D 702 " - " ASN D 546 " " NAG E 701 " - " ASN E 53 " " NAG E 702 " - " ASN E 546 " " NAG F 1 " - " ASN A 122 " " NAG G 1 " - " ASN A 717 " " NAG H 1 " - " ASN A 801 " " NAG I 1 " - " ASN A1074 " " NAG J 1 " - " ASN A1098 " " NAG K 1 " - " ASN A1134 " " NAG L 1 " - " ASN B 122 " " NAG M 1 " - " ASN B 717 " " NAG N 1 " - " ASN B 801 " " NAG O 1 " - " ASN B1074 " " NAG P 1 " - " ASN B1098 " " NAG Q 1 " - " ASN B1134 " " NAG R 1 " - " ASN C 122 " " NAG S 1 " - " ASN C 717 " " NAG T 1 " - " ASN C 801 " " NAG U 1 " - " ASN C1074 " " NAG V 1 " - " ASN C1098 " " NAG W 1 " - " ASN C1134 " Time building additional restraints: 3.40 Conformation dependent library (CDL) restraints added in 1.4 seconds Enol-peptide restraints added in 715.3 nanoseconds 8556 Ramachandran restraints generated. 4278 Oldfield, 0 Emsley, 4278 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8146 Finding SS restraints... Secondary structure from input PDB file: 136 helices and 54 sheets defined 38.0% alpha, 25.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.75 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.679A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 371 Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.279A pdb=" N SER A 408 " --> pdb=" O ASN A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 616 through 620 removed outlier: 4.038A 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: 3.649A 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 849 through 856 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 919 removed outlier: 3.859A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 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: 4.018A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 4.131A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.728A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 371 Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.312A pdb=" N SER B 408 " --> pdb=" O ASN B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 616 through 620 removed outlier: 4.023A 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: 3.645A 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 849 through 856 removed outlier: 3.684A pdb=" N ASN B 856 " --> pdb=" O ALA B 852 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 887 through 891 removed outlier: 3.713A pdb=" N GLY B 891 " --> pdb=" O PHE B 888 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 919 removed outlier: 3.887A 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: 3.917A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 4.124A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.967A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 371 Processing helix chain 'C' and resid 386 through 389 Processing helix chain 'C' and resid 404 through 410 removed outlier: 3.883A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N SER C 408 " --> pdb=" O ASN C 405 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 616 through 620 removed outlier: 3.821A 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: 3.613A 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 849 through 856 removed outlier: 4.175A pdb=" N ASN C 856 " --> pdb=" O ALA C 852 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 887 through 891 removed outlier: 3.756A pdb=" N GLY C 891 " --> pdb=" O PHE C 888 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 912 through 919 removed outlier: 3.922A 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 1032 removed outlier: 4.056A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 4.147A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'D' and resid 21 through 53 removed outlier: 4.081A pdb=" N GLN D 34 " --> pdb=" O ASN D 30 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLU D 35 " --> pdb=" O ASN D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 81 Processing helix chain 'D' and resid 82 through 83 No H-bonds generated for 'chain 'D' and resid 82 through 83' Processing helix chain 'D' and resid 84 through 88 removed outlier: 3.824A pdb=" N GLU D 87 " --> pdb=" O SER D 84 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE D 88 " --> pdb=" O LEU D 85 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 84 through 88' Processing helix chain 'D' and resid 90 through 101 Processing helix chain 'D' and resid 103 through 108 removed outlier: 3.685A pdb=" N SER D 106 " --> pdb=" O SER D 103 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ALA D 107 " --> pdb=" O GLY D 104 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU D 108 " --> pdb=" O SER D 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 103 through 108' Processing helix chain 'D' and resid 109 through 128 Processing helix chain 'D' and resid 147 through 155 Processing helix chain 'D' and resid 157 through 194 removed outlier: 5.019A pdb=" N GLN D 175 " --> pdb=" O GLU D 171 " (cutoff:3.500A) Proline residue: D 178 - end of helix removed outlier: 3.672A pdb=" N VAL D 185 " --> pdb=" O GLU D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 205 Processing helix chain 'D' and resid 206 through 208 No H-bonds generated for 'chain 'D' and resid 206 through 208' Processing helix chain 'D' and resid 218 through 231 removed outlier: 3.611A pdb=" N LEU D 222 " --> pdb=" O ASN D 218 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ILE D 223 " --> pdb=" O ARG D 219 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N GLU D 224 " --> pdb=" O ASN D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 252 Processing helix chain 'D' and resid 275 through 279 removed outlier: 3.711A pdb=" N TYR D 279 " --> pdb=" O THR D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 293 through 300 Processing helix chain 'D' and resid 303 through 318 Processing helix chain 'D' and resid 324 through 331 removed outlier: 3.632A pdb=" N TRP D 328 " --> pdb=" O THR D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 385 removed outlier: 3.712A pdb=" N TYR D 385 " --> pdb=" O TYR D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 386 through 388 No H-bonds generated for 'chain 'D' and resid 386 through 388' Processing helix chain 'D' and resid 389 through 393 Processing helix chain 'D' and resid 399 through 413 removed outlier: 3.876A pdb=" N GLY D 405 " --> pdb=" O HIS D 401 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N MET D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA D 413 " --> pdb=" O SER D 409 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 421 Processing helix chain 'D' and resid 431 through 447 removed outlier: 3.676A pdb=" N GLU D 435 " --> pdb=" O ASP D 431 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 465 removed outlier: 4.435A pdb=" N PHE D 452 " --> pdb=" O GLY D 448 " (cutoff:3.500A) Processing helix chain 'D' and resid 469 through 471 No H-bonds generated for 'chain 'D' and resid 469 through 471' Processing helix chain 'D' and resid 472 through 484 removed outlier: 3.614A pdb=" N LYS D 476 " --> pdb=" O GLN D 472 " (cutoff:3.500A) Processing helix chain 'D' and resid 499 through 502 removed outlier: 3.700A pdb=" N SER D 502 " --> pdb=" O ASP D 499 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 499 through 502' Processing helix chain 'D' and resid 503 through 508 Processing helix chain 'D' and resid 512 through 533 removed outlier: 4.307A pdb=" N TYR D 516 " --> pdb=" O PHE D 512 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N PHE D 523 " --> pdb=" O THR D 519 " (cutoff:3.500A) Processing helix chain 'D' and resid 538 through 542 Processing helix chain 'D' and resid 547 through 561 removed outlier: 4.036A pdb=" N MET D 557 " --> pdb=" O LYS D 553 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU D 560 " --> pdb=" O LYS D 556 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLY D 561 " --> pdb=" O MET D 557 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 575 Processing helix chain 'D' and resid 581 through 588 Processing helix chain 'D' and resid 588 through 598 Processing helix chain 'E' and resid 21 through 53 removed outlier: 3.571A pdb=" N GLN E 34 " --> pdb=" O ASN E 30 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASP E 38 " --> pdb=" O GLN E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 81 Processing helix chain 'E' and resid 82 through 83 No H-bonds generated for 'chain 'E' and resid 82 through 83' Processing helix chain 'E' and resid 84 through 88 removed outlier: 3.850A pdb=" N GLU E 87 " --> pdb=" O SER E 84 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE E 88 " --> pdb=" O LEU E 85 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 84 through 88' Processing helix chain 'E' and resid 90 through 101 Processing helix chain 'E' and resid 103 through 108 removed outlier: 3.694A pdb=" N SER E 106 " --> pdb=" O SER E 103 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA E 107 " --> pdb=" O GLY E 104 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU E 108 " --> pdb=" O SER E 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 103 through 108' Processing helix chain 'E' and resid 109 through 128 Processing helix chain 'E' and resid 147 through 155 Processing helix chain 'E' and resid 157 through 194 removed outlier: 4.978A pdb=" N GLN E 175 " --> pdb=" O GLU E 171 " (cutoff:3.500A) Proline residue: E 178 - end of helix removed outlier: 3.717A pdb=" N VAL E 185 " --> pdb=" O GLU E 181 " (cutoff:3.500A) Processing helix chain 'E' and resid 198 through 205 Processing helix chain 'E' and resid 206 through 208 No H-bonds generated for 'chain 'E' and resid 206 through 208' Processing helix chain 'E' and resid 218 through 231 removed outlier: 3.660A pdb=" N LEU E 222 " --> pdb=" O ASN E 218 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ILE E 223 " --> pdb=" O ARG E 219 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N GLU E 224 " --> pdb=" O ASN E 220 " (cutoff:3.500A) Processing helix chain 'E' and resid 233 through 252 Processing helix chain 'E' and resid 275 through 279 removed outlier: 3.729A pdb=" N TYR E 279 " --> pdb=" O THR E 276 " (cutoff:3.500A) Processing helix chain 'E' and resid 293 through 300 Processing helix chain 'E' and resid 303 through 318 Processing helix chain 'E' and resid 324 through 331 removed outlier: 3.637A pdb=" N TRP E 328 " --> pdb=" O THR E 324 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 385 removed outlier: 3.750A pdb=" N TYR E 385 " --> pdb=" O TYR E 381 " (cutoff:3.500A) Processing helix chain 'E' and resid 386 through 388 No H-bonds generated for 'chain 'E' and resid 386 through 388' Processing helix chain 'E' and resid 389 through 393 Processing helix chain 'E' and resid 399 through 413 removed outlier: 3.897A pdb=" N GLY E 405 " --> pdb=" O HIS E 401 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N MET E 408 " --> pdb=" O VAL E 404 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA E 413 " --> pdb=" O SER E 409 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 421 Processing helix chain 'E' and resid 431 through 447 removed outlier: 3.669A pdb=" N GLU E 435 " --> pdb=" O ASP E 431 " (cutoff:3.500A) Processing helix chain 'E' and resid 448 through 465 removed outlier: 4.456A pdb=" N PHE E 452 " --> pdb=" O GLY E 448 " (cutoff:3.500A) Processing helix chain 'E' and resid 469 through 471 No H-bonds generated for 'chain 'E' and resid 469 through 471' Processing helix chain 'E' and resid 472 through 484 removed outlier: 3.552A pdb=" N LYS E 476 " --> pdb=" O GLN E 472 " (cutoff:3.500A) Processing helix chain 'E' and resid 499 through 502 removed outlier: 3.688A pdb=" N SER E 502 " --> pdb=" O ASP E 499 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 499 through 502' Processing helix chain 'E' and resid 503 through 508 Processing helix chain 'E' and resid 512 through 533 removed outlier: 4.329A pdb=" N TYR E 516 " --> pdb=" O PHE E 512 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N PHE E 523 " --> pdb=" O THR E 519 " (cutoff:3.500A) Processing helix chain 'E' and resid 538 through 542 Processing helix chain 'E' and resid 547 through 561 removed outlier: 4.039A pdb=" N MET E 557 " --> pdb=" O LYS E 553 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU E 560 " --> pdb=" O LYS E 556 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLY E 561 " --> pdb=" O MET E 557 " (cutoff:3.500A) Processing helix chain 'E' and resid 565 through 575 Processing helix chain 'E' and resid 581 through 588 Processing helix chain 'E' and resid 588 through 598 Processing sheet with id=AA1, first strand: chain 'A' and resid 20 through 30 removed outlier: 7.716A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 43 through 44 removed outlier: 6.557A pdb=" N PHE A 43 " --> pdb=" O ARG C 567 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 4.040A 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 Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.793A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N GLN A 134 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 8.864A pdb=" N ASN A 164 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 6.837A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 324 through 326 Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 6.822A pdb=" N ALA A 435 " --> pdb=" O PHE A 375 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB3, first strand: chain 'A' and resid 551 through 554 removed outlier: 4.988A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.913A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.489A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.688A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N LYS B 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.440A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.440A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.319A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 787 through 790 removed outlier: 3.666A pdb=" N LYS A 790 " --> pdb=" O ASN C 703 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AC2, first strand: chain 'B' and resid 20 through 30 removed outlier: 7.984A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.011A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC5, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.676A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N GLU B 132 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N CYS B 166 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N GLN B 134 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 8.876A pdb=" N ASN B 164 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.819A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 324 through 328 removed outlier: 3.631A pdb=" N VAL B 539 " --> pdb=" O GLY B 550 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 354 through 358 removed outlier: 6.853A pdb=" N ALA B 435 " --> pdb=" O PHE B 375 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AD1, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD2, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD3, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.940A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.486A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 701 through 704 removed outlier: 6.653A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N LYS C 790 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N ASN B 703 " --> pdb=" O LYS C 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.420A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.420A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.343A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD9, first strand: chain 'C' and resid 20 through 30 removed outlier: 7.870A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 47 through 55 removed outlier: 4.002A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AE3, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.779A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N GLU C 132 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N CYS C 166 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N GLN C 134 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 8.844A pdb=" N ASN C 164 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.203A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.002A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.002A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE8, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.999A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.500A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.471A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.471A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.402A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AF4, first strand: chain 'D' and resid 131 through 133 Processing sheet with id=AF5, first strand: chain 'D' and resid 262 through 263 removed outlier: 5.906A pdb=" N LEU D 262 " --> pdb=" O VAL D 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF5 Processing sheet with id=AF6, first strand: chain 'D' and resid 347 through 352 removed outlier: 6.312A pdb=" N ASP D 355 " --> pdb=" O LEU D 351 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'E' and resid 131 through 133 Processing sheet with id=AF8, first strand: chain 'E' and resid 262 through 263 removed outlier: 5.849A pdb=" N LEU E 262 " --> pdb=" O VAL E 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF8 Processing sheet with id=AF9, first strand: chain 'E' and resid 347 through 352 removed outlier: 6.327A pdb=" N ASP E 355 " --> pdb=" O LEU E 351 " (cutoff:3.500A) 1691 hydrogen bonds defined for protein. 4773 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 10.11 Time building geometry restraints manager: 4.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 11169 1.35 - 1.47: 9441 1.47 - 1.60: 15155 1.60 - 1.73: 0 1.73 - 1.85: 247 Bond restraints: 36012 Sorted by residual: bond pdb=" C1 NAG C1304 " pdb=" O5 NAG C1304 " ideal model delta sigma weight residual 1.406 1.459 -0.053 2.00e-02 2.50e+03 6.94e+00 bond pdb=" C PRO C 986 " pdb=" N PRO C 987 " ideal model delta sigma weight residual 1.335 1.370 -0.035 1.38e-02 5.25e+03 6.59e+00 bond pdb=" C1 NAG A1305 " pdb=" O5 NAG A1305 " ideal model delta sigma weight residual 1.406 1.455 -0.049 2.00e-02 2.50e+03 5.90e+00 bond pdb=" C1 NAG A1306 " pdb=" O5 NAG A1306 " ideal model delta sigma weight residual 1.406 1.454 -0.048 2.00e-02 2.50e+03 5.78e+00 bond pdb=" C1 NAG D 702 " pdb=" O5 NAG D 702 " ideal model delta sigma weight residual 1.406 1.453 -0.047 2.00e-02 2.50e+03 5.53e+00 ... (remaining 36007 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.28: 47581 2.28 - 4.56: 1266 4.56 - 6.84: 97 6.84 - 9.12: 19 9.12 - 11.40: 2 Bond angle restraints: 48965 Sorted by residual: angle pdb=" C ILE B 197 " pdb=" N ASP B 198 " pdb=" CA ASP B 198 " ideal model delta sigma weight residual 122.46 129.83 -7.37 1.41e+00 5.03e-01 2.73e+01 angle pdb=" N ALA B 372 " pdb=" CA ALA B 372 " pdb=" C ALA B 372 " ideal model delta sigma weight residual 109.81 121.21 -11.40 2.21e+00 2.05e-01 2.66e+01 angle pdb=" C ILE C 197 " pdb=" N ASP C 198 " pdb=" CA ASP C 198 " ideal model delta sigma weight residual 122.46 129.62 -7.16 1.41e+00 5.03e-01 2.58e+01 angle pdb=" C ILE A 197 " pdb=" N ASP A 198 " pdb=" CA ASP A 198 " ideal model delta sigma weight residual 122.46 129.52 -7.06 1.41e+00 5.03e-01 2.51e+01 angle pdb=" N PRO A 986 " pdb=" CA PRO A 986 " pdb=" C PRO A 986 " ideal model delta sigma weight residual 110.70 116.28 -5.58 1.22e+00 6.72e-01 2.09e+01 ... (remaining 48960 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 20295 17.73 - 35.45: 1523 35.45 - 53.18: 302 53.18 - 70.91: 75 70.91 - 88.63: 36 Dihedral angle restraints: 22231 sinusoidal: 9581 harmonic: 12650 Sorted by residual: dihedral pdb=" CB CYS B 391 " pdb=" SG CYS B 391 " pdb=" SG CYS B 525 " pdb=" CB CYS B 525 " ideal model delta sinusoidal sigma weight residual 93.00 54.28 38.72 1 1.00e+01 1.00e-02 2.11e+01 dihedral pdb=" CB CYS A 391 " pdb=" SG CYS A 391 " pdb=" SG CYS A 525 " pdb=" CB CYS A 525 " ideal model delta sinusoidal sigma weight residual 93.00 55.15 37.85 1 1.00e+01 1.00e-02 2.02e+01 dihedral pdb=" CB CYS C 131 " pdb=" SG CYS C 131 " pdb=" SG CYS C 166 " pdb=" CB CYS C 166 " ideal model delta sinusoidal sigma weight residual -86.00 -50.83 -35.17 1 1.00e+01 1.00e-02 1.75e+01 ... (remaining 22228 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 4355 0.064 - 0.128: 1037 0.128 - 0.192: 180 0.192 - 0.256: 15 0.256 - 0.320: 1 Chirality restraints: 5588 Sorted by residual: chirality pdb=" C1 NAG A1305 " pdb=" ND2 ASN A 331 " pdb=" C2 NAG A1305 " pdb=" O5 NAG A1305 " both_signs ideal model delta sigma weight residual False -2.40 -2.08 -0.32 2.00e-01 2.50e+01 2.55e+00 chirality pdb=" CB ILE D 291 " pdb=" CA ILE D 291 " pdb=" CG1 ILE D 291 " pdb=" CG2 ILE D 291 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.24 2.00e-01 2.50e+01 1.46e+00 chirality pdb=" CG LEU C 858 " pdb=" CB LEU C 858 " pdb=" CD1 LEU C 858 " pdb=" CD2 LEU C 858 " both_signs ideal model delta sigma weight residual False -2.59 -2.35 -0.24 2.00e-01 2.50e+01 1.45e+00 ... (remaining 5585 not shown) Planarity restraints: 6300 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY A 594 " -0.017 2.00e-02 2.50e+03 3.45e-02 1.19e+01 pdb=" C GLY A 594 " 0.060 2.00e-02 2.50e+03 pdb=" O GLY A 594 " -0.022 2.00e-02 2.50e+03 pdb=" N VAL A 595 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 952 " 0.016 2.00e-02 2.50e+03 3.15e-02 9.92e+00 pdb=" C VAL A 952 " -0.054 2.00e-02 2.50e+03 pdb=" O VAL A 952 " 0.021 2.00e-02 2.50e+03 pdb=" N ASN A 953 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS A 954 " -0.016 2.00e-02 2.50e+03 3.12e-02 9.75e+00 pdb=" C HIS A 954 " 0.054 2.00e-02 2.50e+03 pdb=" O HIS A 954 " -0.020 2.00e-02 2.50e+03 pdb=" N ASN A 955 " -0.018 2.00e-02 2.50e+03 ... (remaining 6297 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 9903 2.82 - 3.34: 30555 3.34 - 3.86: 60176 3.86 - 4.38: 69556 4.38 - 4.90: 119826 Nonbonded interactions: 290016 Sorted by model distance: nonbonded pdb=" OG1 THR C 323 " pdb=" OE1 GLU C 324 " model vdw 2.296 3.040 nonbonded pdb=" OH TYR A 37 " pdb=" O LEU A 54 " model vdw 2.305 3.040 nonbonded pdb=" OH TYR A 756 " pdb=" OD1 ASP A 994 " model vdw 2.310 3.040 nonbonded pdb=" O ILE D 151 " pdb=" OG SER D 155 " model vdw 2.310 3.040 nonbonded pdb=" O ILE E 151 " pdb=" OG SER E 155 " model vdw 2.313 3.040 ... (remaining 290011 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' } ncs_group { reference = 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' selection = chain 'V' selection = chain 'W' } 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: 4.740 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: 0.050 Extract box with map and model: 0.650 Check model and map are aligned: 0.120 Set scattering table: 0.090 Process input model: 37.560 Find NCS groups from input model: 0.930 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 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 0.069 36119 Z= 0.242 Angle : 0.851 11.403 49240 Z= 0.473 Chirality : 0.056 0.320 5588 Planarity : 0.007 0.070 6257 Dihedral : 13.316 88.635 13947 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 0.58 % Allowed : 3.51 % Favored : 95.91 % 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 aren not related in a simple way. whole: 0.44 (0.12), residues: 4278 helix: 1.26 (0.12), residues: 1424 sheet: 0.80 (0.18), residues: 703 loop : -0.51 (0.12), residues: 2151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 273 TYR 0.035 0.002 TYR D 385 PHE 0.027 0.002 PHE A 377 TRP 0.036 0.002 TRP B 886 HIS 0.019 0.002 HIS C 954 Details of bonding type rmsd covalent geometry : bond 0.00491 (36012) covalent geometry : angle 0.83790 (48965) SS BOND : bond 0.00492 ( 46) SS BOND : angle 1.62823 ( 92) hydrogen bonds : bond 0.12744 ( 1600) hydrogen bonds : angle 6.87295 ( 4773) link_BETA1-4 : bond 0.00747 ( 18) link_BETA1-4 : angle 1.60426 ( 54) link_NAG-ASN : bond 0.00413 ( 43) link_NAG-ASN : angle 2.66946 ( 129) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8556 Ramachandran restraints generated. 4278 Oldfield, 0 Emsley, 4278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8556 Ramachandran restraints generated. 4278 Oldfield, 0 Emsley, 4278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 491 residues out of total 3790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 469 time to evaluate : 1.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8056 (tm-30) cc_final: 0.7737 (tm130) REVERT: A 342 PHE cc_start: 0.7970 (m-80) cc_final: 0.7770 (m-80) REVERT: A 371 PHE cc_start: 0.4326 (OUTLIER) cc_final: 0.4057 (m-80) REVERT: A 448 ASN cc_start: 0.6341 (t0) cc_final: 0.6133 (t0) REVERT: B 740 MET cc_start: 0.8329 (ttt) cc_final: 0.8116 (ttm) REVERT: C 54 LEU cc_start: 0.8902 (mt) cc_final: 0.8621 (mp) REVERT: C 177 MET cc_start: 0.6643 (pmm) cc_final: 0.6182 (ppp) REVERT: C 245 HIS cc_start: 0.6681 (m90) cc_final: 0.6137 (m90) REVERT: D 157 ASP cc_start: 0.0229 (t0) cc_final: 0.0029 (t0) REVERT: D 216 ASN cc_start: 0.4784 (m-40) cc_final: 0.4444 (m-40) REVERT: D 249 MET cc_start: 0.0422 (ttm) cc_final: 0.0081 (tmt) REVERT: D 298 MET cc_start: 0.2317 (mmm) cc_final: 0.1920 (ptt) REVERT: D 322 HIS cc_start: 0.6514 (m-70) cc_final: 0.5915 (m-70) REVERT: D 323 MET cc_start: 0.0222 (mmm) cc_final: -0.1300 (mmm) REVERT: D 332 MET cc_start: 0.2830 (ptm) cc_final: 0.2564 (ppp) REVERT: D 341 LYS cc_start: 0.7357 (mmmm) cc_final: 0.6774 (mppt) REVERT: D 360 MET cc_start: 0.1996 (ttm) cc_final: 0.1331 (ttm) REVERT: D 535 TYR cc_start: 0.0060 (t80) cc_final: -0.0532 (p90) REVERT: E 26 LYS cc_start: 0.6760 (mtpt) cc_final: 0.6510 (mmtt) REVERT: E 62 MET cc_start: 0.3354 (ttp) cc_final: 0.2852 (tpt) REVERT: E 98 GLN cc_start: 0.5556 (mt0) cc_final: 0.5228 (mm110) REVERT: E 135 PRO cc_start: 0.2066 (Cg_endo) cc_final: 0.1335 (Cg_exo) REVERT: E 165 TRP cc_start: 0.0369 (t60) cc_final: -0.0735 (m-90) REVERT: E 246 ARG cc_start: 0.1689 (ttp-110) cc_final: 0.1097 (tmm-80) REVERT: E 249 MET cc_start: 0.2490 (ttm) cc_final: 0.2060 (tpp) REVERT: E 270 MET cc_start: -0.1758 (tpt) cc_final: -0.2184 (tpt) REVERT: E 298 MET cc_start: 0.1731 (mmm) cc_final: 0.0648 (tmm) REVERT: E 328 TRP cc_start: 0.4405 (m100) cc_final: 0.3592 (t-100) REVERT: E 418 LEU cc_start: 0.1073 (mt) cc_final: 0.0815 (mt) REVERT: E 435 GLU cc_start: -0.0319 (mm-30) cc_final: -0.0694 (pt0) REVERT: E 546 ASN cc_start: 0.2596 (m110) cc_final: 0.1243 (t0) outliers start: 22 outliers final: 1 residues processed: 485 average time/residue: 0.7450 time to fit residues: 433.8985 Evaluate side-chains 215 residues out of total 3790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 213 time to evaluate : 1.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 371 PHE Chi-restraints excluded: chain B residue 371 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 430 random chunks: chunk 197 optimal weight: 2.9990 chunk 388 optimal weight: 8.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 20.0000 chunk 132 optimal weight: 0.0870 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 0.5980 chunk 401 optimal weight: 0.6980 chunk 424 optimal weight: 5.9990 chunk 155 optimal weight: 0.9980 overall best weight: 1.0760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 GLN A 66 HIS A 115 GLN A 360 ASN A 613 GLN A 824 ASN A 957 GLN B 23 GLN B 613 GLN B 755 GLN B 824 ASN C 134 GLN C 856 ASN C 926 GLN D 113 ASN D 117 ASN D 239 HIS D 345 HIS D 368 ASN ** D 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 34 GLN E 98 GLN ** E 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 586 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4668 r_free = 0.4668 target = 0.181090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.111179 restraints weight = 75243.741| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 3.92 r_work: 0.3283 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3172 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.1865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 36119 Z= 0.150 Angle : 0.606 17.042 49240 Z= 0.309 Chirality : 0.044 0.238 5588 Planarity : 0.005 0.045 6257 Dihedral : 6.694 59.098 5946 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 1.74 % Allowed : 9.16 % Favored : 89.10 % 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 aren not related in a simple way. whole: 0.82 (0.12), residues: 4278 helix: 1.70 (0.13), residues: 1444 sheet: 0.72 (0.18), residues: 709 loop : -0.29 (0.13), residues: 2125 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 95 TYR 0.024 0.001 TYR B1067 PHE 0.033 0.002 PHE D 369 TRP 0.022 0.002 TRP C 258 HIS 0.010 0.001 HIS D 505 Details of bonding type rmsd covalent geometry : bond 0.00330 (36012) covalent geometry : angle 0.58389 (48965) SS BOND : bond 0.00284 ( 46) SS BOND : angle 1.37074 ( 92) hydrogen bonds : bond 0.04481 ( 1600) hydrogen bonds : angle 5.41125 ( 4773) link_BETA1-4 : bond 0.00287 ( 18) link_BETA1-4 : angle 1.29735 ( 54) link_NAG-ASN : bond 0.00335 ( 43) link_NAG-ASN : angle 2.98536 ( 129) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8556 Ramachandran restraints generated. 4278 Oldfield, 0 Emsley, 4278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8556 Ramachandran restraints generated. 4278 Oldfield, 0 Emsley, 4278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 3790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 239 time to evaluate : 1.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8357 (tm-30) cc_final: 0.7949 (tm130) REVERT: A 258 TRP cc_start: 0.5088 (m-90) cc_final: 0.4762 (m-90) REVERT: A 448 ASN cc_start: 0.5838 (t0) cc_final: 0.5614 (t0) REVERT: A 740 MET cc_start: 0.8631 (OUTLIER) cc_final: 0.7859 (ttp) REVERT: A 1050 MET cc_start: 0.9509 (ptm) cc_final: 0.9249 (ptp) REVERT: B 214 ARG cc_start: 0.7090 (mtp85) cc_final: 0.6513 (tpm170) REVERT: B 394 ASN cc_start: 0.6852 (m-40) cc_final: 0.6638 (t0) REVERT: B 740 MET cc_start: 0.8682 (ttt) cc_final: 0.8325 (ttm) REVERT: C 177 MET cc_start: 0.7427 (pmm) cc_final: 0.5695 (mmm) REVERT: C 200 TYR cc_start: 0.7214 (OUTLIER) cc_final: 0.6853 (t80) REVERT: C 245 HIS cc_start: 0.6663 (m90) cc_final: 0.5778 (m-70) REVERT: C 246 ARG cc_start: 0.4534 (OUTLIER) cc_final: 0.1780 (pmt170) REVERT: C 258 TRP cc_start: 0.6577 (m-90) cc_final: 0.6033 (m100) REVERT: C 517 LEU cc_start: 0.5719 (OUTLIER) cc_final: 0.5189 (tm) REVERT: D 249 MET cc_start: 0.0999 (ttm) cc_final: 0.0640 (tmt) REVERT: D 298 MET cc_start: 0.2335 (mmm) cc_final: 0.2007 (ptt) REVERT: D 332 MET cc_start: 0.4760 (ptm) cc_final: 0.4431 (ppp) REVERT: D 341 LYS cc_start: 0.7396 (mmmm) cc_final: 0.6951 (mppt) REVERT: D 360 MET cc_start: 0.1538 (ttm) cc_final: 0.0903 (ttm) REVERT: D 483 GLU cc_start: 0.5424 (tp30) cc_final: 0.5215 (pt0) REVERT: D 535 TYR cc_start: 0.0816 (t80) cc_final: 0.0040 (p90) REVERT: E 28 PHE cc_start: 0.4775 (t80) cc_final: 0.4571 (t80) REVERT: E 62 MET cc_start: 0.3160 (ttp) cc_final: 0.2837 (tpt) REVERT: E 95 ARG cc_start: 0.2142 (ptp-110) cc_final: 0.1815 (tpp-160) REVERT: E 163 TRP cc_start: 0.2765 (m-90) cc_final: 0.2503 (m-90) REVERT: E 165 TRP cc_start: -0.0230 (t60) cc_final: -0.0807 (m-90) REVERT: E 246 ARG cc_start: 0.1933 (ttp-110) cc_final: 0.1274 (tmm-80) REVERT: E 249 MET cc_start: 0.2902 (ttm) cc_final: 0.2524 (tpp) REVERT: E 270 MET cc_start: -0.1544 (tpt) cc_final: -0.1927 (tpt) REVERT: E 271 TRP cc_start: 0.0950 (OUTLIER) cc_final: 0.0710 (m-90) REVERT: E 298 MET cc_start: 0.1388 (mmm) cc_final: 0.0694 (tmm) REVERT: E 328 TRP cc_start: 0.4260 (m100) cc_final: 0.3879 (t-100) REVERT: E 366 MET cc_start: -0.0003 (tpt) cc_final: -0.0210 (tpt) REVERT: E 462 MET cc_start: 0.1676 (OUTLIER) cc_final: 0.0852 (ttt) REVERT: E 546 ASN cc_start: 0.1670 (m110) cc_final: 0.1194 (p0) outliers start: 66 outliers final: 13 residues processed: 284 average time/residue: 0.6713 time to fit residues: 234.2504 Evaluate side-chains 204 residues out of total 3790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 185 time to evaluate : 1.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 371 PHE Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 371 PHE Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 246 ARG Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 256 ILE Chi-restraints excluded: chain D residue 538 SER Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain E residue 271 TRP Chi-restraints excluded: chain E residue 462 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 430 random chunks: chunk 292 optimal weight: 0.9980 chunk 5 optimal weight: 20.0000 chunk 54 optimal weight: 3.9990 chunk 347 optimal weight: 10.0000 chunk 300 optimal weight: 2.9990 chunk 417 optimal weight: 20.0000 chunk 217 optimal weight: 10.0000 chunk 363 optimal weight: 3.9990 chunk 419 optimal weight: 6.9990 chunk 265 optimal weight: 4.9990 chunk 70 optimal weight: 3.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 30 ASN ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN C 824 ASN D 239 HIS D 330 ASN ** D 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 175 GLN ** E 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 368 ASN ** E 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 540 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4634 r_free = 0.4634 target = 0.187002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.118383 restraints weight = 72095.091| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 3.79 r_work: 0.3192 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work: 0.3084 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.2957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 36119 Z= 0.299 Angle : 0.685 15.068 49240 Z= 0.350 Chirality : 0.049 0.243 5588 Planarity : 0.005 0.040 6257 Dihedral : 6.530 59.539 5946 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.90 % Allowed : 11.37 % Favored : 86.73 % 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 aren not related in a simple way. whole: 0.73 (0.12), residues: 4278 helix: 1.60 (0.13), residues: 1432 sheet: 0.65 (0.18), residues: 728 loop : -0.31 (0.13), residues: 2118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 387 TYR 0.030 0.002 TYR B1067 PHE 0.038 0.002 PHE D 369 TRP 0.025 0.002 TRP A 886 HIS 0.015 0.002 HIS E 540 Details of bonding type rmsd covalent geometry : bond 0.00694 (36012) covalent geometry : angle 0.66611 (48965) SS BOND : bond 0.00368 ( 46) SS BOND : angle 1.28556 ( 92) hydrogen bonds : bond 0.05019 ( 1600) hydrogen bonds : angle 5.49509 ( 4773) link_BETA1-4 : bond 0.00429 ( 18) link_BETA1-4 : angle 1.55876 ( 54) link_NAG-ASN : bond 0.00618 ( 43) link_NAG-ASN : angle 2.88211 ( 129) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8556 Ramachandran restraints generated. 4278 Oldfield, 0 Emsley, 4278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8556 Ramachandran restraints generated. 4278 Oldfield, 0 Emsley, 4278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 3790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 205 time to evaluate : 1.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8408 (tm-30) cc_final: 0.7912 (tm-30) REVERT: A 177 MET cc_start: 0.7191 (pmm) cc_final: 0.5874 (mtt) REVERT: A 258 TRP cc_start: 0.5204 (m-90) cc_final: 0.4930 (m-90) REVERT: A 371 PHE cc_start: 0.5180 (OUTLIER) cc_final: 0.4953 (t80) REVERT: A 448 ASN cc_start: 0.6571 (t0) cc_final: 0.6353 (t0) REVERT: A 740 MET cc_start: 0.8609 (OUTLIER) cc_final: 0.7865 (ttp) REVERT: A 780 GLU cc_start: 0.9123 (OUTLIER) cc_final: 0.8914 (mm-30) REVERT: B 214 ARG cc_start: 0.7308 (mtp85) cc_final: 0.6684 (tpm170) REVERT: B 533 LEU cc_start: 0.8255 (OUTLIER) cc_final: 0.7879 (tt) REVERT: B 740 MET cc_start: 0.8664 (ttt) cc_final: 0.8414 (ttm) REVERT: C 177 MET cc_start: 0.7254 (pmm) cc_final: 0.6703 (ppp) REVERT: C 200 TYR cc_start: 0.7381 (OUTLIER) cc_final: 0.7005 (t80) REVERT: C 220 PHE cc_start: 0.7757 (t80) cc_final: 0.7496 (t80) REVERT: C 245 HIS cc_start: 0.6906 (m90) cc_final: 0.5765 (m-70) REVERT: C 355 ARG cc_start: 0.7346 (OUTLIER) cc_final: 0.7062 (tpp-160) REVERT: C 517 LEU cc_start: 0.6130 (OUTLIER) cc_final: 0.5626 (mm) REVERT: D 89 GLN cc_start: 0.4313 (mp10) cc_final: 0.4004 (tp40) REVERT: D 249 MET cc_start: 0.0777 (ttm) cc_final: 0.0423 (tmt) REVERT: D 270 MET cc_start: 0.1218 (OUTLIER) cc_final: 0.0932 (tmt) REVERT: D 298 MET cc_start: 0.1947 (mmm) cc_final: 0.1513 (ptt) REVERT: D 340 ARG cc_start: 0.3981 (OUTLIER) cc_final: 0.3384 (ptt-90) REVERT: D 341 LYS cc_start: 0.7325 (mmmm) cc_final: 0.6818 (mppt) REVERT: D 408 MET cc_start: 0.3817 (mmp) cc_final: 0.3124 (tpt) REVERT: D 483 GLU cc_start: 0.5599 (tp30) cc_final: 0.5268 (pt0) REVERT: D 535 TYR cc_start: 0.1347 (t80) cc_final: 0.0248 (p90) REVERT: E 62 MET cc_start: 0.3164 (ttp) cc_final: 0.2827 (tpt) REVERT: E 95 ARG cc_start: 0.2274 (ptp-110) cc_final: 0.1976 (ttm110) REVERT: E 163 TRP cc_start: 0.3103 (m-90) cc_final: 0.2852 (m-10) REVERT: E 246 ARG cc_start: 0.1539 (ttp-110) cc_final: 0.0974 (tmm-80) REVERT: E 249 MET cc_start: 0.2931 (ttm) cc_final: 0.2555 (tpp) REVERT: E 271 TRP cc_start: 0.1021 (OUTLIER) cc_final: 0.0775 (m-90) REVERT: E 275 TRP cc_start: 0.4009 (m-10) cc_final: 0.3730 (m-10) REVERT: E 298 MET cc_start: 0.1525 (mmm) cc_final: 0.0684 (tmm) REVERT: E 328 TRP cc_start: 0.4137 (m100) cc_final: 0.3657 (t-100) REVERT: E 366 MET cc_start: -0.0037 (tpt) cc_final: -0.0398 (tpt) REVERT: E 482 ARG cc_start: 0.4796 (ptt90) cc_final: 0.4534 (mtt180) REVERT: E 546 ASN cc_start: 0.2096 (m110) cc_final: 0.1229 (t0) outliers start: 72 outliers final: 23 residues processed: 257 average time/residue: 0.6331 time to fit residues: 198.1454 Evaluate side-chains 211 residues out of total 3790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 178 time to evaluate : 1.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 371 PHE Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 371 PHE Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 355 ARG Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 256 ILE Chi-restraints excluded: chain D residue 270 MET Chi-restraints excluded: chain D residue 340 ARG Chi-restraints excluded: chain D residue 538 SER Chi-restraints excluded: chain D residue 548 THR Chi-restraints excluded: chain D residue 555 LEU Chi-restraints excluded: chain E residue 271 TRP Chi-restraints excluded: chain E residue 315 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 430 random chunks: chunk 174 optimal weight: 0.8980 chunk 42 optimal weight: 6.9990 chunk 240 optimal weight: 1.9990 chunk 113 optimal weight: 6.9990 chunk 154 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 425 optimal weight: 9.9990 chunk 54 optimal weight: 4.9990 chunk 261 optimal weight: 9.9990 chunk 86 optimal weight: 2.9990 chunk 35 optimal weight: 9.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 GLN ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 ASN B 603 ASN D 239 HIS D 345 HIS E 30 ASN ** E 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 378 HIS ** 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 = 0.4618 r_free = 0.4618 target = 0.177235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.107783 restraints weight = 73932.176| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 3.49 r_work: 0.3212 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.3239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 36119 Z= 0.194 Angle : 0.589 13.731 49240 Z= 0.300 Chirality : 0.045 0.214 5588 Planarity : 0.004 0.068 6257 Dihedral : 6.220 59.852 5946 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.79 % Allowed : 12.35 % Favored : 85.86 % 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 aren not related in a simple way. whole: 0.79 (0.12), residues: 4278 helix: 1.75 (0.14), residues: 1427 sheet: 0.45 (0.17), residues: 736 loop : -0.25 (0.13), residues: 2115 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 237 TYR 0.024 0.002 TYR B1067 PHE 0.028 0.002 PHE D 369 TRP 0.019 0.001 TRP D 165 HIS 0.009 0.001 HIS D 239 Details of bonding type rmsd covalent geometry : bond 0.00443 (36012) covalent geometry : angle 0.57231 (48965) SS BOND : bond 0.00441 ( 46) SS BOND : angle 1.07267 ( 92) hydrogen bonds : bond 0.04335 ( 1600) hydrogen bonds : angle 5.32896 ( 4773) link_BETA1-4 : bond 0.00271 ( 18) link_BETA1-4 : angle 1.19964 ( 54) link_NAG-ASN : bond 0.00392 ( 43) link_NAG-ASN : angle 2.56055 ( 129) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8556 Ramachandran restraints generated. 4278 Oldfield, 0 Emsley, 4278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8556 Ramachandran restraints generated. 4278 Oldfield, 0 Emsley, 4278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 3790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 200 time to evaluate : 1.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8353 (tm-30) cc_final: 0.7880 (tm-30) REVERT: A 158 ARG cc_start: 0.5728 (mtt-85) cc_final: 0.5411 (mtt-85) REVERT: A 177 MET cc_start: 0.7344 (pmm) cc_final: 0.5943 (mtt) REVERT: A 258 TRP cc_start: 0.4605 (m-90) cc_final: 0.4368 (m-90) REVERT: A 371 PHE cc_start: 0.4917 (OUTLIER) cc_final: 0.4681 (t80) REVERT: A 448 ASN cc_start: 0.6604 (t0) cc_final: 0.6384 (t0) REVERT: A 740 MET cc_start: 0.8591 (OUTLIER) cc_final: 0.7896 (ttp) REVERT: B 214 ARG cc_start: 0.7356 (mtp85) cc_final: 0.6724 (tpm170) REVERT: B 533 LEU cc_start: 0.8222 (OUTLIER) cc_final: 0.7997 (tt) REVERT: B 697 MET cc_start: 0.9380 (ptt) cc_final: 0.9054 (ptt) REVERT: B 740 MET cc_start: 0.8707 (ttt) cc_final: 0.8455 (ttm) REVERT: C 177 MET cc_start: 0.7237 (pmm) cc_final: 0.6435 (ppp) REVERT: C 188 ASN cc_start: 0.5527 (t0) cc_final: 0.5290 (t0) REVERT: C 200 TYR cc_start: 0.7390 (OUTLIER) cc_final: 0.6981 (t80) REVERT: C 245 HIS cc_start: 0.6730 (m90) cc_final: 0.5718 (m-70) REVERT: C 355 ARG cc_start: 0.7449 (OUTLIER) cc_final: 0.7215 (tpp-160) REVERT: C 987 PRO cc_start: 0.8469 (Cg_exo) cc_final: 0.8252 (Cg_endo) REVERT: D 132 VAL cc_start: -0.3631 (OUTLIER) cc_final: -0.3852 (t) REVERT: D 249 MET cc_start: 0.0473 (ttm) cc_final: 0.0231 (tmt) REVERT: D 298 MET cc_start: 0.2105 (mmm) cc_final: 0.1636 (ptt) REVERT: D 340 ARG cc_start: 0.3853 (OUTLIER) cc_final: 0.3378 (ptt-90) REVERT: D 341 LYS cc_start: 0.7349 (mmmm) cc_final: 0.6855 (mppt) REVERT: D 408 MET cc_start: 0.3755 (mmp) cc_final: 0.3040 (tpt) REVERT: D 483 GLU cc_start: 0.5519 (tp30) cc_final: 0.5227 (pt0) REVERT: D 535 TYR cc_start: 0.1135 (t80) cc_final: -0.0131 (p90) REVERT: E 22 GLU cc_start: 0.2956 (tt0) cc_final: 0.2641 (mm-30) REVERT: E 62 MET cc_start: 0.3119 (ttp) cc_final: 0.2728 (tpt) REVERT: E 95 ARG cc_start: 0.2358 (ptp-110) cc_final: 0.1930 (tpp-160) REVERT: E 144 LEU cc_start: 0.0361 (tm) cc_final: -0.0225 (pt) REVERT: E 210 GLU cc_start: 0.4478 (tp30) cc_final: 0.4243 (mm-30) REVERT: E 246 ARG cc_start: 0.1491 (ttp-110) cc_final: 0.0919 (tmm-80) REVERT: E 249 MET cc_start: 0.2839 (ttm) cc_final: 0.2452 (tpp) REVERT: E 275 TRP cc_start: 0.4069 (m-10) cc_final: 0.3806 (m-10) REVERT: E 298 MET cc_start: 0.1493 (mmm) cc_final: 0.0671 (tmm) REVERT: E 328 TRP cc_start: 0.4127 (m100) cc_final: 0.3715 (t-100) REVERT: E 366 MET cc_start: -0.0258 (tpt) cc_final: -0.0642 (tpt) REVERT: E 482 ARG cc_start: 0.4695 (ptt90) cc_final: 0.4407 (mtt180) REVERT: E 546 ASN cc_start: 0.1939 (m110) cc_final: 0.1169 (t0) outliers start: 68 outliers final: 27 residues processed: 250 average time/residue: 0.6714 time to fit residues: 207.2990 Evaluate side-chains 212 residues out of total 3790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 178 time to evaluate : 1.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 371 PHE Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 371 PHE Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 355 ARG Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 203 TRP Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 256 ILE Chi-restraints excluded: chain D residue 333 LEU Chi-restraints excluded: chain D residue 340 ARG Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 538 SER Chi-restraints excluded: chain D residue 555 LEU Chi-restraints excluded: chain E residue 94 LYS Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain E residue 315 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 430 random chunks: chunk 389 optimal weight: 10.0000 chunk 236 optimal weight: 1.9990 chunk 351 optimal weight: 0.0170 chunk 335 optimal weight: 0.0570 chunk 367 optimal weight: 7.9990 chunk 121 optimal weight: 9.9990 chunk 114 optimal weight: 6.9990 chunk 320 optimal weight: 30.0000 chunk 246 optimal weight: 9.9990 chunk 399 optimal weight: 10.0000 chunk 130 optimal weight: 2.9990 overall best weight: 2.4142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 607 GLN B 115 GLN ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 173 GLN C 30 ASN ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 239 HIS ** D 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4601 r_free = 0.4601 target = 0.176013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.106206 restraints weight = 73821.945| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 3.49 r_work: 0.3179 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.3653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 36119 Z= 0.231 Angle : 0.615 13.480 49240 Z= 0.312 Chirality : 0.046 0.239 5588 Planarity : 0.004 0.044 6257 Dihedral : 6.098 59.457 5946 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.01 % Allowed : 12.72 % Favored : 85.28 % 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 aren not related in a simple way. whole: 0.69 (0.12), residues: 4278 helix: 1.64 (0.13), residues: 1436 sheet: 0.44 (0.18), residues: 707 loop : -0.32 (0.13), residues: 2135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 237 TYR 0.024 0.002 TYR B1067 PHE 0.027 0.002 PHE D 369 TRP 0.017 0.002 TRP D 165 HIS 0.012 0.001 HIS D 239 Details of bonding type rmsd covalent geometry : bond 0.00535 (36012) covalent geometry : angle 0.59900 (48965) SS BOND : bond 0.00559 ( 46) SS BOND : angle 1.18292 ( 92) hydrogen bonds : bond 0.04478 ( 1600) hydrogen bonds : angle 5.37340 ( 4773) link_BETA1-4 : bond 0.00284 ( 18) link_BETA1-4 : angle 1.31958 ( 54) link_NAG-ASN : bond 0.00489 ( 43) link_NAG-ASN : angle 2.58368 ( 129) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8556 Ramachandran restraints generated. 4278 Oldfield, 0 Emsley, 4278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8556 Ramachandran restraints generated. 4278 Oldfield, 0 Emsley, 4278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 3790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 192 time to evaluate : 1.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8241 (tm-30) cc_final: 0.7763 (tm-30) REVERT: A 258 TRP cc_start: 0.4745 (m-90) cc_final: 0.4301 (m-90) REVERT: A 448 ASN cc_start: 0.6482 (t0) cc_final: 0.6187 (t0) REVERT: A 497 PHE cc_start: 0.5432 (m-80) cc_final: 0.4416 (m-80) REVERT: A 740 MET cc_start: 0.8644 (OUTLIER) cc_final: 0.7919 (ttp) REVERT: A 820 ASP cc_start: 0.8700 (OUTLIER) cc_final: 0.8409 (m-30) REVERT: A 994 ASP cc_start: 0.8454 (OUTLIER) cc_final: 0.8087 (t70) REVERT: B 214 ARG cc_start: 0.7491 (mtp85) cc_final: 0.6805 (tpm170) REVERT: B 533 LEU cc_start: 0.8196 (OUTLIER) cc_final: 0.7953 (tt) REVERT: B 697 MET cc_start: 0.9389 (ptt) cc_final: 0.9108 (ptt) REVERT: B 740 MET cc_start: 0.8712 (ttt) cc_final: 0.8465 (ttm) REVERT: C 177 MET cc_start: 0.7304 (pmm) cc_final: 0.6797 (ppp) REVERT: C 200 TYR cc_start: 0.7560 (OUTLIER) cc_final: 0.7293 (t80) REVERT: C 355 ARG cc_start: 0.7231 (OUTLIER) cc_final: 0.6983 (tpp-160) REVERT: C 987 PRO cc_start: 0.8492 (Cg_exo) cc_final: 0.8270 (Cg_endo) REVERT: D 89 GLN cc_start: 0.4247 (mp10) cc_final: 0.3687 (tp40) REVERT: D 249 MET cc_start: 0.0331 (ttm) cc_final: 0.0040 (tmt) REVERT: D 298 MET cc_start: 0.2215 (mmm) cc_final: 0.1815 (ptt) REVERT: D 340 ARG cc_start: 0.3709 (OUTLIER) cc_final: 0.3317 (ptt-90) REVERT: D 341 LYS cc_start: 0.7338 (mmmm) cc_final: 0.6887 (mppt) REVERT: D 408 MET cc_start: 0.3685 (mmp) cc_final: 0.2998 (tpt) REVERT: D 483 GLU cc_start: 0.5416 (tp30) cc_final: 0.5178 (pt0) REVERT: D 535 TYR cc_start: 0.1178 (t80) cc_final: -0.0168 (p90) REVERT: E 62 MET cc_start: 0.3135 (ttp) cc_final: 0.2759 (tpt) REVERT: E 95 ARG cc_start: 0.2345 (ptp-110) cc_final: 0.1976 (tpp-160) REVERT: E 144 LEU cc_start: 0.1888 (tm) cc_final: 0.1260 (pp) REVERT: E 165 TRP cc_start: -0.0023 (OUTLIER) cc_final: -0.0336 (p-90) REVERT: E 210 GLU cc_start: 0.4297 (tp30) cc_final: 0.4054 (mm-30) REVERT: E 246 ARG cc_start: 0.1686 (ttp-110) cc_final: 0.1110 (tmm-80) REVERT: E 249 MET cc_start: 0.2830 (ttm) cc_final: 0.2451 (tpp) REVERT: E 275 TRP cc_start: 0.4027 (m-10) cc_final: 0.3793 (m-10) REVERT: E 281 LEU cc_start: 0.0816 (OUTLIER) cc_final: 0.0608 (pt) REVERT: E 298 MET cc_start: 0.1512 (mmm) cc_final: 0.0792 (tmm) REVERT: E 366 MET cc_start: -0.0342 (tpt) cc_final: -0.0715 (tpt) REVERT: E 482 ARG cc_start: 0.4547 (ptt90) cc_final: 0.4280 (mtt180) REVERT: E 546 ASN cc_start: 0.1849 (m110) cc_final: 0.1136 (t0) outliers start: 76 outliers final: 31 residues processed: 253 average time/residue: 0.6799 time to fit residues: 211.3317 Evaluate side-chains 207 residues out of total 3790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 167 time to evaluate : 1.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 371 PHE Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 355 ARG Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 203 TRP Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 256 ILE Chi-restraints excluded: chain D residue 333 LEU Chi-restraints excluded: chain D residue 340 ARG Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 555 LEU Chi-restraints excluded: chain E residue 94 LYS Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain E residue 165 TRP Chi-restraints excluded: chain E residue 281 LEU Chi-restraints excluded: chain E residue 315 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 430 random chunks: chunk 110 optimal weight: 0.9990 chunk 1 optimal weight: 4.9990 chunk 193 optimal weight: 0.9980 chunk 401 optimal weight: 20.0000 chunk 283 optimal weight: 8.9990 chunk 306 optimal weight: 0.6980 chunk 244 optimal weight: 8.9990 chunk 393 optimal weight: 20.0000 chunk 352 optimal weight: 4.9990 chunk 380 optimal weight: 20.0000 chunk 231 optimal weight: 1.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 188 ASN D 239 HIS ** D 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 42 GLN E 96 GLN ** E 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4602 r_free = 0.4602 target = 0.176449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.105920 restraints weight = 73292.611| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 3.38 r_work: 0.3199 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.3908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 36119 Z= 0.192 Angle : 0.591 12.957 49240 Z= 0.299 Chirality : 0.045 0.226 5588 Planarity : 0.004 0.043 6257 Dihedral : 5.862 59.510 5944 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.11 % Allowed : 12.96 % Favored : 84.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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 aren not related in a simple way. whole: 0.70 (0.12), residues: 4278 helix: 1.72 (0.14), residues: 1413 sheet: 0.43 (0.18), residues: 704 loop : -0.33 (0.13), residues: 2161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 403 TYR 0.023 0.001 TYR B1067 PHE 0.029 0.002 PHE D 464 TRP 0.021 0.001 TRP E 271 HIS 0.013 0.001 HIS D 239 Details of bonding type rmsd covalent geometry : bond 0.00441 (36012) covalent geometry : angle 0.57589 (48965) SS BOND : bond 0.00304 ( 46) SS BOND : angle 1.10526 ( 92) hydrogen bonds : bond 0.04222 ( 1600) hydrogen bonds : angle 5.26698 ( 4773) link_BETA1-4 : bond 0.00297 ( 18) link_BETA1-4 : angle 1.17042 ( 54) link_NAG-ASN : bond 0.00399 ( 43) link_NAG-ASN : angle 2.42749 ( 129) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8556 Ramachandran restraints generated. 4278 Oldfield, 0 Emsley, 4278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8556 Ramachandran restraints generated. 4278 Oldfield, 0 Emsley, 4278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 3790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 180 time to evaluate : 1.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8199 (tm-30) cc_final: 0.7706 (tm-30) REVERT: A 158 ARG cc_start: 0.5604 (mtt-85) cc_final: 0.5382 (mtt-85) REVERT: A 258 TRP cc_start: 0.4584 (m-90) cc_final: 0.4274 (m-90) REVERT: A 448 ASN cc_start: 0.6472 (t0) cc_final: 0.6270 (t0) REVERT: A 524 VAL cc_start: 0.5473 (OUTLIER) cc_final: 0.5245 (m) REVERT: A 740 MET cc_start: 0.8557 (OUTLIER) cc_final: 0.7827 (ttp) REVERT: A 820 ASP cc_start: 0.8711 (OUTLIER) cc_final: 0.8377 (m-30) REVERT: A 994 ASP cc_start: 0.8420 (OUTLIER) cc_final: 0.8034 (t70) REVERT: B 214 ARG cc_start: 0.7476 (mtp85) cc_final: 0.6791 (tpm170) REVERT: B 528 LYS cc_start: 0.6790 (OUTLIER) cc_final: 0.6488 (pptt) REVERT: B 533 LEU cc_start: 0.8268 (OUTLIER) cc_final: 0.8064 (tt) REVERT: B 697 MET cc_start: 0.9387 (ptt) cc_final: 0.9068 (ptt) REVERT: B 740 MET cc_start: 0.8623 (ttt) cc_final: 0.8366 (ttm) REVERT: B 1142 GLN cc_start: 0.8461 (mm110) cc_final: 0.8258 (mm-40) REVERT: C 177 MET cc_start: 0.7217 (pmm) cc_final: 0.6825 (ppp) REVERT: C 200 TYR cc_start: 0.7570 (OUTLIER) cc_final: 0.7265 (t80) REVERT: C 237 ARG cc_start: 0.7686 (OUTLIER) cc_final: 0.7424 (ttp-110) REVERT: C 987 PRO cc_start: 0.8531 (Cg_exo) cc_final: 0.8309 (Cg_endo) REVERT: D 89 GLN cc_start: 0.4321 (mp10) cc_final: 0.3737 (tp40) REVERT: D 249 MET cc_start: 0.0264 (ttm) cc_final: 0.0009 (tmt) REVERT: D 298 MET cc_start: 0.2272 (mmm) cc_final: 0.1885 (ptt) REVERT: D 340 ARG cc_start: 0.3806 (OUTLIER) cc_final: 0.3492 (ptt-90) REVERT: D 341 LYS cc_start: 0.7308 (mmmm) cc_final: 0.6897 (mptt) REVERT: D 408 MET cc_start: 0.3885 (mmp) cc_final: 0.3139 (tpt) REVERT: D 464 PHE cc_start: 0.0278 (OUTLIER) cc_final: -0.0173 (t80) REVERT: D 483 GLU cc_start: 0.5456 (tp30) cc_final: 0.5201 (pt0) REVERT: D 535 TYR cc_start: 0.1201 (t80) cc_final: -0.0188 (p90) REVERT: E 62 MET cc_start: 0.3183 (ttp) cc_final: 0.2765 (tpt) REVERT: E 144 LEU cc_start: 0.1181 (tm) cc_final: 0.0459 (pp) REVERT: E 165 TRP cc_start: -0.0147 (OUTLIER) cc_final: -0.0529 (p-90) REVERT: E 246 ARG cc_start: 0.1580 (ttp-110) cc_final: 0.0993 (tmm-80) REVERT: E 249 MET cc_start: 0.2474 (ttm) cc_final: 0.2029 (tpp) REVERT: E 275 TRP cc_start: 0.4150 (m-10) cc_final: 0.3805 (m-10) REVERT: E 281 LEU cc_start: 0.1066 (OUTLIER) cc_final: 0.0808 (pt) REVERT: E 298 MET cc_start: 0.1301 (mmm) cc_final: 0.0558 (tmm) REVERT: E 366 MET cc_start: -0.0336 (tpt) cc_final: -0.0668 (tpt) REVERT: E 482 ARG cc_start: 0.4567 (ptt90) cc_final: 0.4267 (mtt180) REVERT: E 546 ASN cc_start: 0.1878 (m110) cc_final: 0.1097 (t0) outliers start: 80 outliers final: 37 residues processed: 243 average time/residue: 0.6767 time to fit residues: 202.4815 Evaluate side-chains 214 residues out of total 3790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 165 time to evaluate : 1.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 144 TYR Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 764 LYS Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 371 PHE Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 237 ARG Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 256 ILE Chi-restraints excluded: chain D residue 333 LEU Chi-restraints excluded: chain D residue 340 ARG Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 464 PHE Chi-restraints excluded: chain D residue 555 LEU Chi-restraints excluded: chain E residue 94 LYS Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain E residue 165 TRP Chi-restraints excluded: chain E residue 203 TRP Chi-restraints excluded: chain E residue 281 LEU Chi-restraints excluded: chain E residue 315 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 430 random chunks: chunk 215 optimal weight: 8.9990 chunk 236 optimal weight: 7.9990 chunk 244 optimal weight: 7.9990 chunk 110 optimal weight: 0.9990 chunk 362 optimal weight: 7.9990 chunk 230 optimal weight: 4.9990 chunk 397 optimal weight: 10.0000 chunk 167 optimal weight: 0.9980 chunk 241 optimal weight: 8.9990 chunk 83 optimal weight: 2.9990 chunk 200 optimal weight: 0.6980 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN A 125 ASN ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 GLN C 314 GLN D 188 ASN D 309 GLN D 345 HIS ** D 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 30 ASN ** E 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4594 r_free = 0.4594 target = 0.177445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.106196 restraints weight = 72029.436| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 3.38 r_work: 0.3197 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3074 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.4188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 36119 Z= 0.208 Angle : 0.606 13.010 49240 Z= 0.305 Chirality : 0.045 0.237 5588 Planarity : 0.004 0.045 6257 Dihedral : 5.773 59.631 5944 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.06 % Allowed : 13.51 % Favored : 84.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.64 (0.12), residues: 4278 helix: 1.64 (0.13), residues: 1435 sheet: 0.39 (0.18), residues: 700 loop : -0.35 (0.13), residues: 2143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 21 TYR 0.023 0.002 TYR B1067 PHE 0.029 0.002 PHE D 464 TRP 0.019 0.001 TRP D 165 HIS 0.008 0.001 HIS D 239 Details of bonding type rmsd covalent geometry : bond 0.00480 (36012) covalent geometry : angle 0.59127 (48965) SS BOND : bond 0.00306 ( 46) SS BOND : angle 1.24903 ( 92) hydrogen bonds : bond 0.04300 ( 1600) hydrogen bonds : angle 5.28710 ( 4773) link_BETA1-4 : bond 0.00279 ( 18) link_BETA1-4 : angle 1.22194 ( 54) link_NAG-ASN : bond 0.00428 ( 43) link_NAG-ASN : angle 2.43503 ( 129) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8556 Ramachandran restraints generated. 4278 Oldfield, 0 Emsley, 4278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8556 Ramachandran restraints generated. 4278 Oldfield, 0 Emsley, 4278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 3790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 174 time to evaluate : 1.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 ARG cc_start: 0.5645 (mtt-85) cc_final: 0.5317 (mtt-85) REVERT: A 168 PHE cc_start: 0.6940 (t80) cc_final: 0.6512 (t80) REVERT: A 258 TRP cc_start: 0.4450 (m-90) cc_final: 0.4186 (m-90) REVERT: A 524 VAL cc_start: 0.5582 (OUTLIER) cc_final: 0.5305 (m) REVERT: A 740 MET cc_start: 0.8529 (OUTLIER) cc_final: 0.7711 (ttp) REVERT: A 820 ASP cc_start: 0.8703 (OUTLIER) cc_final: 0.8387 (m-30) REVERT: A 994 ASP cc_start: 0.8431 (OUTLIER) cc_final: 0.8049 (t70) REVERT: B 153 MET cc_start: 0.4385 (OUTLIER) cc_final: 0.3624 (mpt) REVERT: B 214 ARG cc_start: 0.7524 (mtp85) cc_final: 0.6798 (tpm170) REVERT: B 533 LEU cc_start: 0.8251 (OUTLIER) cc_final: 0.8037 (tt) REVERT: B 697 MET cc_start: 0.9376 (ptt) cc_final: 0.9047 (ptt) REVERT: B 740 MET cc_start: 0.8589 (ttt) cc_final: 0.8332 (ttm) REVERT: C 177 MET cc_start: 0.7273 (pmm) cc_final: 0.6851 (ppp) REVERT: C 200 TYR cc_start: 0.7702 (OUTLIER) cc_final: 0.7394 (t80) REVERT: C 355 ARG cc_start: 0.7186 (OUTLIER) cc_final: 0.6934 (tpp-160) REVERT: C 580 GLN cc_start: 0.8036 (tt0) cc_final: 0.7670 (mm-40) REVERT: C 987 PRO cc_start: 0.8475 (Cg_exo) cc_final: 0.8263 (Cg_endo) REVERT: D 89 GLN cc_start: 0.4361 (mp10) cc_final: 0.3749 (tp40) REVERT: D 249 MET cc_start: 0.0348 (ttm) cc_final: 0.0096 (tmt) REVERT: D 298 MET cc_start: 0.2270 (mmm) cc_final: 0.1906 (ptt) REVERT: D 408 MET cc_start: 0.3848 (mmp) cc_final: 0.3149 (tpt) REVERT: D 483 GLU cc_start: 0.5500 (tp30) cc_final: 0.5264 (pt0) REVERT: D 535 TYR cc_start: 0.1354 (t80) cc_final: -0.0106 (p90) REVERT: E 22 GLU cc_start: 0.2788 (tt0) cc_final: 0.2348 (mm-30) REVERT: E 62 MET cc_start: 0.3139 (ttp) cc_final: 0.2754 (tpt) REVERT: E 144 LEU cc_start: 0.1411 (tm) cc_final: 0.0823 (pp) REVERT: E 165 TRP cc_start: -0.0216 (OUTLIER) cc_final: -0.0529 (p-90) REVERT: E 246 ARG cc_start: 0.1788 (ttp-110) cc_final: 0.1204 (tmm-80) REVERT: E 249 MET cc_start: 0.2751 (ttm) cc_final: 0.2351 (tpp) REVERT: E 281 LEU cc_start: 0.0649 (OUTLIER) cc_final: 0.0446 (pt) REVERT: E 298 MET cc_start: 0.1256 (mmm) cc_final: 0.0576 (tmm) REVERT: E 315 PHE cc_start: 0.1276 (OUTLIER) cc_final: 0.0709 (m-10) REVERT: E 366 MET cc_start: -0.0272 (tpt) cc_final: -0.0586 (tpt) REVERT: E 482 ARG cc_start: 0.4689 (ptt90) cc_final: 0.4412 (mtt180) REVERT: E 546 ASN cc_start: 0.2040 (m110) cc_final: 0.1311 (t0) outliers start: 78 outliers final: 38 residues processed: 234 average time/residue: 0.6772 time to fit residues: 195.9195 Evaluate side-chains 209 residues out of total 3790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 160 time to evaluate : 1.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 144 TYR Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 764 LYS Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 371 PHE Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 355 ARG Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 163 TRP Chi-restraints excluded: chain D residue 203 TRP Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 256 ILE Chi-restraints excluded: chain D residue 333 LEU Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 548 THR Chi-restraints excluded: chain D residue 555 LEU Chi-restraints excluded: chain E residue 94 LYS Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain E residue 165 TRP Chi-restraints excluded: chain E residue 203 TRP Chi-restraints excluded: chain E residue 281 LEU Chi-restraints excluded: chain E residue 315 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 55.1142 > 50: distance: 34 - 38: 3.011 distance: 38 - 39: 5.487 distance: 39 - 40: 7.890 distance: 40 - 41: 7.522 distance: 40 - 47: 3.719 distance: 42 - 43: 8.524 distance: 43 - 44: 4.150 distance: 44 - 45: 4.255 distance: 47 - 48: 3.853 distance: 48 - 49: 15.274 distance: 48 - 51: 11.978 distance: 49 - 50: 20.213 distance: 49 - 54: 13.807 distance: 51 - 52: 3.939 distance: 51 - 53: 8.158 distance: 54 - 55: 7.653 distance: 55 - 56: 4.912 distance: 55 - 58: 8.065 distance: 56 - 57: 10.456 distance: 56 - 60: 4.147 distance: 57 - 176: 25.236 distance: 58 - 59: 10.405 distance: 61 - 62: 6.925 distance: 61 - 64: 7.554 distance: 62 - 63: 7.021 distance: 62 - 68: 3.824 distance: 64 - 65: 22.077 distance: 65 - 66: 11.703 distance: 65 - 67: 21.395 distance: 68 - 69: 3.648 distance: 68 - 171: 6.849 distance: 69 - 70: 4.341 distance: 69 - 72: 3.851 distance: 70 - 71: 9.372 distance: 70 - 79: 8.405 distance: 71 - 168: 13.052 distance: 72 - 73: 3.039 distance: 73 - 74: 5.730 distance: 73 - 75: 5.054 distance: 74 - 76: 3.719 distance: 75 - 77: 6.636 distance: 76 - 78: 4.823 distance: 77 - 78: 4.515 distance: 79 - 80: 8.107 distance: 80 - 81: 7.476 distance: 80 - 83: 8.840 distance: 81 - 82: 15.492 distance: 81 - 90: 8.077 distance: 84 - 85: 17.287 distance: 85 - 86: 17.667 distance: 86 - 87: 14.453 distance: 87 - 88: 17.041 distance: 87 - 89: 9.684 distance: 90 - 91: 15.772 distance: 91 - 92: 26.297 distance: 91 - 94: 20.309 distance: 92 - 93: 9.751 distance: 92 - 97: 38.405 distance: 94 - 95: 24.719 distance: 94 - 96: 5.961 distance: 97 - 98: 17.319 distance: 98 - 99: 16.739 distance: 98 - 101: 12.516 distance: 99 - 106: 9.449 distance: 101 - 102: 18.419 distance: 102 - 103: 27.936 distance: 103 - 104: 10.683 distance: 103 - 105: 10.694 distance: 106 - 107: 7.683 distance: 106 - 112: 18.857 distance: 107 - 108: 27.983 distance: 107 - 110: 19.964 distance: 108 - 109: 14.046 distance: 108 - 113: 12.530 distance: 110 - 111: 12.731 distance: 111 - 112: 5.473 distance: 113 - 114: 4.945 distance: 114 - 117: 7.044 distance: 115 - 116: 5.816 distance: 115 - 120: 8.459 distance: 117 - 118: 6.389