Starting phenix.real_space_refine on Mon Jun 23 09:33:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tf0_25857/06_2025/7tf0_25857.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tf0_25857/06_2025/7tf0_25857.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.02 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7tf0_25857/06_2025/7tf0_25857.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tf0_25857/06_2025/7tf0_25857.map" model { file = "/net/cci-nas-00/data/ceres_data/7tf0_25857/06_2025/7tf0_25857.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tf0_25857/06_2025/7tf0_25857.cif" } resolution = 3.02 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= -0.000 sd= 0.018 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 121 5.16 5 C 17086 2.51 5 N 4399 2.21 5 O 5243 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 26849 Number of models: 1 Model: "" Number of chains: 26 Chain: "A" Number of atoms: 6513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 836, 6513 Classifications: {'peptide': 836} Link IDs: {'PTRANS': 45, 'TRANS': 790} Chain breaks: 8 Chain: "B" Number of atoms: 8093 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1035, 8093 Classifications: {'peptide': 1035} Link IDs: {'PTRANS': 56, 'TRANS': 978} Chain breaks: 7 Chain: "C" Number of atoms: 6513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 836, 6513 Classifications: {'peptide': 836} Link IDs: {'PTRANS': 45, 'TRANS': 790} Chain breaks: 8 Chain: "E" Number of atoms: 4862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 568} 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: "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: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "C" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "E" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 15.27, per 1000 atoms: 0.57 Number of scatterers: 26849 At special positions: 0 Unit cell: (141, 158, 236, 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 121 16.00 O 5243 8.00 N 4399 7.00 C 17086 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, 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 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=2.04 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 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 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS E 133 " - pdb=" SG CYS E 141 " distance=2.04 Simple disulfide: pdb=" SG CYS E 530 " - pdb=" SG CYS E 542 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG 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-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 165 " " NAG A1304 " - " ASN A 234 " " NAG A1305 " - " ASN A 282 " " NAG A1306 " - " ASN A 709 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 165 " " NAG B1304 " - " ASN B 234 " " NAG B1305 " - " ASN B 282 " " NAG B1306 " - " ASN B 331 " " NAG B1307 " - " ASN B 343 " " NAG B1308 " - " ASN B 709 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 122 " " NAG C1303 " - " ASN C 165 " " NAG C1304 " - " ASN C 234 " " NAG C1305 " - " ASN C 282 " " NAG C1306 " - " ASN C 709 " " NAG D 1 " - " ASN A 17 " " NAG E 701 " - " ASN E 53 " " NAG E 702 " - " ASN E 90 " " NAG E 703 " - " ASN E 103 " " NAG E 704 " - " ASN E 322 " " NAG E 705 " - " ASN E 432 " " NAG E 706 " - " ASN E 546 " " NAG F 1 " - " ASN A 717 " " NAG G 1 " - " ASN A 801 " " NAG H 1 " - " ASN A1074 " " NAG I 1 " - " ASN A1098 " " NAG J 1 " - " ASN A1134 " " NAG K 1 " - " ASN B 17 " " NAG L 1 " - " ASN B 717 " " NAG M 1 " - " ASN B 801 " " NAG N 1 " - " ASN B1074 " " NAG O 1 " - " ASN B1098 " " NAG P 1 " - " ASN B1134 " " NAG Q 1 " - " ASN C 17 " " NAG R 1 " - " ASN C 717 " " NAG S 1 " - " ASN C 801 " " NAG T 1 " - " ASN C1074 " " NAG U 1 " - " ASN C1098 " " NAG V 1 " - " ASN C1134 " Time building additional restraints: 7.47 Conformation dependent library (CDL) restraints added in 3.5 seconds 6498 Ramachandran restraints generated. 3249 Oldfield, 0 Emsley, 3249 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6206 Finding SS restraints... Secondary structure from input PDB file: 89 helices and 47 sheets defined 34.5% alpha, 27.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.79 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 616 through 620 removed outlier: 3.861A 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: 3.599A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 919 removed outlier: 3.925A 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 removed outlier: 3.528A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.182A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1147 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 383 through 387 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.673A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 620 removed outlier: 4.048A pdb=" N VAL B 620 " --> pdb=" O CYS B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 744 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: 3.602A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 919 removed outlier: 3.916A 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 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.058A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1147 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 616 through 620 removed outlier: 3.542A pdb=" N GLU C 619 " --> pdb=" O ASN C 616 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N VAL C 620 " --> pdb=" O CYS C 617 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 616 through 620' 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: 3.581A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.748A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 912 through 919 removed outlier: 3.915A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.057A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1147 Processing helix chain 'E' and resid 20 through 53 removed outlier: 4.072A pdb=" N ASP E 38 " --> pdb=" O HIS E 34 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N LEU E 39 " --> pdb=" O GLU E 35 " (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: 3.770A pdb=" N GLU E 87 " --> pdb=" O PRO E 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 101 Processing helix chain 'E' and resid 103 through 108 removed outlier: 4.133A pdb=" N VAL E 107 " --> pdb=" O GLY E 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 129 Processing helix chain 'E' and resid 146 through 155 removed outlier: 3.955A pdb=" N ILE E 151 " --> pdb=" O GLY E 147 " (cutoff:3.500A) Processing helix chain 'E' and resid 157 through 194 Proline residue: E 178 - end of helix removed outlier: 3.651A 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 252 removed outlier: 3.764A pdb=" N LEU E 222 " --> pdb=" O SER E 218 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N ILE E 223 " --> pdb=" O ARG E 219 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLU E 224 " --> pdb=" O GLY E 220 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLU E 232 " --> pdb=" O HIS E 228 " (cutoff:3.500A) Proline residue: E 235 - end of helix Processing helix chain 'E' and resid 265 through 267 No H-bonds generated for 'chain 'E' and resid 265 through 267' Processing helix chain 'E' and resid 275 through 279 removed outlier: 3.818A 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: 3.531A pdb=" N TRP E 328 " --> pdb=" O THR E 324 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 385 removed outlier: 3.679A 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 397 through 413 removed outlier: 4.112A pdb=" N HIS E 401 " --> pdb=" O ASN E 397 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N GLU E 402 " --> pdb=" O GLU E 398 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLY E 405 " --> pdb=" O HIS E 401 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N MET E 408 " --> pdb=" O VAL E 404 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 421 Processing helix chain 'E' and resid 431 through 447 removed outlier: 3.535A pdb=" N GLU E 435 " --> pdb=" O ASP E 431 " (cutoff:3.500A) Processing helix chain 'E' and resid 448 through 466 removed outlier: 4.288A 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 Processing helix chain 'E' and resid 499 through 502 removed outlier: 3.596A 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 513 through 533 removed outlier: 3.600A 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 559 removed outlier: 3.781A pdb=" N MET E 557 " --> pdb=" O LYS E 553 " (cutoff:3.500A) Processing helix chain 'E' and resid 565 through 574 Processing helix chain 'E' and resid 581 through 588 Processing helix chain 'E' and resid 588 through 599 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 Processing sheet with id=AA2, first strand: chain 'A' and resid 27 through 30 removed outlier: 8.140A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 42 through 44 removed outlier: 5.319A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 48 through 55 removed outlier: 4.115A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 83 through 85 removed outlier: 3.993A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL A 126 " --> pdb=" O SER A 172 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 133 through 135 removed outlier: 6.444A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 141 through 144 removed outlier: 6.858A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N ARG A 246 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N VAL A 143 " --> pdb=" O ARG A 246 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.244A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.167A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.187A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.531A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.585A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N LYS B 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.541A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.541A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.337A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 787 through 790 removed outlier: 5.921A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB8, first strand: chain 'B' and resid 27 through 30 Processing sheet with id=AB9, first strand: chain 'B' and resid 27 through 30 removed outlier: 8.026A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.051A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.705A pdb=" N LEU B 84 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N GLU B 132 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N CYS B 166 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 10.200A pdb=" N GLN B 134 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 9.264A pdb=" N ASN B 164 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 141 through 144 removed outlier: 6.872A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N ARG B 246 " --> pdb=" O LEU B 141 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N VAL B 143 " --> pdb=" O ARG B 246 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 318 removed outlier: 6.738A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.183A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.989A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 391 through 392 Processing sheet with id=AC8, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC9, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD1, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.051A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.649A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 701 through 704 removed outlier: 6.713A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) removed outlier: 8.229A pdb=" N LYS C 790 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N ASN B 703 " --> pdb=" O LYS C 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.549A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.549A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.276A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD7, first strand: chain 'C' and resid 27 through 30 Processing sheet with id=AD8, first strand: chain 'C' and resid 27 through 30 removed outlier: 8.245A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 48 through 55 removed outlier: 4.092A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 83 through 85 removed outlier: 3.794A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N GLU C 132 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N CYS C 166 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 9.735A pdb=" N GLN C 134 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 8.885A pdb=" N ASN C 164 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 140 through 144 removed outlier: 6.752A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N ARG C 246 " --> pdb=" O LEU C 141 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N VAL C 143 " --> pdb=" O ARG C 246 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 311 through 317 removed outlier: 6.584A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.082A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.671A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.562A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.562A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.307A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AE9, first strand: chain 'E' and resid 131 through 132 removed outlier: 3.903A pdb=" N LEU E 142 " --> pdb=" O VAL E 132 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'E' and resid 262 through 263 removed outlier: 6.196A pdb=" N LEU E 262 " --> pdb=" O VAL E 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF1 Processing sheet with id=AF2, first strand: chain 'E' and resid 347 through 352 removed outlier: 6.392A pdb=" N ASP E 355 " --> pdb=" O LEU E 351 " (cutoff:3.500A) 1294 hydrogen bonds defined for protein. 3642 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: 12.52 Time building geometry restraints manager: 8.04 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: 8512 1.35 - 1.47: 6971 1.47 - 1.60: 11812 1.60 - 1.72: 0 1.72 - 1.85: 166 Bond restraints: 27461 Sorted by residual: bond pdb=" C1 NAG B1307 " pdb=" O5 NAG B1307 " ideal model delta sigma weight residual 1.406 1.475 -0.069 2.00e-02 2.50e+03 1.20e+01 bond pdb=" C1 NAG E 706 " pdb=" O5 NAG E 706 " ideal model delta sigma weight residual 1.406 1.474 -0.068 2.00e-02 2.50e+03 1.15e+01 bond pdb=" C1 NAG A1303 " pdb=" O5 NAG A1303 " ideal model delta sigma weight residual 1.406 1.469 -0.063 2.00e-02 2.50e+03 9.90e+00 bond pdb=" C1 NAG C1303 " pdb=" O5 NAG C1303 " ideal model delta sigma weight residual 1.406 1.465 -0.059 2.00e-02 2.50e+03 8.81e+00 bond pdb=" C1 NAG B1303 " pdb=" O5 NAG B1303 " ideal model delta sigma weight residual 1.406 1.464 -0.058 2.00e-02 2.50e+03 8.28e+00 ... (remaining 27456 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.05: 36117 2.05 - 4.09: 1147 4.09 - 6.14: 77 6.14 - 8.19: 26 8.19 - 10.23: 3 Bond angle restraints: 37370 Sorted by residual: angle pdb=" C LYS B 528 " pdb=" N LYS B 529 " pdb=" CA LYS B 529 " ideal model delta sigma weight residual 121.54 131.77 -10.23 1.91e+00 2.74e-01 2.87e+01 angle pdb=" N PRO B 986 " pdb=" CA PRO B 986 " pdb=" C PRO B 986 " ideal model delta sigma weight residual 110.70 116.26 -5.56 1.22e+00 6.72e-01 2.08e+01 angle pdb=" N PRO A 986 " pdb=" CA PRO A 986 " pdb=" C PRO A 986 " ideal model delta sigma weight residual 110.70 116.22 -5.52 1.22e+00 6.72e-01 2.04e+01 angle pdb=" N PRO C 986 " pdb=" CA PRO C 986 " pdb=" C PRO C 986 " ideal model delta sigma weight residual 110.70 116.13 -5.43 1.22e+00 6.72e-01 1.98e+01 angle pdb=" C SER B 359 " pdb=" N ASN B 360 " pdb=" CA ASN B 360 " ideal model delta sigma weight residual 122.36 128.54 -6.18 1.42e+00 4.96e-01 1.90e+01 ... (remaining 37365 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 15787 17.82 - 35.64: 1075 35.64 - 53.45: 210 53.45 - 71.27: 58 71.27 - 89.09: 34 Dihedral angle restraints: 17164 sinusoidal: 7546 harmonic: 9618 Sorted by residual: dihedral pdb=" CB CYS E 133 " pdb=" SG CYS E 133 " pdb=" SG CYS E 141 " pdb=" CB CYS E 141 " ideal model delta sinusoidal sigma weight residual -86.00 -51.75 -34.25 1 1.00e+01 1.00e-02 1.66e+01 dihedral pdb=" SG CYS B 391 " pdb=" CB CYS B 525 " pdb=" SG CYS B 525 " pdb=" CA CYS B 525 " ideal model delta sinusoidal sigma weight residual 79.00 17.20 61.80 1 2.00e+01 2.50e-03 1.27e+01 dihedral pdb=" CB CYS A 291 " pdb=" SG CYS A 291 " pdb=" SG CYS A 301 " pdb=" CB CYS A 301 " ideal model delta sinusoidal sigma weight residual 93.00 65.65 27.35 1 1.00e+01 1.00e-02 1.07e+01 ... (remaining 17161 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 3579 0.074 - 0.148: 748 0.148 - 0.221: 61 0.221 - 0.295: 7 0.295 - 0.369: 2 Chirality restraints: 4397 Sorted by residual: chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN A 17 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-01 2.50e+01 3.41e+00 chirality pdb=" C1 NAG Q 1 " pdb=" ND2 ASN C 17 " pdb=" C2 NAG Q 1 " pdb=" O5 NAG Q 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-01 2.50e+01 3.05e+00 chirality pdb=" C1 NAG K 1 " pdb=" ND2 ASN B 17 " pdb=" C2 NAG K 1 " pdb=" O5 NAG K 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-01 2.50e+01 2.04e+00 ... (remaining 4394 not shown) Planarity restraints: 4796 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY C 550 " 0.014 2.00e-02 2.50e+03 2.81e-02 7.92e+00 pdb=" C GLY C 550 " -0.049 2.00e-02 2.50e+03 pdb=" O GLY C 550 " 0.019 2.00e-02 2.50e+03 pdb=" N VAL C 551 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU E 589 " -0.046 5.00e-02 4.00e+02 6.86e-02 7.53e+00 pdb=" N PRO E 590 " 0.119 5.00e-02 4.00e+02 pdb=" CA PRO E 590 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO E 590 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP E 499 " -0.044 5.00e-02 4.00e+02 6.48e-02 6.73e+00 pdb=" N PRO E 500 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO E 500 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO E 500 " -0.037 5.00e-02 4.00e+02 ... (remaining 4793 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 6503 2.80 - 3.32: 23098 3.32 - 3.85: 45804 3.85 - 4.37: 52442 4.37 - 4.90: 90912 Nonbonded interactions: 218759 Sorted by model distance: nonbonded pdb=" OH TYR B 37 " pdb=" O LEU B 54 " model vdw 2.269 3.040 nonbonded pdb=" OH TYR C 37 " pdb=" O LEU C 54 " model vdw 2.286 3.040 nonbonded pdb=" OD1 ASN A 540 " pdb=" OG1 THR A 549 " model vdw 2.288 3.040 nonbonded pdb=" OE1 GLN C 52 " pdb=" OG1 THR C 274 " model vdw 2.296 3.040 nonbonded pdb=" OG1 THR A 323 " pdb=" OE1 GLU A 324 " model vdw 2.322 3.040 ... (remaining 218754 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' } 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: 4.840 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: 0.020 Extract box with map and model: 0.990 Check model and map are aligned: 0.170 Set scattering table: 0.210 Process input model: 62.150 Find NCS groups from input model: 0.870 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:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 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 27559 Z= 0.241 Angle : 0.842 15.066 37628 Z= 0.458 Chirality : 0.057 0.369 4397 Planarity : 0.006 0.075 4752 Dihedral : 13.051 89.092 10850 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.45 % Favored : 98.52 % Rotamer: Outliers : 0.10 % Allowed : 3.55 % Favored : 96.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.13), residues: 3249 helix: 1.74 (0.14), residues: 987 sheet: 1.15 (0.20), residues: 591 loop : -0.65 (0.13), residues: 1671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP E 69 HIS 0.007 0.001 HIS E 378 PHE 0.028 0.002 PHE A 238 TYR 0.032 0.002 TYR E 385 ARG 0.021 0.001 ARG B 158 Details of bonding type rmsd link_NAG-ASN : bond 0.00752 ( 44) link_NAG-ASN : angle 3.69507 ( 132) link_BETA1-4 : bond 0.00606 ( 18) link_BETA1-4 : angle 1.41869 ( 54) hydrogen bonds : bond 0.12671 ( 1246) hydrogen bonds : angle 6.97897 ( 3642) SS BOND : bond 0.00284 ( 36) SS BOND : angle 1.58550 ( 72) covalent geometry : bond 0.00483 (27461) covalent geometry : angle 0.81080 (37370) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6498 Ramachandran restraints generated. 3249 Oldfield, 0 Emsley, 3249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6498 Ramachandran restraints generated. 3249 Oldfield, 0 Emsley, 3249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 341 time to evaluate : 2.839 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.7348 (tp-100) cc_final: 0.7124 (tp-100) REVERT: A 200 TYR cc_start: 0.8610 (m-80) cc_final: 0.8408 (m-80) REVERT: A 238 PHE cc_start: 0.7691 (p90) cc_final: 0.7264 (p90) REVERT: B 188 ASN cc_start: 0.7190 (m-40) cc_final: 0.6817 (m-40) REVERT: C 237 ARG cc_start: 0.8969 (mtp180) cc_final: 0.8705 (mtm-85) REVERT: C 787 GLN cc_start: 0.8341 (mm-40) cc_final: 0.8061 (mm-40) REVERT: C 823 PHE cc_start: 0.8237 (m-80) cc_final: 0.7945 (m-10) REVERT: E 63 ASN cc_start: 0.8335 (m-40) cc_final: 0.8119 (m-40) REVERT: E 240 LEU cc_start: 0.6644 (tp) cc_final: 0.6423 (mt) REVERT: E 552 GLN cc_start: 0.7526 (tp-100) cc_final: 0.6903 (tm-30) REVERT: E 554 LEU cc_start: 0.5980 (tp) cc_final: 0.5595 (tp) outliers start: 3 outliers final: 0 residues processed: 344 average time/residue: 0.4279 time to fit residues: 226.7617 Evaluate side-chains 136 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 2.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 276 optimal weight: 4.9990 chunk 248 optimal weight: 3.9990 chunk 137 optimal weight: 4.9990 chunk 84 optimal weight: 5.9990 chunk 167 optimal weight: 1.9990 chunk 132 optimal weight: 0.8980 chunk 257 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 156 optimal weight: 3.9990 chunk 191 optimal weight: 5.9990 chunk 297 optimal weight: 10.0000 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 121 ASN ** A 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 GLN A1071 HIS B 448 ASN B 450 ASN B 957 GLN ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1071 HIS C 218 GLN C 824 ASN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1071 HIS E 64 ASN E 228 HIS E 374 HIS E 493 HIS E 586 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.116120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.076017 restraints weight = 86224.437| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 3.55 r_work: 0.3111 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.1852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 27559 Z= 0.210 Angle : 0.627 11.061 37628 Z= 0.314 Chirality : 0.045 0.243 4397 Planarity : 0.005 0.068 4752 Dihedral : 6.252 59.651 4823 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.03 % Allowed : 0.86 % Favored : 99.11 % Rotamer: Outliers : 1.07 % Allowed : 6.69 % Favored : 92.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.14), residues: 3249 helix: 2.37 (0.16), residues: 994 sheet: 0.86 (0.20), residues: 631 loop : -0.46 (0.14), residues: 1624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP E 165 HIS 0.007 0.001 HIS A 66 PHE 0.025 0.002 PHE A 133 TYR 0.024 0.002 TYR A 170 ARG 0.011 0.001 ARG A 34 Details of bonding type rmsd link_NAG-ASN : bond 0.00616 ( 44) link_NAG-ASN : angle 2.95804 ( 132) link_BETA1-4 : bond 0.00272 ( 18) link_BETA1-4 : angle 1.15972 ( 54) hydrogen bonds : bond 0.04483 ( 1246) hydrogen bonds : angle 5.64573 ( 3642) SS BOND : bond 0.00212 ( 36) SS BOND : angle 1.07649 ( 72) covalent geometry : bond 0.00469 (27461) covalent geometry : angle 0.60056 (37370) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6498 Ramachandran restraints generated. 3249 Oldfield, 0 Emsley, 3249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6498 Ramachandran restraints generated. 3249 Oldfield, 0 Emsley, 3249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 143 time to evaluate : 2.996 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 TYR cc_start: 0.8905 (m-80) cc_final: 0.8615 (m-80) REVERT: B 92 PHE cc_start: 0.8808 (t80) cc_final: 0.8295 (t80) REVERT: B 188 ASN cc_start: 0.7710 (m-40) cc_final: 0.7227 (m-40) REVERT: B 394 ASN cc_start: 0.9005 (m-40) cc_final: 0.8798 (t0) REVERT: C 900 MET cc_start: 0.8949 (mtp) cc_final: 0.8690 (mtp) REVERT: E 240 LEU cc_start: 0.6607 (tp) cc_final: 0.6346 (mt) REVERT: E 329 GLU cc_start: 0.7671 (mt-10) cc_final: 0.7451 (pt0) outliers start: 31 outliers final: 16 residues processed: 168 average time/residue: 0.4002 time to fit residues: 108.7610 Evaluate side-chains 132 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 116 time to evaluate : 3.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 94 LYS Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 440 LEU Chi-restraints excluded: chain E residue 505 HIS Chi-restraints excluded: chain E residue 555 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 193 optimal weight: 6.9990 chunk 8 optimal weight: 10.0000 chunk 235 optimal weight: 2.9990 chunk 156 optimal weight: 4.9990 chunk 250 optimal weight: 4.9990 chunk 275 optimal weight: 20.0000 chunk 168 optimal weight: 5.9990 chunk 82 optimal weight: 0.8980 chunk 128 optimal weight: 3.9990 chunk 211 optimal weight: 0.9980 chunk 4 optimal weight: 4.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 824 ASN ** A 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 ASN ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 211 ASN ** C 901 GLN ** 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 = 0.4124 r_free = 0.4124 target = 0.118768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.078669 restraints weight = 86557.285| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 3.57 r_work: 0.3052 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.2590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 27559 Z= 0.249 Angle : 0.625 10.760 37628 Z= 0.313 Chirality : 0.045 0.269 4397 Planarity : 0.004 0.059 4752 Dihedral : 6.006 57.783 4823 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.55 % Allowed : 8.03 % Favored : 90.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.14), residues: 3249 helix: 2.35 (0.16), residues: 992 sheet: 0.50 (0.20), residues: 621 loop : -0.49 (0.14), residues: 1636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 165 HIS 0.006 0.001 HIS A 207 PHE 0.024 0.002 PHE A 238 TYR 0.025 0.002 TYR B1067 ARG 0.014 0.001 ARG B 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00625 ( 44) link_NAG-ASN : angle 2.79120 ( 132) link_BETA1-4 : bond 0.00325 ( 18) link_BETA1-4 : angle 1.08222 ( 54) hydrogen bonds : bond 0.04436 ( 1246) hydrogen bonds : angle 5.48972 ( 3642) SS BOND : bond 0.00240 ( 36) SS BOND : angle 0.97074 ( 72) covalent geometry : bond 0.00564 (27461) covalent geometry : angle 0.60213 (37370) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6498 Ramachandran restraints generated. 3249 Oldfield, 0 Emsley, 3249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6498 Ramachandran restraints generated. 3249 Oldfield, 0 Emsley, 3249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 118 time to evaluate : 2.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 983 ARG cc_start: 0.8377 (mtp180) cc_final: 0.8025 (tpm170) REVERT: A 1138 TYR cc_start: 0.8877 (t80) cc_final: 0.8597 (t80) REVERT: B 92 PHE cc_start: 0.8771 (t80) cc_final: 0.8203 (t80) REVERT: B 188 ASN cc_start: 0.7762 (m110) cc_final: 0.7280 (m-40) REVERT: C 900 MET cc_start: 0.9025 (mtp) cc_final: 0.8767 (mtp) REVERT: E 190 MET cc_start: 0.3740 (ppp) cc_final: 0.3284 (ppp) REVERT: E 215 TYR cc_start: 0.3671 (OUTLIER) cc_final: 0.3375 (t80) REVERT: E 240 LEU cc_start: 0.6577 (tp) cc_final: 0.6301 (mt) REVERT: E 455 MET cc_start: 0.5526 (ptm) cc_final: 0.5310 (ptm) outliers start: 45 outliers final: 26 residues processed: 155 average time/residue: 0.3473 time to fit residues: 90.1707 Evaluate side-chains 130 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 103 time to evaluate : 2.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 923 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 449 TYR Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain C residue 211 ASN Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 94 LYS Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 215 TYR Chi-restraints excluded: chain E residue 440 LEU Chi-restraints excluded: chain E residue 505 HIS Chi-restraints excluded: chain E residue 535 HIS Chi-restraints excluded: chain E residue 548 THR Chi-restraints excluded: chain E residue 555 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 206 optimal weight: 8.9990 chunk 150 optimal weight: 0.7980 chunk 242 optimal weight: 0.6980 chunk 284 optimal weight: 4.9990 chunk 59 optimal weight: 0.6980 chunk 303 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 chunk 160 optimal weight: 1.9990 chunk 6 optimal weight: 9.9990 chunk 102 optimal weight: 2.9990 chunk 268 optimal weight: 0.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN A 613 GLN ** A 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 ASN B 493 GLN B 907 ASN ** B1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 86 GLN E 221 GLN ** E 228 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 = 0.4139 r_free = 0.4139 target = 0.117698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.077999 restraints weight = 86148.770| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 3.64 r_work: 0.3088 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.2697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 27559 Z= 0.125 Angle : 0.538 10.410 37628 Z= 0.268 Chirality : 0.043 0.267 4397 Planarity : 0.004 0.053 4752 Dihedral : 5.555 54.367 4823 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 1.07 % Allowed : 9.07 % Favored : 89.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.14), residues: 3249 helix: 2.49 (0.16), residues: 998 sheet: 0.45 (0.20), residues: 620 loop : -0.45 (0.14), residues: 1631 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 165 HIS 0.009 0.001 HIS E 228 PHE 0.026 0.001 PHE A 133 TYR 0.022 0.001 TYR A1067 ARG 0.006 0.000 ARG E 482 Details of bonding type rmsd link_NAG-ASN : bond 0.00503 ( 44) link_NAG-ASN : angle 2.62508 ( 132) link_BETA1-4 : bond 0.00245 ( 18) link_BETA1-4 : angle 0.94189 ( 54) hydrogen bonds : bond 0.03918 ( 1246) hydrogen bonds : angle 5.26717 ( 3642) SS BOND : bond 0.00150 ( 36) SS BOND : angle 0.78865 ( 72) covalent geometry : bond 0.00274 (27461) covalent geometry : angle 0.51483 (37370) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6498 Ramachandran restraints generated. 3249 Oldfield, 0 Emsley, 3249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6498 Ramachandran restraints generated. 3249 Oldfield, 0 Emsley, 3249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 117 time to evaluate : 3.014 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 983 ARG cc_start: 0.8361 (mtp180) cc_final: 0.7994 (tpm170) REVERT: A 1138 TYR cc_start: 0.8889 (t80) cc_final: 0.8609 (t80) REVERT: B 92 PHE cc_start: 0.8791 (t80) cc_final: 0.8263 (t80) REVERT: B 188 ASN cc_start: 0.7567 (m110) cc_final: 0.7082 (m-40) REVERT: E 190 MET cc_start: 0.3604 (ppp) cc_final: 0.3164 (ppp) REVERT: E 240 LEU cc_start: 0.6741 (tp) cc_final: 0.6380 (mt) REVERT: E 557 MET cc_start: 0.5327 (ptp) cc_final: 0.5045 (ptp) outliers start: 31 outliers final: 18 residues processed: 140 average time/residue: 0.3346 time to fit residues: 81.0581 Evaluate side-chains 126 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 108 time to evaluate : 3.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 923 ILE Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 449 TYR Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 440 LEU Chi-restraints excluded: chain E residue 505 HIS Chi-restraints excluded: chain E residue 535 HIS Chi-restraints excluded: chain E residue 555 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 255 optimal weight: 4.9990 chunk 320 optimal weight: 0.4980 chunk 149 optimal weight: 1.9990 chunk 268 optimal weight: 0.8980 chunk 197 optimal weight: 1.9990 chunk 196 optimal weight: 6.9990 chunk 62 optimal weight: 3.9990 chunk 230 optimal weight: 2.9990 chunk 258 optimal weight: 0.0000 chunk 315 optimal weight: 9.9990 chunk 91 optimal weight: 9.9990 overall best weight: 1.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN E 86 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.114048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.074305 restraints weight = 87112.784| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 3.55 r_work: 0.3098 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.2851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 27559 Z= 0.125 Angle : 0.518 10.228 37628 Z= 0.258 Chirality : 0.043 0.270 4397 Planarity : 0.003 0.051 4752 Dihedral : 5.144 55.280 4823 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 1.21 % Allowed : 9.34 % Favored : 89.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.14), residues: 3249 helix: 2.56 (0.16), residues: 998 sheet: 0.39 (0.19), residues: 630 loop : -0.38 (0.15), residues: 1621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 165 HIS 0.005 0.001 HIS E 228 PHE 0.026 0.001 PHE A 133 TYR 0.022 0.001 TYR B1067 ARG 0.003 0.000 ARG C 158 Details of bonding type rmsd link_NAG-ASN : bond 0.00505 ( 44) link_NAG-ASN : angle 2.51418 ( 132) link_BETA1-4 : bond 0.00273 ( 18) link_BETA1-4 : angle 0.93934 ( 54) hydrogen bonds : bond 0.03741 ( 1246) hydrogen bonds : angle 5.11210 ( 3642) SS BOND : bond 0.00151 ( 36) SS BOND : angle 0.76509 ( 72) covalent geometry : bond 0.00275 (27461) covalent geometry : angle 0.49542 (37370) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6498 Ramachandran restraints generated. 3249 Oldfield, 0 Emsley, 3249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6498 Ramachandran restraints generated. 3249 Oldfield, 0 Emsley, 3249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 116 time to evaluate : 3.541 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 983 ARG cc_start: 0.8328 (mtp180) cc_final: 0.8001 (tpm170) REVERT: B 92 PHE cc_start: 0.8787 (t80) cc_final: 0.8245 (t80) REVERT: B 188 ASN cc_start: 0.7615 (m110) cc_final: 0.7132 (m-40) REVERT: C 1010 GLN cc_start: 0.9252 (OUTLIER) cc_final: 0.8811 (mp10) REVERT: E 190 MET cc_start: 0.3581 (ppp) cc_final: 0.3117 (ppp) REVERT: E 240 LEU cc_start: 0.6736 (tp) cc_final: 0.6359 (mt) REVERT: E 323 MET cc_start: 0.5334 (mmt) cc_final: 0.3553 (mtp) REVERT: E 557 MET cc_start: 0.5492 (ptp) cc_final: 0.5198 (ptp) outliers start: 35 outliers final: 24 residues processed: 143 average time/residue: 0.3846 time to fit residues: 96.2859 Evaluate side-chains 129 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 104 time to evaluate : 3.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 923 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 449 TYR Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 215 TYR Chi-restraints excluded: chain E residue 440 LEU Chi-restraints excluded: chain E residue 505 HIS Chi-restraints excluded: chain E residue 535 HIS Chi-restraints excluded: chain E residue 555 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 251 optimal weight: 5.9990 chunk 53 optimal weight: 4.9990 chunk 247 optimal weight: 2.9990 chunk 262 optimal weight: 0.6980 chunk 101 optimal weight: 0.0270 chunk 243 optimal weight: 3.9990 chunk 191 optimal weight: 10.0000 chunk 113 optimal weight: 2.9990 chunk 105 optimal weight: 3.9990 chunk 18 optimal weight: 7.9990 chunk 213 optimal weight: 0.9980 overall best weight: 1.5442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 86 GLN E 221 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.113478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.073697 restraints weight = 86981.355| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 3.54 r_work: 0.3083 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.3021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 27559 Z= 0.152 Angle : 0.528 10.151 37628 Z= 0.264 Chirality : 0.043 0.276 4397 Planarity : 0.003 0.047 4752 Dihedral : 4.972 55.480 4823 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 1.14 % Allowed : 9.90 % Favored : 88.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.14), residues: 3249 helix: 2.54 (0.16), residues: 998 sheet: 0.32 (0.19), residues: 632 loop : -0.40 (0.15), residues: 1619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 165 HIS 0.005 0.001 HIS E 228 PHE 0.027 0.001 PHE A 133 TYR 0.022 0.001 TYR A1067 ARG 0.002 0.000 ARG E 482 Details of bonding type rmsd link_NAG-ASN : bond 0.00509 ( 44) link_NAG-ASN : angle 2.48217 ( 132) link_BETA1-4 : bond 0.00251 ( 18) link_BETA1-4 : angle 0.96614 ( 54) hydrogen bonds : bond 0.03784 ( 1246) hydrogen bonds : angle 5.09493 ( 3642) SS BOND : bond 0.00162 ( 36) SS BOND : angle 0.76445 ( 72) covalent geometry : bond 0.00341 (27461) covalent geometry : angle 0.50691 (37370) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6498 Ramachandran restraints generated. 3249 Oldfield, 0 Emsley, 3249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6498 Ramachandran restraints generated. 3249 Oldfield, 0 Emsley, 3249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 105 time to evaluate : 3.092 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 902 MET cc_start: 0.9158 (tpp) cc_final: 0.8894 (tpt) REVERT: A 983 ARG cc_start: 0.8308 (mtp180) cc_final: 0.8009 (tpm170) REVERT: A 1050 MET cc_start: 0.9278 (ptm) cc_final: 0.9070 (ptm) REVERT: B 92 PHE cc_start: 0.8789 (t80) cc_final: 0.8234 (t80) REVERT: B 188 ASN cc_start: 0.7637 (m110) cc_final: 0.7130 (m-40) REVERT: C 1010 GLN cc_start: 0.9281 (OUTLIER) cc_final: 0.9009 (mm110) REVERT: E 240 LEU cc_start: 0.6801 (tp) cc_final: 0.6438 (mt) REVERT: E 557 MET cc_start: 0.5314 (ptp) cc_final: 0.4996 (ptp) outliers start: 33 outliers final: 26 residues processed: 129 average time/residue: 0.3829 time to fit residues: 85.7381 Evaluate side-chains 126 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 99 time to evaluate : 3.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 923 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 449 TYR Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 215 TYR Chi-restraints excluded: chain E residue 221 GLN Chi-restraints excluded: chain E residue 440 LEU Chi-restraints excluded: chain E residue 535 HIS Chi-restraints excluded: chain E residue 555 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 18 optimal weight: 7.9990 chunk 14 optimal weight: 9.9990 chunk 11 optimal weight: 3.9990 chunk 122 optimal weight: 10.0000 chunk 46 optimal weight: 5.9990 chunk 74 optimal weight: 0.8980 chunk 167 optimal weight: 0.9980 chunk 96 optimal weight: 10.0000 chunk 182 optimal weight: 0.8980 chunk 54 optimal weight: 0.9990 chunk 69 optimal weight: 4.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN ** B1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 86 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.113538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.073766 restraints weight = 87293.429| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 3.53 r_work: 0.3083 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.3142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 27559 Z= 0.152 Angle : 0.529 10.024 37628 Z= 0.264 Chirality : 0.043 0.281 4397 Planarity : 0.003 0.050 4752 Dihedral : 4.885 55.949 4823 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 1.28 % Allowed : 10.14 % Favored : 88.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.14), residues: 3249 helix: 2.52 (0.16), residues: 1010 sheet: 0.25 (0.19), residues: 660 loop : -0.40 (0.15), residues: 1579 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 165 HIS 0.004 0.001 HIS E 228 PHE 0.027 0.001 PHE A 133 TYR 0.022 0.001 TYR A1067 ARG 0.003 0.000 ARG E 482 Details of bonding type rmsd link_NAG-ASN : bond 0.00504 ( 44) link_NAG-ASN : angle 2.44022 ( 132) link_BETA1-4 : bond 0.00267 ( 18) link_BETA1-4 : angle 0.95263 ( 54) hydrogen bonds : bond 0.03760 ( 1246) hydrogen bonds : angle 5.07386 ( 3642) SS BOND : bond 0.00154 ( 36) SS BOND : angle 0.74676 ( 72) covalent geometry : bond 0.00342 (27461) covalent geometry : angle 0.50787 (37370) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6498 Ramachandran restraints generated. 3249 Oldfield, 0 Emsley, 3249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6498 Ramachandran restraints generated. 3249 Oldfield, 0 Emsley, 3249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 102 time to evaluate : 3.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 983 ARG cc_start: 0.8283 (mtp180) cc_final: 0.8007 (tpm170) REVERT: B 92 PHE cc_start: 0.8810 (t80) cc_final: 0.8235 (t80) REVERT: B 188 ASN cc_start: 0.7594 (m110) cc_final: 0.7093 (m-40) REVERT: C 1010 GLN cc_start: 0.9296 (OUTLIER) cc_final: 0.9025 (mm110) REVERT: E 190 MET cc_start: 0.3328 (ppp) cc_final: 0.2674 (ppp) REVERT: E 240 LEU cc_start: 0.6787 (tp) cc_final: 0.6408 (mt) REVERT: E 376 MET cc_start: 0.4498 (ptm) cc_final: 0.4297 (ppp) REVERT: E 535 HIS cc_start: 0.5345 (OUTLIER) cc_final: 0.4952 (t-90) outliers start: 37 outliers final: 25 residues processed: 132 average time/residue: 0.3433 time to fit residues: 79.4795 Evaluate side-chains 126 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 99 time to evaluate : 2.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 923 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 449 TYR Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 215 TYR Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 440 LEU Chi-restraints excluded: chain E residue 535 HIS Chi-restraints excluded: chain E residue 555 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 158 optimal weight: 0.6980 chunk 210 optimal weight: 5.9990 chunk 285 optimal weight: 5.9990 chunk 81 optimal weight: 0.7980 chunk 103 optimal weight: 7.9990 chunk 317 optimal weight: 9.9990 chunk 204 optimal weight: 5.9990 chunk 303 optimal weight: 20.0000 chunk 112 optimal weight: 10.0000 chunk 16 optimal weight: 9.9990 chunk 86 optimal weight: 4.9990 overall best weight: 3.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 755 GLN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 824 ASN ** B1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 211 ASN E 86 GLN E 221 GLN E 239 HIS E 580 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.116424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.076292 restraints weight = 87157.039| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 3.52 r_work: 0.3020 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.3645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.059 27559 Z= 0.318 Angle : 0.674 10.149 37628 Z= 0.335 Chirality : 0.047 0.285 4397 Planarity : 0.004 0.054 4752 Dihedral : 5.544 54.746 4823 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.52 % Allowed : 10.24 % Favored : 88.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.14), residues: 3249 helix: 2.17 (0.16), residues: 1013 sheet: 0.07 (0.18), residues: 713 loop : -0.61 (0.15), residues: 1523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP B 258 HIS 0.008 0.001 HIS E 373 PHE 0.029 0.002 PHE A 133 TYR 0.024 0.002 TYR B1067 ARG 0.005 0.001 ARG B 190 Details of bonding type rmsd link_NAG-ASN : bond 0.00705 ( 44) link_NAG-ASN : angle 2.70041 ( 132) link_BETA1-4 : bond 0.00276 ( 18) link_BETA1-4 : angle 1.21769 ( 54) hydrogen bonds : bond 0.04570 ( 1246) hydrogen bonds : angle 5.45407 ( 3642) SS BOND : bond 0.00242 ( 36) SS BOND : angle 0.95277 ( 72) covalent geometry : bond 0.00723 (27461) covalent geometry : angle 0.65361 (37370) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6498 Ramachandran restraints generated. 3249 Oldfield, 0 Emsley, 3249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6498 Ramachandran restraints generated. 3249 Oldfield, 0 Emsley, 3249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 102 time to evaluate : 2.770 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 PHE cc_start: 0.6959 (p90) cc_final: 0.6736 (p90) REVERT: A 983 ARG cc_start: 0.8218 (mtp180) cc_final: 0.8006 (tpm170) REVERT: B 92 PHE cc_start: 0.8835 (t80) cc_final: 0.8252 (t80) REVERT: B 188 ASN cc_start: 0.7605 (m110) cc_final: 0.7113 (m-40) REVERT: B 867 ASP cc_start: 0.8811 (m-30) cc_final: 0.8435 (t0) REVERT: E 190 MET cc_start: 0.3495 (ppp) cc_final: 0.2847 (ppp) REVERT: E 240 LEU cc_start: 0.6598 (tp) cc_final: 0.6274 (mt) REVERT: E 557 MET cc_start: 0.5445 (ptp) cc_final: 0.5089 (ptp) outliers start: 44 outliers final: 32 residues processed: 137 average time/residue: 0.3509 time to fit residues: 83.1796 Evaluate side-chains 124 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 92 time to evaluate : 2.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 211 ASN Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain E residue 215 TYR Chi-restraints excluded: chain E residue 221 GLN Chi-restraints excluded: chain E residue 334 THR Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 440 LEU Chi-restraints excluded: chain E residue 505 HIS Chi-restraints excluded: chain E residue 535 HIS Chi-restraints excluded: chain E residue 555 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 69 optimal weight: 0.8980 chunk 76 optimal weight: 0.7980 chunk 55 optimal weight: 0.0980 chunk 131 optimal weight: 1.9990 chunk 313 optimal weight: 4.9990 chunk 287 optimal weight: 20.0000 chunk 233 optimal weight: 0.9990 chunk 57 optimal weight: 0.3980 chunk 73 optimal weight: 0.5980 chunk 265 optimal weight: 0.9990 chunk 97 optimal weight: 10.0000 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 907 ASN A 955 ASN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN E 86 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.113193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.073511 restraints weight = 87078.798| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 3.61 r_work: 0.3076 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.3525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 27559 Z= 0.109 Angle : 0.554 13.947 37628 Z= 0.274 Chirality : 0.044 0.286 4397 Planarity : 0.003 0.049 4752 Dihedral : 5.175 57.761 4823 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 0.97 % Allowed : 10.93 % Favored : 88.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.15), residues: 3249 helix: 2.42 (0.16), residues: 1012 sheet: 0.19 (0.19), residues: 695 loop : -0.48 (0.15), residues: 1542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 258 HIS 0.005 0.001 HIS E 228 PHE 0.034 0.001 PHE A 133 TYR 0.022 0.001 TYR A1067 ARG 0.004 0.000 ARG E 482 Details of bonding type rmsd link_NAG-ASN : bond 0.00419 ( 44) link_NAG-ASN : angle 2.65061 ( 132) link_BETA1-4 : bond 0.00562 ( 18) link_BETA1-4 : angle 1.12046 ( 54) hydrogen bonds : bond 0.03781 ( 1246) hydrogen bonds : angle 5.18631 ( 3642) SS BOND : bond 0.00161 ( 36) SS BOND : angle 0.75876 ( 72) covalent geometry : bond 0.00232 (27461) covalent geometry : angle 0.53035 (37370) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6498 Ramachandran restraints generated. 3249 Oldfield, 0 Emsley, 3249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6498 Ramachandran restraints generated. 3249 Oldfield, 0 Emsley, 3249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 100 time to evaluate : 3.014 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 983 ARG cc_start: 0.8203 (mtp180) cc_final: 0.7962 (tpm170) REVERT: B 92 PHE cc_start: 0.8844 (t80) cc_final: 0.8290 (t80) REVERT: B 188 ASN cc_start: 0.7726 (m110) cc_final: 0.7233 (m-40) REVERT: E 190 MET cc_start: 0.3367 (ppp) cc_final: 0.2745 (ppp) REVERT: E 240 LEU cc_start: 0.6692 (tp) cc_final: 0.6362 (mt) REVERT: E 535 HIS cc_start: 0.5334 (OUTLIER) cc_final: 0.4878 (t-90) REVERT: E 557 MET cc_start: 0.5459 (ptp) cc_final: 0.5083 (ptp) outliers start: 28 outliers final: 22 residues processed: 122 average time/residue: 0.3451 time to fit residues: 73.4335 Evaluate side-chains 120 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 97 time to evaluate : 3.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 215 TYR Chi-restraints excluded: chain E residue 334 THR Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 535 HIS Chi-restraints excluded: chain E residue 555 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 153 optimal weight: 0.6980 chunk 258 optimal weight: 2.9990 chunk 141 optimal weight: 1.9990 chunk 216 optimal weight: 2.9990 chunk 233 optimal weight: 6.9990 chunk 61 optimal weight: 2.9990 chunk 87 optimal weight: 8.9990 chunk 2 optimal weight: 4.9990 chunk 173 optimal weight: 4.9990 chunk 223 optimal weight: 0.0170 chunk 204 optimal weight: 3.9990 overall best weight: 1.7424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN E 221 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.112355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.072578 restraints weight = 86798.202| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 3.60 r_work: 0.3060 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.3611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 27559 Z= 0.171 Angle : 0.561 10.068 37628 Z= 0.278 Chirality : 0.044 0.286 4397 Planarity : 0.003 0.050 4752 Dihedral : 5.103 56.725 4823 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 0.93 % Allowed : 10.93 % Favored : 88.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.15), residues: 3249 helix: 2.44 (0.16), residues: 1012 sheet: 0.14 (0.19), residues: 709 loop : -0.47 (0.15), residues: 1528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 258 HIS 0.005 0.001 HIS E 228 PHE 0.032 0.001 PHE A 133 TYR 0.022 0.001 TYR B1067 ARG 0.003 0.000 ARG E 482 Details of bonding type rmsd link_NAG-ASN : bond 0.00492 ( 44) link_NAG-ASN : angle 2.41318 ( 132) link_BETA1-4 : bond 0.00259 ( 18) link_BETA1-4 : angle 1.00797 ( 54) hydrogen bonds : bond 0.03833 ( 1246) hydrogen bonds : angle 5.16089 ( 3642) SS BOND : bond 0.00157 ( 36) SS BOND : angle 0.79081 ( 72) covalent geometry : bond 0.00387 (27461) covalent geometry : angle 0.54226 (37370) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6498 Ramachandran restraints generated. 3249 Oldfield, 0 Emsley, 3249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6498 Ramachandran restraints generated. 3249 Oldfield, 0 Emsley, 3249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 95 time to evaluate : 2.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 983 ARG cc_start: 0.8208 (mtp180) cc_final: 0.7955 (tpm170) REVERT: B 92 PHE cc_start: 0.8837 (t80) cc_final: 0.8248 (t80) REVERT: B 188 ASN cc_start: 0.7663 (m110) cc_final: 0.7167 (m-40) REVERT: B 867 ASP cc_start: 0.8774 (m-30) cc_final: 0.8406 (t0) REVERT: E 190 MET cc_start: 0.3342 (ppp) cc_final: 0.2745 (ppp) REVERT: E 240 LEU cc_start: 0.6689 (tp) cc_final: 0.6349 (mt) REVERT: E 535 HIS cc_start: 0.5382 (OUTLIER) cc_final: 0.4971 (t-90) REVERT: E 557 MET cc_start: 0.5451 (ptp) cc_final: 0.5094 (ptp) outliers start: 27 outliers final: 24 residues processed: 118 average time/residue: 0.3313 time to fit residues: 68.8954 Evaluate side-chains 118 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 93 time to evaluate : 2.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 215 TYR Chi-restraints excluded: chain E residue 334 THR Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 535 HIS Chi-restraints excluded: chain E residue 555 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 99 optimal weight: 1.9990 chunk 289 optimal weight: 9.9990 chunk 202 optimal weight: 3.9990 chunk 107 optimal weight: 7.9990 chunk 239 optimal weight: 2.9990 chunk 248 optimal weight: 0.5980 chunk 129 optimal weight: 9.9990 chunk 287 optimal weight: 20.0000 chunk 126 optimal weight: 6.9990 chunk 119 optimal weight: 9.9990 chunk 249 optimal weight: 0.0870 overall best weight: 1.9364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN E 86 GLN E 221 GLN ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.102718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.063413 restraints weight = 87885.823| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 3.43 r_work: 0.3058 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.3668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 27559 Z= 0.180 Angle : 0.560 9.984 37628 Z= 0.277 Chirality : 0.044 0.290 4397 Planarity : 0.003 0.049 4752 Dihedral : 5.109 56.959 4823 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 0.97 % Allowed : 11.03 % Favored : 88.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.15), residues: 3249 helix: 2.44 (0.16), residues: 1012 sheet: 0.11 (0.19), residues: 708 loop : -0.47 (0.15), residues: 1529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 258 HIS 0.006 0.001 HIS E 228 PHE 0.032 0.001 PHE A 133 TYR 0.022 0.001 TYR A1067 ARG 0.006 0.000 ARG C 905 Details of bonding type rmsd link_NAG-ASN : bond 0.00463 ( 44) link_NAG-ASN : angle 2.36569 ( 132) link_BETA1-4 : bond 0.00248 ( 18) link_BETA1-4 : angle 0.97780 ( 54) hydrogen bonds : bond 0.03833 ( 1246) hydrogen bonds : angle 5.16262 ( 3642) SS BOND : bond 0.00159 ( 36) SS BOND : angle 0.79629 ( 72) covalent geometry : bond 0.00408 (27461) covalent geometry : angle 0.54138 (37370) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 24890.35 seconds wall clock time: 435 minutes 42.61 seconds (26142.61 seconds total)