Starting phenix.real_space_refine on Tue Jun 24 19:44:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sxz_25511/06_2025/7sxz_25511.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sxz_25511/06_2025/7sxz_25511.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.61 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7sxz_25511/06_2025/7sxz_25511.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sxz_25511/06_2025/7sxz_25511.map" model { file = "/net/cci-nas-00/data/ceres_data/7sxz_25511/06_2025/7sxz_25511.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sxz_25511/06_2025/7sxz_25511.cif" } resolution = 2.61 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= -0.001 sd= 0.039 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 132 5.16 5 C 18191 2.51 5 N 4679 2.21 5 O 5581 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 28583 Number of models: 1 Model: "" Number of chains: 26 Chain: "A" Number of atoms: 6555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 841, 6555 Classifications: {'peptide': 841} Link IDs: {'PTRANS': 45, 'TRANS': 795} Chain breaks: 8 Chain: "B" Number of atoms: 8135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1040, 8135 Classifications: {'peptide': 1040} Link IDs: {'PTRANS': 56, 'TRANS': 983} Chain breaks: 7 Chain: "C" Number of atoms: 8135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1040, 8135 Classifications: {'peptide': 1040} Link IDs: {'PTRANS': 56, 'TRANS': 983} Chain breaks: 7 Chain: "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: 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: "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: 17.01, per 1000 atoms: 0.60 Number of scatterers: 28583 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 132 16.00 O 5581 8.00 N 4679 7.00 C 18191 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=40, 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=2.04 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.04 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 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 331 " " NAG C1307 " - " ASN C 343 " " NAG C1308 " - " 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: 7.41 Conformation dependent library (CDL) restraints added in 3.6 seconds 6930 Ramachandran restraints generated. 3465 Oldfield, 0 Emsley, 3465 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6604 Finding SS restraints... Secondary structure from input PDB file: 93 helices and 42 sheets defined 33.2% alpha, 21.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.64 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 616 through 620 removed outlier: 3.890A 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: 3.640A 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: 3.942A 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: 3.564A 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 1032 removed outlier: 4.265A 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 406 through 410 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.697A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 620 removed outlier: 4.084A 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: 3.609A 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: 3.927A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.047A 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 337 through 343 removed outlier: 3.839A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 386 through 390 removed outlier: 3.842A pdb=" N LEU C 390 " --> pdb=" O LEU C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 409 removed outlier: 3.895A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 removed outlier: 3.611A pdb=" N ASP C 420 " --> pdb=" O GLY C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 616 through 620 removed outlier: 3.549A pdb=" N GLU C 619 " --> pdb=" O ASN C 616 " (cutoff:3.500A) removed outlier: 3.972A 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: 3.598A 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 897 through 909 removed outlier: 3.549A pdb=" N ALA C 903 " --> pdb=" O PRO C 899 " (cutoff:3.500A) Processing helix chain 'C' and resid 912 through 919 removed outlier: 3.888A 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 removed outlier: 3.503A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1032 removed outlier: 4.118A 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: 4.153A pdb=" N ASP E 38 " --> pdb=" O HIS E 34 " (cutoff:3.500A) removed outlier: 4.114A 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: 3.823A 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: 4.084A 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: 3.988A 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: 3.706A 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: 3.700A pdb=" N LEU E 222 " --> pdb=" O SER E 218 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N ILE E 223 " --> pdb=" O ARG E 219 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N GLU E 224 " --> pdb=" O GLY E 220 " (cutoff:3.500A) removed outlier: 3.854A 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: 3.796A pdb=" N TYR E 279 " --> pdb=" O THR E 276 " (cutoff:3.500A) Processing helix chain 'E' and resid 293 through 301 Processing helix chain 'E' and resid 303 through 318 Processing helix chain 'E' and resid 324 through 331 removed outlier: 3.548A pdb=" N TRP E 328 " --> pdb=" O THR E 324 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 385 removed outlier: 3.684A 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: 4.252A pdb=" N HIS E 401 " --> pdb=" O ASN E 397 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N GLU E 402 " --> pdb=" O GLU E 398 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLY E 405 " --> pdb=" O HIS E 401 " (cutoff:3.500A) removed outlier: 3.949A 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: 3.529A pdb=" N GLU E 435 " --> pdb=" O ASP E 431 " (cutoff:3.500A) Processing helix chain 'E' and resid 448 through 465 removed outlier: 4.388A 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: 3.768A pdb=" N SER E 502 " --> pdb=" O ASP E 499 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 499 through 502' Processing helix chain 'E' and resid 503 through 508 Processing helix chain 'E' and resid 512 through 533 removed outlier: 4.447A pdb=" N TYR E 516 " --> pdb=" O PHE E 512 " (cutoff:3.500A) removed outlier: 3.571A 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: 3.875A 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 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 78 through 79 current: chain 'A' and resid 188 through 197 removed outlier: 6.306A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 4.108A pdb=" N ARG C 567 " --> pdb=" O PHE A 43 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 4.178A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 83 through 85 removed outlier: 3.932A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL A 126 " --> pdb=" O SER A 172 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 154 through 163 removed outlier: 9.490A pdb=" N SER A 155 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 11.361A pdb=" N PHE A 140 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 9.807A pdb=" N PHE A 157 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 11.279A pdb=" N ASP A 138 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N VAL A 159 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 8.114A pdb=" N LEU A 244 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N ARG A 246 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N VAL A 143 " --> pdb=" O ARG A 246 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.210A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.114A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.108A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.452A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.596A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N LYS B 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 711 through 728 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 711 through 728 current: chain 'A' and resid 1059 through 1078 removed outlier: 3.848A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.312A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 787 through 790 removed outlier: 5.911A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB5, first strand: chain 'B' and resid 27 through 30 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 78 through 79 current: chain 'B' and resid 188 through 197 removed outlier: 6.342A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.008A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 84 through 85 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 84 through 85 current: chain 'B' and resid 116 through 121 removed outlier: 11.407A pdb=" N VAL B 126 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 10.004A pdb=" N GLU B 169 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 11.295A pdb=" N ILE B 128 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 8.646A pdb=" N THR B 167 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N VAL B 130 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ASN B 165 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N GLU B 132 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N ALA B 163 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N GLN B 134 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N VAL B 159 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 11.041A pdb=" N ASP B 138 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 9.368A pdb=" N PHE B 157 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 11.515A pdb=" N PHE B 140 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 9.451A pdb=" N SER B 155 " --> pdb=" O PHE B 140 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 154 through 172 current: chain 'B' and resid 259 through 260 Processing sheet with id=AB8, first strand: chain 'B' and resid 311 through 318 removed outlier: 6.708A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.146A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.250A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 391 through 392 Processing sheet with id=AC3, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC4, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC5, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.123A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.721A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 701 through 704 removed outlier: 3.820A pdb=" N LYS C 790 " --> pdb=" O ASN B 703 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 711 through 728 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 711 through 728 current: chain 'B' and resid 1059 through 1078 removed outlier: 3.886A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.259A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD1, first strand: chain 'C' and resid 27 through 30 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 78 through 79 current: chain 'C' and resid 188 through 197 removed outlier: 5.938A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 48 through 55 removed outlier: 4.124A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 83 through 85 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 83 through 85 current: chain 'C' and resid 116 through 121 removed outlier: 3.585A pdb=" N VAL C 126 " --> pdb=" O SER C 172 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N GLU C 132 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N CYS C 166 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 9.953A pdb=" N GLN C 134 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 9.036A pdb=" N ASN C 164 " --> pdb=" O GLN C 134 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N CYS C 136 " --> pdb=" O SER C 162 " (cutoff:3.500A) removed outlier: 10.230A pdb=" N SER C 162 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 9.913A pdb=" N ASP C 138 " --> pdb=" O TYR C 160 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N TYR C 160 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLU C 156 " --> pdb=" O GLY C 142 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N TYR C 144 " --> pdb=" O GLU C 154 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N GLU C 154 " --> pdb=" O TYR C 144 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 154 through 172 current: chain 'C' and resid 259 through 260 Processing sheet with id=AD4, first strand: chain 'C' and resid 311 through 319 removed outlier: 6.695A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.841A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.863A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AD8, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.535A pdb=" N TYR C 473 " --> pdb=" O TYR C 489 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.030A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.593A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 711 through 728 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 711 through 728 current: chain 'C' and resid 1059 through 1078 removed outlier: 3.912A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.327A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AE4, first strand: chain 'E' and resid 131 through 132 removed outlier: 3.752A pdb=" N LEU E 142 " --> pdb=" O VAL E 132 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 262 through 263 removed outlier: 5.939A pdb=" N LEU E 262 " --> pdb=" O VAL E 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'E' and resid 347 through 352 removed outlier: 6.333A pdb=" N ASP E 355 " --> pdb=" O LEU E 351 " (cutoff:3.500A) 1148 hydrogen bonds defined for protein. 3228 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: 12.16 Time building geometry restraints manager: 8.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9009 1.34 - 1.47: 7369 1.47 - 1.59: 12683 1.59 - 1.72: 0 1.72 - 1.84: 180 Bond restraints: 29241 Sorted by residual: bond pdb=" C1 NAG D 1 " pdb=" O5 NAG D 1 " ideal model delta sigma weight residual 1.406 1.462 -0.056 2.00e-02 2.50e+03 7.93e+00 bond pdb=" C1 NAG A1303 " pdb=" O5 NAG A1303 " ideal model delta sigma weight residual 1.406 1.461 -0.055 2.00e-02 2.50e+03 7.55e+00 bond pdb=" C1 NAG U 1 " pdb=" O5 NAG U 1 " ideal model delta sigma weight residual 1.406 1.461 -0.055 2.00e-02 2.50e+03 7.48e+00 bond pdb=" C1 NAG I 1 " pdb=" O5 NAG I 1 " ideal model delta sigma weight residual 1.406 1.461 -0.055 2.00e-02 2.50e+03 7.47e+00 bond pdb=" C1 NAG C1303 " pdb=" O5 NAG C1303 " ideal model delta sigma weight residual 1.406 1.460 -0.054 2.00e-02 2.50e+03 7.38e+00 ... (remaining 29236 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.01: 38351 2.01 - 4.02: 1285 4.02 - 6.03: 112 6.03 - 8.04: 28 8.04 - 10.05: 11 Bond angle restraints: 39787 Sorted by residual: angle pdb=" C SER B 359 " pdb=" N ASN B 360 " pdb=" CA ASN B 360 " ideal model delta sigma weight residual 122.82 129.36 -6.54 1.42e+00 4.96e-01 2.12e+01 angle pdb=" N PRO C 986 " pdb=" CA PRO C 986 " pdb=" C PRO C 986 " ideal model delta sigma weight residual 110.70 116.27 -5.57 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 110.70 116.23 -5.53 1.22e+00 6.72e-01 2.05e+01 angle pdb=" N PRO B 986 " pdb=" CA PRO B 986 " pdb=" C PRO B 986 " ideal model delta sigma weight residual 110.70 115.88 -5.18 1.22e+00 6.72e-01 1.81e+01 angle pdb=" CA GLU C 583 " pdb=" CB GLU C 583 " pdb=" CG GLU C 583 " ideal model delta sigma weight residual 114.10 122.06 -7.96 2.00e+00 2.50e-01 1.58e+01 ... (remaining 39782 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 16803 17.92 - 35.85: 1178 35.85 - 53.77: 177 53.77 - 71.70: 58 71.70 - 89.62: 36 Dihedral angle restraints: 18252 sinusoidal: 8006 harmonic: 10246 Sorted by residual: dihedral pdb=" CA LEU C 517 " pdb=" C LEU C 517 " pdb=" N LEU C 518 " pdb=" CA LEU C 518 " ideal model delta harmonic sigma weight residual 180.00 154.55 25.45 0 5.00e+00 4.00e-02 2.59e+01 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 -46.34 -39.66 1 1.00e+01 1.00e-02 2.21e+01 dihedral pdb=" CA PHE C 515 " pdb=" C PHE C 515 " pdb=" N GLU C 516 " pdb=" CA GLU C 516 " ideal model delta harmonic sigma weight residual 180.00 157.53 22.47 0 5.00e+00 4.00e-02 2.02e+01 ... (remaining 18249 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 3762 0.071 - 0.143: 799 0.143 - 0.214: 85 0.214 - 0.286: 6 0.286 - 0.357: 1 Chirality restraints: 4653 Sorted by residual: 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 -2.04 -0.36 2.00e-01 2.50e+01 3.19e+00 chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN A 17 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.12 -0.28 2.00e-01 2.50e+01 2.03e+00 chirality pdb=" CB VAL B 576 " pdb=" CA VAL B 576 " pdb=" CG1 VAL B 576 " pdb=" CG2 VAL B 576 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.66e+00 ... (remaining 4650 not shown) Planarity restraints: 5116 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 394 " -0.035 2.00e-02 2.50e+03 7.13e-02 5.08e+01 pdb=" CG ASN C 394 " 0.123 2.00e-02 2.50e+03 pdb=" OD1 ASN C 394 " -0.047 2.00e-02 2.50e+03 pdb=" ND2 ASN C 394 " -0.040 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA E 36 " 0.021 2.00e-02 2.50e+03 4.15e-02 1.72e+01 pdb=" C ALA E 36 " -0.072 2.00e-02 2.50e+03 pdb=" O ALA E 36 " 0.027 2.00e-02 2.50e+03 pdb=" N GLU E 37 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG E 169 " 0.015 2.00e-02 2.50e+03 3.08e-02 9.47e+00 pdb=" C ARG E 169 " -0.053 2.00e-02 2.50e+03 pdb=" O ARG E 169 " 0.020 2.00e-02 2.50e+03 pdb=" N SER E 170 " 0.018 2.00e-02 2.50e+03 ... (remaining 5113 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 7451 2.80 - 3.33: 24622 3.33 - 3.85: 49344 3.85 - 4.38: 56706 4.38 - 4.90: 97196 Nonbonded interactions: 235319 Sorted by model distance: nonbonded pdb=" OG1 THR C 323 " pdb=" OE1 GLU C 324 " model vdw 2.280 3.040 nonbonded pdb=" OH TYR C 37 " pdb=" O LEU C 54 " model vdw 2.291 3.040 nonbonded pdb=" OH TYR B 37 " pdb=" O LEU B 54 " model vdw 2.292 3.040 nonbonded pdb=" OE1 GLN A 115 " pdb=" OG1 THR A 167 " model vdw 2.301 3.040 nonbonded pdb=" OD1 ASN A 540 " pdb=" OG1 THR A 549 " model vdw 2.305 3.040 ... (remaining 235314 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 'B' 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: 4.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.270 Check model and map are aligned: 0.200 Set scattering table: 0.300 Process input model: 66.170 Find NCS groups from input model: 0.910 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: 0.000 Load rotamer database and sin/cos tables:12.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 85.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 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 0.058 29345 Z= 0.240 Angle : 0.853 15.325 40059 Z= 0.453 Chirality : 0.057 0.357 4653 Planarity : 0.006 0.071 5070 Dihedral : 12.887 89.619 11528 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.54 % 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: -0.12 (0.13), residues: 3465 helix: 0.71 (0.14), residues: 1003 sheet: 0.55 (0.19), residues: 688 loop : -0.78 (0.13), residues: 1774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 886 HIS 0.007 0.001 HIS E 378 PHE 0.034 0.002 PHE A 238 TYR 0.033 0.002 TYR A 200 ARG 0.008 0.001 ARG A 328 Details of bonding type rmsd link_NAG-ASN : bond 0.00666 ( 46) link_NAG-ASN : angle 3.83602 ( 138) link_BETA1-4 : bond 0.00563 ( 18) link_BETA1-4 : angle 1.87566 ( 54) hydrogen bonds : bond 0.12446 ( 1148) hydrogen bonds : angle 6.79532 ( 3228) SS BOND : bond 0.00282 ( 40) SS BOND : angle 1.59772 ( 80) covalent geometry : bond 0.00490 (29241) covalent geometry : angle 0.81923 (39787) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6930 Ramachandran restraints generated. 3465 Oldfield, 0 Emsley, 3465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6930 Ramachandran restraints generated. 3465 Oldfield, 0 Emsley, 3465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 290 time to evaluate : 3.127 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 175 PHE cc_start: 0.5120 (m-10) cc_final: 0.4429 (m-10) REVERT: A 1029 MET cc_start: 0.9141 (tpp) cc_final: 0.8908 (tpp) REVERT: B 54 LEU cc_start: 0.9228 (mp) cc_final: 0.8804 (tp) REVERT: B 88 ASP cc_start: 0.8933 (m-30) cc_final: 0.8649 (p0) REVERT: B 153 MET cc_start: 0.5775 (ptt) cc_final: 0.4789 (pmt) REVERT: B 369 TYR cc_start: 0.8443 (t80) cc_final: 0.8080 (t80) REVERT: B 370 ASN cc_start: 0.8908 (m-40) cc_final: 0.7823 (p0) REVERT: C 565 PHE cc_start: 0.8149 (p90) cc_final: 0.7895 (p90) REVERT: E 341 LYS cc_start: 0.7989 (mmtt) cc_final: 0.7729 (ptpp) REVERT: E 480 MET cc_start: 0.1418 (mtp) cc_final: 0.0923 (mpp) REVERT: E 559 ARG cc_start: 0.7420 (ptm-80) cc_final: 0.7186 (ttp80) outliers start: 0 outliers final: 2 residues processed: 290 average time/residue: 1.4980 time to fit residues: 507.4935 Evaluate side-chains 132 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 130 time to evaluate : 3.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain C residue 360 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 296 optimal weight: 30.0000 chunk 266 optimal weight: 0.9990 chunk 147 optimal weight: 0.6980 chunk 90 optimal weight: 6.9990 chunk 179 optimal weight: 3.9990 chunk 142 optimal weight: 6.9990 chunk 275 optimal weight: 2.9990 chunk 106 optimal weight: 5.9990 chunk 167 optimal weight: 0.7980 chunk 204 optimal weight: 1.9990 chunk 318 optimal weight: 6.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN A 926 GLN A1011 GLN B 115 GLN B 173 GLN B 354 ASN ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN C 394 ASN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 578 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4545 r_free = 0.4545 target = 0.137601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.095260 restraints weight = 103402.161| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 5.34 r_work: 0.3052 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.1559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 29345 Z= 0.166 Angle : 0.592 11.050 40059 Z= 0.298 Chirality : 0.044 0.246 4653 Planarity : 0.004 0.055 5070 Dihedral : 5.388 52.200 5109 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 0.94 % Allowed : 7.61 % Favored : 91.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.54 % 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: 0.47 (0.14), residues: 3465 helix: 1.74 (0.16), residues: 1017 sheet: 0.58 (0.20), residues: 654 loop : -0.63 (0.13), residues: 1794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 353 HIS 0.005 0.001 HIS E 505 PHE 0.024 0.001 PHE A 238 TYR 0.016 0.001 TYR A 170 ARG 0.009 0.001 ARG A 765 Details of bonding type rmsd link_NAG-ASN : bond 0.00566 ( 46) link_NAG-ASN : angle 3.03125 ( 138) link_BETA1-4 : bond 0.00325 ( 18) link_BETA1-4 : angle 1.07189 ( 54) hydrogen bonds : bond 0.04257 ( 1148) hydrogen bonds : angle 5.44308 ( 3228) SS BOND : bond 0.00211 ( 40) SS BOND : angle 1.04388 ( 80) covalent geometry : bond 0.00368 (29241) covalent geometry : angle 0.56302 (39787) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6930 Ramachandran restraints generated. 3465 Oldfield, 0 Emsley, 3465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6930 Ramachandran restraints generated. 3465 Oldfield, 0 Emsley, 3465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 146 time to evaluate : 3.088 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: A 88 ASP cc_start: 0.8366 (OUTLIER) cc_final: 0.8025 (p0) REVERT: A 153 MET cc_start: 0.5437 (ptt) cc_final: 0.5145 (ppp) REVERT: A 168 PHE cc_start: 0.8199 (t80) cc_final: 0.7740 (t80) REVERT: A 170 TYR cc_start: 0.8739 (t80) cc_final: 0.8358 (t80) REVERT: A 200 TYR cc_start: 0.8355 (m-80) cc_final: 0.8056 (m-80) REVERT: A 226 LEU cc_start: 0.8532 (mt) cc_final: 0.8274 (pt) REVERT: B 54 LEU cc_start: 0.9443 (mp) cc_final: 0.8843 (tp) REVERT: B 88 ASP cc_start: 0.9137 (m-30) cc_final: 0.8594 (p0) REVERT: B 153 MET cc_start: 0.5711 (ptt) cc_final: 0.4702 (pmt) REVERT: B 369 TYR cc_start: 0.8661 (t80) cc_final: 0.8315 (t80) REVERT: B 370 ASN cc_start: 0.8971 (m-40) cc_final: 0.7998 (p0) REVERT: B 451 TYR cc_start: 0.5887 (m-80) cc_final: 0.5597 (m-80) REVERT: B 1002 GLN cc_start: 0.8112 (tm-30) cc_final: 0.7720 (tm-30) REVERT: C 565 PHE cc_start: 0.8009 (p90) cc_final: 0.7728 (p90) REVERT: E 474 MET cc_start: 0.1505 (mmm) cc_final: 0.0242 (mmm) REVERT: E 559 ARG cc_start: 0.7438 (ptm-80) cc_final: 0.7175 (ttp-110) outliers start: 29 outliers final: 9 residues processed: 165 average time/residue: 1.3594 time to fit residues: 266.8970 Evaluate side-chains 128 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 118 time to evaluate : 3.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain E residue 90 ASN Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 571 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 245 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 132 optimal weight: 10.0000 chunk 29 optimal weight: 8.9990 chunk 172 optimal weight: 0.8980 chunk 123 optimal weight: 20.0000 chunk 180 optimal weight: 1.9990 chunk 329 optimal weight: 10.0000 chunk 148 optimal weight: 3.9990 chunk 168 optimal weight: 0.7980 chunk 32 optimal weight: 9.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN B 580 GLN ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 824 ASN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN ** C1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 374 HIS E 524 GLN E 552 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4534 r_free = 0.4534 target = 0.136944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.095036 restraints weight = 103307.930| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 5.69 r_work: 0.3022 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.2022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 29345 Z= 0.160 Angle : 0.555 11.017 40059 Z= 0.277 Chirality : 0.044 0.268 4653 Planarity : 0.004 0.040 5070 Dihedral : 4.977 52.259 5105 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.23 % Allowed : 8.23 % Favored : 90.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.54 % 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: 0.67 (0.14), residues: 3465 helix: 2.00 (0.16), residues: 1032 sheet: 0.49 (0.20), residues: 642 loop : -0.48 (0.14), residues: 1791 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 353 HIS 0.004 0.001 HIS E 505 PHE 0.024 0.001 PHE C 79 TYR 0.020 0.001 TYR B 365 ARG 0.007 0.000 ARG C 567 Details of bonding type rmsd link_NAG-ASN : bond 0.00633 ( 46) link_NAG-ASN : angle 2.77297 ( 138) link_BETA1-4 : bond 0.00265 ( 18) link_BETA1-4 : angle 1.00551 ( 54) hydrogen bonds : bond 0.04070 ( 1148) hydrogen bonds : angle 5.16793 ( 3228) SS BOND : bond 0.00283 ( 40) SS BOND : angle 0.96059 ( 80) covalent geometry : bond 0.00359 (29241) covalent geometry : angle 0.52904 (39787) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6930 Ramachandran restraints generated. 3465 Oldfield, 0 Emsley, 3465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6930 Ramachandran restraints generated. 3465 Oldfield, 0 Emsley, 3465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 137 time to evaluate : 3.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 ASP cc_start: 0.8541 (OUTLIER) cc_final: 0.8189 (p0) REVERT: A 153 MET cc_start: 0.5283 (ptt) cc_final: 0.5034 (ppp) REVERT: A 168 PHE cc_start: 0.8370 (t80) cc_final: 0.7959 (t80) REVERT: A 170 TYR cc_start: 0.8558 (t80) cc_final: 0.8311 (t80) REVERT: A 175 PHE cc_start: 0.4136 (m-10) cc_final: 0.3914 (m-10) REVERT: A 200 TYR cc_start: 0.8246 (m-80) cc_final: 0.8019 (m-80) REVERT: A 773 GLU cc_start: 0.8836 (tt0) cc_final: 0.8506 (tt0) REVERT: A 1005 GLN cc_start: 0.8897 (tt0) cc_final: 0.8692 (tt0) REVERT: B 54 LEU cc_start: 0.9450 (mp) cc_final: 0.8815 (tp) REVERT: B 88 ASP cc_start: 0.9211 (m-30) cc_final: 0.8473 (p0) REVERT: B 153 MET cc_start: 0.5647 (ptt) cc_final: 0.4809 (pmt) REVERT: B 369 TYR cc_start: 0.8831 (t80) cc_final: 0.8448 (t80) REVERT: B 370 ASN cc_start: 0.8947 (m-40) cc_final: 0.8071 (p0) REVERT: B 425 LEU cc_start: 0.6507 (mm) cc_final: 0.6188 (mp) REVERT: B 451 TYR cc_start: 0.6058 (m-80) cc_final: 0.5736 (m-80) REVERT: B 1002 GLN cc_start: 0.8267 (tm-30) cc_final: 0.7637 (tm-30) REVERT: C 130 VAL cc_start: 0.8169 (t) cc_final: 0.7873 (p) REVERT: C 245 HIS cc_start: 0.6851 (OUTLIER) cc_final: 0.6431 (m-70) REVERT: C 584 ILE cc_start: 0.7098 (OUTLIER) cc_final: 0.6871 (mm) REVERT: C 957 GLN cc_start: 0.8710 (tm-30) cc_final: 0.8501 (tm-30) REVERT: E 474 MET cc_start: 0.0723 (mmm) cc_final: 0.0401 (mmm) REVERT: E 559 ARG cc_start: 0.7637 (ptm-80) cc_final: 0.7340 (ttp-110) REVERT: E 579 MET cc_start: 0.5580 (tpp) cc_final: 0.4986 (tpt) REVERT: E 606 TRP cc_start: 0.1804 (p90) cc_final: 0.1343 (p90) REVERT: E 613 TYR cc_start: 0.4970 (t80) cc_final: 0.4536 (m-10) outliers start: 38 outliers final: 13 residues processed: 160 average time/residue: 1.5216 time to fit residues: 301.0385 Evaluate side-chains 137 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 121 time to evaluate : 3.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain C residue 175 PHE Chi-restraints excluded: chain C residue 245 HIS Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain E residue 90 ASN Chi-restraints excluded: chain E residue 479 GLU Chi-restraints excluded: chain E residue 548 THR Chi-restraints excluded: chain E residue 571 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 47 optimal weight: 3.9990 chunk 1 optimal weight: 0.0370 chunk 63 optimal weight: 6.9990 chunk 275 optimal weight: 3.9990 chunk 277 optimal weight: 4.9990 chunk 308 optimal weight: 9.9990 chunk 198 optimal weight: 10.0000 chunk 50 optimal weight: 0.9990 chunk 118 optimal weight: 10.0000 chunk 254 optimal weight: 4.9990 chunk 255 optimal weight: 1.9990 overall best weight: 2.2066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 824 ASN A 955 ASN B 824 ASN B 907 ASN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN ** C1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 96 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.126072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.072328 restraints weight = 84342.534| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 5.24 r_work: 0.2974 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 29345 Z= 0.209 Angle : 0.576 11.125 40059 Z= 0.285 Chirality : 0.044 0.260 4653 Planarity : 0.004 0.038 5070 Dihedral : 4.988 52.356 5105 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.33 % Allowed : 8.84 % Favored : 89.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.54 % 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 (0.14), residues: 3465 helix: 2.08 (0.16), residues: 1029 sheet: 0.21 (0.20), residues: 639 loop : -0.45 (0.14), residues: 1797 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP E 594 HIS 0.004 0.001 HIS E 505 PHE 0.025 0.001 PHE A 157 TYR 0.024 0.001 TYR B 351 ARG 0.004 0.000 ARG C 567 Details of bonding type rmsd link_NAG-ASN : bond 0.00650 ( 46) link_NAG-ASN : angle 2.73857 ( 138) link_BETA1-4 : bond 0.00209 ( 18) link_BETA1-4 : angle 1.11878 ( 54) hydrogen bonds : bond 0.04137 ( 1148) hydrogen bonds : angle 5.14806 ( 3228) SS BOND : bond 0.00224 ( 40) SS BOND : angle 0.91760 ( 80) covalent geometry : bond 0.00470 (29241) covalent geometry : angle 0.55247 (39787) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6930 Ramachandran restraints generated. 3465 Oldfield, 0 Emsley, 3465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6930 Ramachandran restraints generated. 3465 Oldfield, 0 Emsley, 3465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 120 time to evaluate : 3.529 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: A 88 ASP cc_start: 0.8533 (OUTLIER) cc_final: 0.8282 (p0) REVERT: A 168 PHE cc_start: 0.8280 (t80) cc_final: 0.7820 (t80) REVERT: A 329 PHE cc_start: 0.8364 (OUTLIER) cc_final: 0.8093 (m-10) REVERT: A 773 GLU cc_start: 0.8816 (tt0) cc_final: 0.8459 (tt0) REVERT: A 1010 GLN cc_start: 0.8829 (OUTLIER) cc_final: 0.8581 (mp10) REVERT: B 54 LEU cc_start: 0.9467 (mp) cc_final: 0.8787 (tp) REVERT: B 88 ASP cc_start: 0.9169 (m-30) cc_final: 0.8503 (p0) REVERT: B 153 MET cc_start: 0.6010 (ptt) cc_final: 0.5044 (pmt) REVERT: B 369 TYR cc_start: 0.8827 (t80) cc_final: 0.8453 (t80) REVERT: B 370 ASN cc_start: 0.8971 (m-40) cc_final: 0.8123 (p0) REVERT: B 425 LEU cc_start: 0.6571 (mm) cc_final: 0.6309 (mp) REVERT: B 451 TYR cc_start: 0.6027 (m-80) cc_final: 0.5814 (m-80) REVERT: B 1002 GLN cc_start: 0.8464 (tm-30) cc_final: 0.7850 (tm-30) REVERT: C 130 VAL cc_start: 0.8339 (t) cc_final: 0.8055 (p) REVERT: C 245 HIS cc_start: 0.6742 (OUTLIER) cc_final: 0.6228 (m-70) REVERT: C 993 ILE cc_start: 0.9023 (OUTLIER) cc_final: 0.8716 (mp) REVERT: E 140 GLU cc_start: 0.1511 (OUTLIER) cc_final: 0.1219 (tt0) REVERT: E 358 ILE cc_start: 0.2794 (OUTLIER) cc_final: 0.2571 (tt) REVERT: E 553 LYS cc_start: 0.6996 (OUTLIER) cc_final: 0.6781 (ttpt) REVERT: E 559 ARG cc_start: 0.7613 (ptm-80) cc_final: 0.7409 (ttp-110) REVERT: E 606 TRP cc_start: 0.2248 (p90) cc_final: 0.2028 (p90) REVERT: E 613 TYR cc_start: 0.5011 (t80) cc_final: 0.4651 (m-10) outliers start: 41 outliers final: 13 residues processed: 143 average time/residue: 1.1488 time to fit residues: 201.4966 Evaluate side-chains 134 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 113 time to evaluate : 3.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 1146 ASP Chi-restraints excluded: chain C residue 175 PHE Chi-restraints excluded: chain C residue 245 HIS Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain E residue 90 ASN Chi-restraints excluded: chain E residue 140 GLU Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 358 ILE Chi-restraints excluded: chain E residue 479 GLU Chi-restraints excluded: chain E residue 553 LYS Chi-restraints excluded: chain E residue 571 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 282 optimal weight: 2.9990 chunk 2 optimal weight: 6.9990 chunk 279 optimal weight: 3.9990 chunk 59 optimal weight: 0.5980 chunk 295 optimal weight: 20.0000 chunk 198 optimal weight: 9.9990 chunk 140 optimal weight: 6.9990 chunk 257 optimal weight: 0.9980 chunk 64 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 133 optimal weight: 5.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 779 GLN A 955 ASN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.124997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 87)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.069842 restraints weight = 84104.858| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 4.34 r_work: 0.2972 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.2870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 29345 Z= 0.230 Angle : 0.584 12.258 40059 Z= 0.289 Chirality : 0.045 0.264 4653 Planarity : 0.004 0.038 5070 Dihedral : 5.072 53.308 5105 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.10 % Allowed : 9.72 % Favored : 89.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.54 % 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: 0.61 (0.14), residues: 3465 helix: 2.12 (0.16), residues: 1027 sheet: 0.00 (0.19), residues: 700 loop : -0.44 (0.14), residues: 1738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP E 594 HIS 0.004 0.001 HIS E 265 PHE 0.020 0.002 PHE A 157 TYR 0.026 0.001 TYR B 351 ARG 0.008 0.001 ARG E 169 Details of bonding type rmsd link_NAG-ASN : bond 0.00652 ( 46) link_NAG-ASN : angle 2.73076 ( 138) link_BETA1-4 : bond 0.00178 ( 18) link_BETA1-4 : angle 1.10300 ( 54) hydrogen bonds : bond 0.04203 ( 1148) hydrogen bonds : angle 5.16192 ( 3228) SS BOND : bond 0.00211 ( 40) SS BOND : angle 0.85470 ( 80) covalent geometry : bond 0.00521 (29241) covalent geometry : angle 0.56116 (39787) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6930 Ramachandran restraints generated. 3465 Oldfield, 0 Emsley, 3465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6930 Ramachandran restraints generated. 3465 Oldfield, 0 Emsley, 3465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 116 time to evaluate : 3.012 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.5496 (ptt) cc_final: 0.5176 (ppp) REVERT: A 168 PHE cc_start: 0.8202 (t80) cc_final: 0.7840 (t80) REVERT: A 170 TYR cc_start: 0.8758 (t80) cc_final: 0.8524 (t80) REVERT: A 200 TYR cc_start: 0.8581 (m-80) cc_final: 0.8162 (m-10) REVERT: A 329 PHE cc_start: 0.8424 (OUTLIER) cc_final: 0.8090 (m-80) REVERT: A 773 GLU cc_start: 0.8797 (tt0) cc_final: 0.8454 (tt0) REVERT: B 88 ASP cc_start: 0.9124 (m-30) cc_final: 0.8783 (p0) REVERT: B 153 MET cc_start: 0.6139 (ptt) cc_final: 0.5077 (pmt) REVERT: B 369 TYR cc_start: 0.8662 (t80) cc_final: 0.8332 (t80) REVERT: B 370 ASN cc_start: 0.8995 (m-40) cc_final: 0.8065 (p0) REVERT: B 425 LEU cc_start: 0.6456 (mm) cc_final: 0.6177 (mp) REVERT: B 451 TYR cc_start: 0.6171 (m-80) cc_final: 0.5843 (m-80) REVERT: C 130 VAL cc_start: 0.8389 (t) cc_final: 0.8095 (p) REVERT: C 245 HIS cc_start: 0.6710 (OUTLIER) cc_final: 0.6176 (m-70) REVERT: C 584 ILE cc_start: 0.7352 (OUTLIER) cc_final: 0.7110 (mm) REVERT: C 993 ILE cc_start: 0.8969 (OUTLIER) cc_final: 0.8665 (mp) REVERT: E 140 GLU cc_start: 0.1214 (OUTLIER) cc_final: 0.0894 (tt0) REVERT: E 474 MET cc_start: 0.0245 (mmm) cc_final: -0.0086 (mmm) REVERT: E 553 LYS cc_start: 0.7311 (mptt) cc_final: 0.7006 (ttpt) REVERT: E 559 ARG cc_start: 0.7688 (ptm-80) cc_final: 0.7480 (ttp80) REVERT: E 606 TRP cc_start: 0.2062 (p90) cc_final: 0.1834 (p90) REVERT: E 613 TYR cc_start: 0.4943 (t80) cc_final: 0.4598 (m-10) outliers start: 34 outliers final: 11 residues processed: 138 average time/residue: 1.1956 time to fit residues: 202.1556 Evaluate side-chains 123 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 107 time to evaluate : 3.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain C residue 175 PHE Chi-restraints excluded: chain C residue 245 HIS Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain E residue 90 ASN Chi-restraints excluded: chain E residue 140 GLU Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 479 GLU Chi-restraints excluded: chain E residue 571 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 276 optimal weight: 1.9990 chunk 302 optimal weight: 9.9990 chunk 113 optimal weight: 7.9990 chunk 226 optimal weight: 10.0000 chunk 65 optimal weight: 2.9990 chunk 347 optimal weight: 7.9990 chunk 328 optimal weight: 20.0000 chunk 178 optimal weight: 0.6980 chunk 213 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 208 optimal weight: 7.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1005 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN ** C1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 241 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.125140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.069949 restraints weight = 83544.057| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 4.31 r_work: 0.2961 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.3218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 29345 Z= 0.233 Angle : 0.581 11.416 40059 Z= 0.289 Chirality : 0.045 0.265 4653 Planarity : 0.004 0.048 5070 Dihedral : 5.147 54.395 5105 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.17 % Allowed : 10.30 % Favored : 88.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.54 % 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: 0.61 (0.14), residues: 3465 helix: 2.16 (0.16), residues: 1024 sheet: -0.08 (0.19), residues: 711 loop : -0.42 (0.14), residues: 1730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP E 473 HIS 0.003 0.001 HIS E 345 PHE 0.022 0.001 PHE C 106 TYR 0.027 0.001 TYR E 497 ARG 0.012 0.001 ARG E 245 Details of bonding type rmsd link_NAG-ASN : bond 0.00660 ( 46) link_NAG-ASN : angle 2.71027 ( 138) link_BETA1-4 : bond 0.00227 ( 18) link_BETA1-4 : angle 1.08312 ( 54) hydrogen bonds : bond 0.04179 ( 1148) hydrogen bonds : angle 5.11947 ( 3228) SS BOND : bond 0.00217 ( 40) SS BOND : angle 0.80634 ( 80) covalent geometry : bond 0.00527 (29241) covalent geometry : angle 0.55794 (39787) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6930 Ramachandran restraints generated. 3465 Oldfield, 0 Emsley, 3465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6930 Ramachandran restraints generated. 3465 Oldfield, 0 Emsley, 3465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 110 time to evaluate : 3.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 THR cc_start: 0.8053 (p) cc_final: 0.7840 (p) REVERT: A 153 MET cc_start: 0.5452 (ptt) cc_final: 0.5062 (ppp) REVERT: A 200 TYR cc_start: 0.8547 (m-80) cc_final: 0.8330 (m-10) REVERT: A 773 GLU cc_start: 0.8797 (tt0) cc_final: 0.8430 (tt0) REVERT: A 1010 GLN cc_start: 0.8891 (OUTLIER) cc_final: 0.8623 (mp10) REVERT: B 88 ASP cc_start: 0.9088 (m-30) cc_final: 0.8636 (p0) REVERT: B 153 MET cc_start: 0.6040 (ptt) cc_final: 0.5125 (pmt) REVERT: B 369 TYR cc_start: 0.8687 (t80) cc_final: 0.8341 (t80) REVERT: B 370 ASN cc_start: 0.9013 (m-40) cc_final: 0.8076 (p0) REVERT: B 425 LEU cc_start: 0.6411 (mm) cc_final: 0.6125 (mp) REVERT: B 451 TYR cc_start: 0.6167 (m-80) cc_final: 0.5816 (m-80) REVERT: C 130 VAL cc_start: 0.8357 (t) cc_final: 0.8066 (p) REVERT: C 324 GLU cc_start: 0.8700 (OUTLIER) cc_final: 0.8191 (pm20) REVERT: E 553 LYS cc_start: 0.7343 (mptt) cc_final: 0.7070 (ttpt) REVERT: E 559 ARG cc_start: 0.7809 (ptm-80) cc_final: 0.7540 (ttp-110) REVERT: E 606 TRP cc_start: 0.2329 (p90) cc_final: 0.2012 (p90) REVERT: E 613 TYR cc_start: 0.4937 (t80) cc_final: 0.4597 (m-10) outliers start: 36 outliers final: 15 residues processed: 136 average time/residue: 1.3411 time to fit residues: 222.2558 Evaluate side-chains 119 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 102 time to evaluate : 3.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain C residue 175 PHE Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain E residue 90 ASN Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 479 GLU Chi-restraints excluded: chain E residue 548 THR Chi-restraints excluded: chain E residue 571 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 37 optimal weight: 4.9990 chunk 109 optimal weight: 0.2980 chunk 160 optimal weight: 0.6980 chunk 223 optimal weight: 0.0020 chunk 301 optimal weight: 10.0000 chunk 93 optimal weight: 7.9990 chunk 118 optimal weight: 2.9990 chunk 108 optimal weight: 8.9990 chunk 89 optimal weight: 10.0000 chunk 265 optimal weight: 0.7980 chunk 321 optimal weight: 30.0000 overall best weight: 0.9590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN C1011 GLN E 241 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.123172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.073579 restraints weight = 87605.218| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 3.64 r_work: 0.3004 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.3226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 29345 Z= 0.121 Angle : 0.522 11.307 40059 Z= 0.259 Chirality : 0.043 0.276 4653 Planarity : 0.003 0.037 5070 Dihedral : 4.841 53.848 5105 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.84 % Allowed : 11.24 % Favored : 87.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.54 % 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: 0.78 (0.14), residues: 3465 helix: 2.34 (0.16), residues: 1030 sheet: -0.15 (0.19), residues: 676 loop : -0.26 (0.14), residues: 1759 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 353 HIS 0.003 0.001 HIS E 34 PHE 0.022 0.001 PHE A 168 TYR 0.025 0.001 TYR A 170 ARG 0.008 0.000 ARG E 245 Details of bonding type rmsd link_NAG-ASN : bond 0.00541 ( 46) link_NAG-ASN : angle 2.52528 ( 138) link_BETA1-4 : bond 0.00294 ( 18) link_BETA1-4 : angle 0.88980 ( 54) hydrogen bonds : bond 0.03737 ( 1148) hydrogen bonds : angle 4.90741 ( 3228) SS BOND : bond 0.00142 ( 40) SS BOND : angle 0.62876 ( 80) covalent geometry : bond 0.00269 (29241) covalent geometry : angle 0.50026 (39787) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6930 Ramachandran restraints generated. 3465 Oldfield, 0 Emsley, 3465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6930 Ramachandran restraints generated. 3465 Oldfield, 0 Emsley, 3465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 114 time to evaluate : 3.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.5666 (ptt) cc_final: 0.5278 (ppp) REVERT: A 168 PHE cc_start: 0.8133 (t80) cc_final: 0.7834 (t80) REVERT: A 200 TYR cc_start: 0.8593 (m-80) cc_final: 0.8283 (m-10) REVERT: A 201 PHE cc_start: 0.8859 (t80) cc_final: 0.8654 (t80) REVERT: A 304 LYS cc_start: 0.9338 (mmmm) cc_final: 0.9069 (mptp) REVERT: A 773 GLU cc_start: 0.8775 (tt0) cc_final: 0.8395 (tt0) REVERT: B 88 ASP cc_start: 0.9072 (m-30) cc_final: 0.8647 (p0) REVERT: B 153 MET cc_start: 0.6223 (ptt) cc_final: 0.5242 (pmt) REVERT: B 369 TYR cc_start: 0.8595 (t80) cc_final: 0.8267 (t80) REVERT: B 370 ASN cc_start: 0.8993 (m-40) cc_final: 0.7976 (p0) REVERT: B 425 LEU cc_start: 0.6281 (mm) cc_final: 0.6004 (mp) REVERT: B 451 TYR cc_start: 0.6202 (m-80) cc_final: 0.5803 (m-80) REVERT: C 130 VAL cc_start: 0.8354 (t) cc_final: 0.8076 (p) REVERT: C 173 GLN cc_start: 0.7774 (OUTLIER) cc_final: 0.7396 (tm-30) REVERT: E 192 ARG cc_start: 0.5016 (OUTLIER) cc_final: 0.4692 (tmt-80) REVERT: E 606 TRP cc_start: 0.2077 (p90) cc_final: 0.1687 (p90) REVERT: E 613 TYR cc_start: 0.4781 (t80) cc_final: 0.4425 (m-10) outliers start: 26 outliers final: 9 residues processed: 134 average time/residue: 1.3085 time to fit residues: 215.0754 Evaluate side-chains 114 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 103 time to evaluate : 3.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain C residue 173 GLN Chi-restraints excluded: chain C residue 175 PHE Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain E residue 90 ASN Chi-restraints excluded: chain E residue 192 ARG Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 571 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 315 optimal weight: 10.0000 chunk 199 optimal weight: 0.0170 chunk 4 optimal weight: 3.9990 chunk 259 optimal weight: 0.6980 chunk 119 optimal weight: 20.0000 chunk 212 optimal weight: 0.7980 chunk 312 optimal weight: 6.9990 chunk 321 optimal weight: 30.0000 chunk 218 optimal weight: 0.0870 chunk 92 optimal weight: 7.9990 chunk 319 optimal weight: 0.8980 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 613 GLN C 901 GLN ** C1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 241 HIS E 493 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.124379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 109)---------------| | r_work = 0.3496 r_free = 0.3496 target = 0.070065 restraints weight = 86265.450| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 4.50 r_work: 0.3042 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.3247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 29345 Z= 0.099 Angle : 0.516 11.256 40059 Z= 0.256 Chirality : 0.043 0.277 4653 Planarity : 0.003 0.043 5070 Dihedral : 4.627 54.209 5105 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 0.75 % Allowed : 11.40 % Favored : 87.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.54 % 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 (0.14), residues: 3465 helix: 2.39 (0.16), residues: 1036 sheet: -0.13 (0.19), residues: 684 loop : -0.22 (0.14), residues: 1745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP C 353 HIS 0.004 0.000 HIS E 505 PHE 0.021 0.001 PHE A 168 TYR 0.014 0.001 TYR B1067 ARG 0.007 0.000 ARG C 214 Details of bonding type rmsd link_NAG-ASN : bond 0.00524 ( 46) link_NAG-ASN : angle 2.44877 ( 138) link_BETA1-4 : bond 0.00313 ( 18) link_BETA1-4 : angle 0.92086 ( 54) hydrogen bonds : bond 0.03550 ( 1148) hydrogen bonds : angle 4.77624 ( 3228) SS BOND : bond 0.00153 ( 40) SS BOND : angle 0.70390 ( 80) covalent geometry : bond 0.00214 (29241) covalent geometry : angle 0.49485 (39787) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6930 Ramachandran restraints generated. 3465 Oldfield, 0 Emsley, 3465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6930 Ramachandran restraints generated. 3465 Oldfield, 0 Emsley, 3465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 106 time to evaluate : 3.030 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.5850 (ptt) cc_final: 0.5533 (ppp) REVERT: A 168 PHE cc_start: 0.7969 (t80) cc_final: 0.7748 (t80) REVERT: A 170 TYR cc_start: 0.8578 (t80) cc_final: 0.8273 (t80) REVERT: A 200 TYR cc_start: 0.8620 (m-80) cc_final: 0.8356 (m-10) REVERT: A 304 LYS cc_start: 0.9361 (mmmm) cc_final: 0.9119 (mptp) REVERT: A 773 GLU cc_start: 0.8771 (tt0) cc_final: 0.8435 (tt0) REVERT: B 88 ASP cc_start: 0.9027 (m-30) cc_final: 0.8667 (p0) REVERT: B 153 MET cc_start: 0.6327 (ptt) cc_final: 0.5342 (pmt) REVERT: B 369 TYR cc_start: 0.8687 (t80) cc_final: 0.8313 (t80) REVERT: B 370 ASN cc_start: 0.8996 (m-40) cc_final: 0.7981 (p0) REVERT: B 425 LEU cc_start: 0.6531 (mm) cc_final: 0.6237 (mp) REVERT: B 451 TYR cc_start: 0.6044 (m-80) cc_final: 0.5706 (m-80) REVERT: B 740 MET cc_start: 0.8828 (OUTLIER) cc_final: 0.8502 (tpt) REVERT: B 780 GLU cc_start: 0.9304 (OUTLIER) cc_final: 0.8767 (mp0) REVERT: C 130 VAL cc_start: 0.8416 (t) cc_final: 0.8129 (p) REVERT: C 173 GLN cc_start: 0.7753 (OUTLIER) cc_final: 0.7413 (tm-30) REVERT: C 324 GLU cc_start: 0.8672 (OUTLIER) cc_final: 0.8053 (pm20) REVERT: E 613 TYR cc_start: 0.5029 (t80) cc_final: 0.4737 (m-10) outliers start: 23 outliers final: 8 residues processed: 123 average time/residue: 1.2821 time to fit residues: 189.7531 Evaluate side-chains 111 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 99 time to evaluate : 3.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain C residue 173 GLN Chi-restraints excluded: chain C residue 175 PHE Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain E residue 90 ASN Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 571 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 149 optimal weight: 0.9990 chunk 143 optimal weight: 4.9990 chunk 150 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 321 optimal weight: 30.0000 chunk 112 optimal weight: 2.9990 chunk 196 optimal weight: 9.9990 chunk 323 optimal weight: 20.0000 chunk 37 optimal weight: 1.9990 chunk 290 optimal weight: 2.9990 chunk 154 optimal weight: 0.7980 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.122192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.072972 restraints weight = 87703.002| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 3.63 r_work: 0.2981 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work: 0.2870 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.3417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 29345 Z= 0.175 Angle : 0.556 15.534 40059 Z= 0.275 Chirality : 0.044 0.267 4653 Planarity : 0.003 0.039 5070 Dihedral : 4.717 55.100 5105 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.71 % Allowed : 11.66 % Favored : 87.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.54 % 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: 0.82 (0.14), residues: 3465 helix: 2.35 (0.16), residues: 1042 sheet: -0.11 (0.19), residues: 687 loop : -0.26 (0.14), residues: 1736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP E 594 HIS 0.005 0.001 HIS E 493 PHE 0.019 0.001 PHE A 898 TYR 0.018 0.001 TYR B1067 ARG 0.006 0.000 ARG E 245 Details of bonding type rmsd link_NAG-ASN : bond 0.00560 ( 46) link_NAG-ASN : angle 2.51233 ( 138) link_BETA1-4 : bond 0.00205 ( 18) link_BETA1-4 : angle 1.07319 ( 54) hydrogen bonds : bond 0.03854 ( 1148) hydrogen bonds : angle 4.86701 ( 3228) SS BOND : bond 0.00173 ( 40) SS BOND : angle 0.74261 ( 80) covalent geometry : bond 0.00396 (29241) covalent geometry : angle 0.53589 (39787) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6930 Ramachandran restraints generated. 3465 Oldfield, 0 Emsley, 3465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6930 Ramachandran restraints generated. 3465 Oldfield, 0 Emsley, 3465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 102 time to evaluate : 3.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.5958 (ptt) cc_final: 0.5640 (ppp) REVERT: A 168 PHE cc_start: 0.8227 (t80) cc_final: 0.7926 (t80) REVERT: A 200 TYR cc_start: 0.8645 (m-80) cc_final: 0.8396 (m-80) REVERT: A 773 GLU cc_start: 0.8997 (tt0) cc_final: 0.8618 (tt0) REVERT: B 88 ASP cc_start: 0.9133 (m-30) cc_final: 0.8711 (p0) REVERT: B 153 MET cc_start: 0.6278 (ptt) cc_final: 0.5354 (pmt) REVERT: B 369 TYR cc_start: 0.8645 (t80) cc_final: 0.8313 (t80) REVERT: B 370 ASN cc_start: 0.9012 (m-40) cc_final: 0.8004 (p0) REVERT: B 425 LEU cc_start: 0.6449 (mm) cc_final: 0.6169 (mp) REVERT: B 451 TYR cc_start: 0.6267 (m-80) cc_final: 0.5885 (m-80) REVERT: B 780 GLU cc_start: 0.9517 (OUTLIER) cc_final: 0.8985 (mp0) REVERT: C 130 VAL cc_start: 0.8424 (t) cc_final: 0.8128 (p) REVERT: C 173 GLN cc_start: 0.7919 (OUTLIER) cc_final: 0.7505 (tm-30) REVERT: E 579 MET cc_start: 0.7856 (tpt) cc_final: 0.7026 (mmt) REVERT: E 613 TYR cc_start: 0.4783 (t80) cc_final: 0.4418 (m-10) outliers start: 22 outliers final: 11 residues processed: 116 average time/residue: 1.4465 time to fit residues: 203.3900 Evaluate side-chains 110 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 97 time to evaluate : 3.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain C residue 173 GLN Chi-restraints excluded: chain C residue 175 PHE Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain E residue 90 ASN Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 571 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 12 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 chunk 201 optimal weight: 0.9980 chunk 85 optimal weight: 0.4980 chunk 204 optimal weight: 0.8980 chunk 36 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 8 optimal weight: 7.9990 chunk 103 optimal weight: 1.9990 chunk 80 optimal weight: 0.7980 chunk 61 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4521 r_free = 0.4521 target = 0.136262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.095746 restraints weight = 102847.438| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 4.89 r_work: 0.3012 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.3434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 29345 Z= 0.112 Angle : 0.530 12.812 40059 Z= 0.262 Chirality : 0.043 0.298 4653 Planarity : 0.003 0.040 5070 Dihedral : 4.588 54.334 5105 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 0.49 % Allowed : 11.95 % Favored : 87.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.54 % 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: 0.91 (0.14), residues: 3465 helix: 2.44 (0.16), residues: 1031 sheet: -0.05 (0.20), residues: 675 loop : -0.19 (0.14), residues: 1759 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP E 594 HIS 0.003 0.001 HIS E 505 PHE 0.025 0.001 PHE C 338 TYR 0.027 0.001 TYR A 170 ARG 0.005 0.000 ARG E 245 Details of bonding type rmsd link_NAG-ASN : bond 0.00511 ( 46) link_NAG-ASN : angle 2.41191 ( 138) link_BETA1-4 : bond 0.00319 ( 18) link_BETA1-4 : angle 0.89240 ( 54) hydrogen bonds : bond 0.03569 ( 1148) hydrogen bonds : angle 4.74808 ( 3228) SS BOND : bond 0.00121 ( 40) SS BOND : angle 0.66539 ( 80) covalent geometry : bond 0.00250 (29241) covalent geometry : angle 0.51088 (39787) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6930 Ramachandran restraints generated. 3465 Oldfield, 0 Emsley, 3465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6930 Ramachandran restraints generated. 3465 Oldfield, 0 Emsley, 3465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 100 time to evaluate : 3.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 PHE cc_start: 0.8370 (t80) cc_final: 0.8128 (t80) REVERT: A 170 TYR cc_start: 0.8589 (t80) cc_final: 0.8360 (t80) REVERT: A 200 TYR cc_start: 0.8646 (m-80) cc_final: 0.8353 (m-10) REVERT: A 773 GLU cc_start: 0.8820 (tt0) cc_final: 0.8498 (tt0) REVERT: A 869 MET cc_start: 0.9334 (mtp) cc_final: 0.9073 (mtm) REVERT: B 88 ASP cc_start: 0.9188 (m-30) cc_final: 0.8619 (p0) REVERT: B 153 MET cc_start: 0.6096 (ptt) cc_final: 0.5258 (pmt) REVERT: B 369 TYR cc_start: 0.8713 (t80) cc_final: 0.8381 (t80) REVERT: B 370 ASN cc_start: 0.9013 (m-40) cc_final: 0.8030 (p0) REVERT: B 425 LEU cc_start: 0.6373 (mm) cc_final: 0.6127 (mp) REVERT: B 451 TYR cc_start: 0.6145 (m-80) cc_final: 0.5687 (m-80) REVERT: B 740 MET cc_start: 0.8838 (OUTLIER) cc_final: 0.8512 (tpt) REVERT: B 780 GLU cc_start: 0.9321 (OUTLIER) cc_final: 0.8766 (mp0) REVERT: C 130 VAL cc_start: 0.8277 (t) cc_final: 0.7996 (p) REVERT: C 173 GLN cc_start: 0.7814 (OUTLIER) cc_final: 0.7480 (tm-30) REVERT: E 579 MET cc_start: 0.7576 (tpt) cc_final: 0.6082 (mmt) REVERT: E 613 TYR cc_start: 0.4592 (t80) cc_final: 0.4255 (m-10) outliers start: 15 outliers final: 9 residues processed: 110 average time/residue: 1.3203 time to fit residues: 177.4097 Evaluate side-chains 108 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 96 time to evaluate : 3.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain C residue 173 GLN Chi-restraints excluded: chain C residue 175 PHE Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain E residue 90 ASN Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 571 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 216 optimal weight: 2.9990 chunk 325 optimal weight: 20.0000 chunk 341 optimal weight: 20.0000 chunk 268 optimal weight: 0.8980 chunk 3 optimal weight: 5.9990 chunk 104 optimal weight: 9.9990 chunk 290 optimal weight: 1.9990 chunk 281 optimal weight: 1.9990 chunk 128 optimal weight: 5.9990 chunk 68 optimal weight: 1.9990 chunk 99 optimal weight: 4.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.122014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.071810 restraints weight = 87590.404| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 3.69 r_work: 0.3002 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.3625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 29345 Z= 0.189 Angle : 0.564 12.134 40059 Z= 0.278 Chirality : 0.044 0.276 4653 Planarity : 0.003 0.040 5070 Dihedral : 4.735 55.374 5105 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 0.62 % Allowed : 11.82 % Favored : 87.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.54 % 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: 0.82 (0.14), residues: 3465 helix: 2.37 (0.16), residues: 1043 sheet: -0.17 (0.19), residues: 699 loop : -0.24 (0.15), residues: 1723 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP E 594 HIS 0.006 0.001 HIS E 493 PHE 0.023 0.001 PHE C 338 TYR 0.029 0.001 TYR A 170 ARG 0.006 0.000 ARG E 245 Details of bonding type rmsd link_NAG-ASN : bond 0.00560 ( 46) link_NAG-ASN : angle 2.51338 ( 138) link_BETA1-4 : bond 0.00207 ( 18) link_BETA1-4 : angle 1.13006 ( 54) hydrogen bonds : bond 0.03885 ( 1148) hydrogen bonds : angle 4.87959 ( 3228) SS BOND : bond 0.00174 ( 40) SS BOND : angle 0.68482 ( 80) covalent geometry : bond 0.00428 (29241) covalent geometry : angle 0.54417 (39787) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 36436.08 seconds wall clock time: 626 minutes 24.15 seconds (37584.15 seconds total)