Starting phenix.real_space_refine on Tue Jun 24 20:02:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sy7_25519/06_2025/7sy7_25519.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sy7_25519/06_2025/7sy7_25519.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7sy7_25519/06_2025/7sy7_25519.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sy7_25519/06_2025/7sy7_25519.map" model { file = "/net/cci-nas-00/data/ceres_data/7sy7_25519/06_2025/7sy7_25519.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sy7_25519/06_2025/7sy7_25519.cif" } resolution = 2.81 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= 0.037 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 18199 2.51 5 N 4671 2.21 5 O 5579 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 28581 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: 8134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1040, 8134 Classifications: {'peptide': 1040} Link IDs: {'PTRANS': 56, 'TRANS': 983} Chain breaks: 7 Chain: "C" Number of atoms: 8134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1040, 8134 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: 16.68, per 1000 atoms: 0.58 Number of scatterers: 28581 At special positions: 0 Unit cell: (140, 156, 237, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 132 16.00 O 5579 8.00 N 4671 7.00 C 18199 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=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.04 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 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=2.02 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: 6.51 Conformation dependent library (CDL) restraints added in 3.9 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: 91 helices and 42 sheets defined 33.1% alpha, 20.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.95 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 616 through 620 removed outlier: 3.900A 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: 3.630A 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: 3.961A 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: 3.558A 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: 4.301A 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 364 through 370 removed outlier: 4.226A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 388 removed outlier: 4.340A pdb=" N ASN B 388 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.668A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 620 removed outlier: 4.096A pdb=" N VAL B 620 " --> pdb=" O CYS B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.602A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 919 removed outlier: 3.927A 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: 3.998A 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: 3.820A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 383 through 390 removed outlier: 3.772A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU C 390 " --> pdb=" O LEU C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 410 removed outlier: 3.912A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 removed outlier: 3.583A pdb=" N ASP C 420 " --> pdb=" O GLY C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 616 through 620 removed outlier: 3.547A pdb=" N GLU C 619 " --> pdb=" O ASN C 616 " (cutoff:3.500A) removed outlier: 3.997A 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: 3.585A 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: 3.541A pdb=" N ALA C 903 " --> pdb=" O PRO C 899 " (cutoff:3.500A) Processing helix chain 'C' and resid 912 through 919 removed outlier: 3.891A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1032 removed outlier: 4.100A 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: 4.064A pdb=" N ASN E 33 " --> pdb=" O LEU E 29 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N HIS E 34 " --> pdb=" O ASP E 30 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 81 removed outlier: 3.618A pdb=" N GLN E 81 " --> pdb=" O SER E 77 " (cutoff:3.500A) Processing helix chain 'E' and resid 84 through 88 removed outlier: 3.756A 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: 4.045A 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: 3.914A 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: 3.683A 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: 3.712A pdb=" N LEU E 222 " --> pdb=" O SER E 218 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N ILE E 223 " --> pdb=" O ARG E 219 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLU E 224 " --> pdb=" O GLY E 220 " (cutoff:3.500A) removed outlier: 3.747A 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: 3.793A 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: 3.590A pdb=" N TRP E 328 " --> pdb=" O THR E 324 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 385 removed outlier: 3.672A 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: 4.256A pdb=" N HIS E 401 " --> pdb=" O ASN E 397 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N GLU E 402 " --> pdb=" O GLU E 398 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLY E 405 " --> pdb=" O HIS E 401 " (cutoff:3.500A) removed outlier: 3.918A 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: 3.599A pdb=" N GLU E 435 " --> pdb=" O ASP E 431 " (cutoff:3.500A) Processing helix chain 'E' and resid 448 through 465 removed outlier: 4.335A pdb=" N PHE E 452 " --> pdb=" O GLY E 448 " (cutoff:3.500A) Processing helix chain 'E' and resid 469 through 471 No H-bonds generated for 'chain 'E' and resid 469 through 471' Processing helix chain 'E' and resid 472 through 484 removed outlier: 3.503A pdb=" N GLU E 479 " --> pdb=" O LYS E 475 " (cutoff:3.500A) Processing helix chain 'E' and resid 499 through 502 removed outlier: 3.689A 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: 4.449A pdb=" N TYR E 516 " --> pdb=" O PHE E 512 " (cutoff:3.500A) removed outlier: 3.589A 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: 3.900A 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: 6.368A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.780A 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: 4.538A pdb=" N ARG C 567 " --> pdb=" O PHE A 43 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE C 326 " --> pdb=" O ASN C 540 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 4.165A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.933A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL A 126 " --> pdb=" O SER A 172 " (cutoff:3.500A) removed outlier: 3.669A 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: 9.494A pdb=" N SER A 155 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 11.375A pdb=" N PHE A 140 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 9.876A pdb=" N PHE A 157 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 11.359A pdb=" N ASP A 138 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N VAL A 159 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 8.137A pdb=" N LEU A 244 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N ARG A 246 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 6.901A 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: 5.233A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 4.027A 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: 5.082A 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: 6.106A 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: 6.423A 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: 6.601A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N LYS B 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.419A 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: 3.890A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.605A 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: 4.308A 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: 5.945A 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: 6.319A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.852A 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: 4.014A 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: 11.474A pdb=" N VAL B 126 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 10.066A pdb=" N GLU B 169 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 11.334A pdb=" N ILE B 128 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 8.668A 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: 6.781A pdb=" N ASN B 165 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N GLU B 132 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N ALA B 163 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N GLN B 134 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N VAL B 159 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 11.111A pdb=" N ASP B 138 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 9.442A pdb=" N PHE B 157 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 11.566A pdb=" N PHE B 140 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 9.539A 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: 6.726A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 3.858A 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: 5.165A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.408A 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: 4.052A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.889A 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: 6.066A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.652A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.351A 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: 3.824A 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: 3.948A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.646A 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: 4.304A 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: 5.966A 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: 4.151A 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 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 126 through 131 current: chain 'C' and resid 154 through 163 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 154 through 163 current: chain 'C' and resid 259 through 260 Processing sheet with id=AD4, first strand: chain 'C' and resid 311 through 319 removed outlier: 6.698A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 3.763A 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: 3.617A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.895A 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: 3.604A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.089A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.667A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.395A 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: 3.911A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.586A 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: 4.358A 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: 3.503A pdb=" N VAL E 132 " --> pdb=" O LEU E 142 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LEU E 142 " --> pdb=" O VAL E 132 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'E' and resid 262 through 263 removed outlier: 6.056A 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: 6.348A pdb=" N ASP E 355 " --> pdb=" O LEU E 351 " (cutoff:3.500A) 1139 hydrogen bonds defined for protein. 3204 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: 12.01 Time building geometry restraints manager: 7.78 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: 9011 1.34 - 1.47: 7374 1.47 - 1.59: 12676 1.59 - 1.72: 0 1.72 - 1.84: 180 Bond restraints: 29241 Sorted by residual: bond pdb=" C LEU C 560 " pdb=" N PRO C 561 " ideal model delta sigma weight residual 1.334 1.389 -0.055 1.51e-02 4.39e+03 1.31e+01 bond pdb=" C1 NAG E 702 " pdb=" O5 NAG E 702 " ideal model delta sigma weight residual 1.406 1.470 -0.064 2.00e-02 2.50e+03 1.02e+01 bond pdb=" C1 NAG D 1 " pdb=" O5 NAG D 1 " ideal model delta sigma weight residual 1.406 1.464 -0.058 2.00e-02 2.50e+03 8.44e+00 bond pdb=" C1 NAG E 706 " pdb=" O5 NAG E 706 " ideal model delta sigma weight residual 1.406 1.462 -0.056 2.00e-02 2.50e+03 7.83e+00 bond pdb=" C1 NAG B1307 " pdb=" O5 NAG B1307 " ideal model delta sigma weight residual 1.406 1.461 -0.055 2.00e-02 2.50e+03 7.61e+00 ... (remaining 29236 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.20: 38603 2.20 - 4.40: 1076 4.40 - 6.61: 78 6.61 - 8.81: 31 8.81 - 11.01: 3 Bond angle restraints: 39791 Sorted by residual: angle pdb=" N PRO A 986 " pdb=" CA PRO A 986 " pdb=" C PRO A 986 " ideal model delta sigma weight residual 110.70 116.43 -5.73 1.22e+00 6.72e-01 2.21e+01 angle pdb=" N PRO C 986 " pdb=" CA PRO C 986 " pdb=" C PRO C 986 " ideal model delta sigma weight residual 110.70 116.23 -5.53 1.22e+00 6.72e-01 2.06e+01 angle pdb=" C SER B 359 " pdb=" N ASN B 360 " pdb=" CA ASN B 360 " ideal model delta sigma weight residual 122.46 128.59 -6.13 1.41e+00 5.03e-01 1.89e+01 angle pdb=" N PRO B 986 " pdb=" CA PRO B 986 " pdb=" C PRO B 986 " ideal model delta sigma weight residual 110.70 115.97 -5.27 1.22e+00 6.72e-01 1.87e+01 angle pdb=" CA GLU C 583 " pdb=" CB GLU C 583 " pdb=" CG GLU C 583 " ideal model delta sigma weight residual 114.10 122.31 -8.21 2.00e+00 2.50e-01 1.69e+01 ... (remaining 39786 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 16785 17.95 - 35.89: 1178 35.89 - 53.84: 189 53.84 - 71.78: 57 71.78 - 89.73: 35 Dihedral angle restraints: 18244 sinusoidal: 7996 harmonic: 10248 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 180.00 154.01 25.99 0 5.00e+00 4.00e-02 2.70e+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 -46.03 -39.97 1 1.00e+01 1.00e-02 2.24e+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 180.00 157.33 22.67 0 5.00e+00 4.00e-02 2.06e+01 ... (remaining 18241 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 3665 0.067 - 0.135: 860 0.135 - 0.202: 122 0.202 - 0.269: 7 0.269 - 0.336: 3 Chirality restraints: 4657 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 -2.06 -0.34 2.00e-01 2.50e+01 2.83e+00 chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN A 17 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.08 -0.32 2.00e-01 2.50e+01 2.60e+00 chirality pdb=" C1 NAG K 1 " pdb=" ND2 ASN B 17 " pdb=" C2 NAG K 1 " pdb=" O5 NAG K 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.10 -0.30 2.00e-01 2.50e+01 2.31e+00 ... (remaining 4654 not shown) Planarity restraints: 5112 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE E 40 " -0.018 2.00e-02 2.50e+03 3.63e-02 1.32e+01 pdb=" C PHE E 40 " 0.063 2.00e-02 2.50e+03 pdb=" O PHE E 40 " -0.024 2.00e-02 2.50e+03 pdb=" N TYR E 41 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET A 902 " -0.014 2.00e-02 2.50e+03 2.84e-02 8.07e+00 pdb=" C MET A 902 " 0.049 2.00e-02 2.50e+03 pdb=" O MET A 902 " -0.018 2.00e-02 2.50e+03 pdb=" N ALA A 903 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU E 589 " -0.046 5.00e-02 4.00e+02 6.84e-02 7.48e+00 pdb=" N PRO E 590 " 0.118 5.00e-02 4.00e+02 pdb=" CA PRO E 590 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO E 590 " -0.039 5.00e-02 4.00e+02 ... (remaining 5109 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 7470 2.80 - 3.33: 24659 3.33 - 3.85: 49250 3.85 - 4.38: 56435 4.38 - 4.90: 96949 Nonbonded interactions: 234763 Sorted by model distance: nonbonded pdb=" OG1 THR C 323 " pdb=" OE1 GLU C 324 " model vdw 2.281 3.040 nonbonded pdb=" OH TYR B 37 " pdb=" O LEU B 54 " model vdw 2.294 3.040 nonbonded pdb=" O ASP B 80 " pdb=" OH TYR B 265 " model vdw 2.294 3.040 nonbonded pdb=" OH TYR C 37 " pdb=" O LEU C 54 " model vdw 2.301 3.040 nonbonded pdb=" OE1 GLN C 52 " pdb=" OG1 THR C 274 " model vdw 2.311 3.040 ... (remaining 234758 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: 5.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.110 Check model and map are aligned: 0.180 Set scattering table: 0.230 Process input model: 63.610 Find NCS groups from input model: 1.060 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 86.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 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 0.064 29345 Z= 0.240 Angle : 0.854 14.834 40063 Z= 0.455 Chirality : 0.057 0.336 4657 Planarity : 0.006 0.068 5066 Dihedral : 12.959 89.731 11520 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % 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: -0.05 (0.13), residues: 3465 helix: 0.87 (0.15), residues: 992 sheet: 0.57 (0.18), residues: 700 loop : -0.79 (0.13), residues: 1773 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP E 69 HIS 0.006 0.001 HIS E 378 PHE 0.033 0.002 PHE C 238 TYR 0.046 0.002 TYR A 200 ARG 0.009 0.001 ARG E 460 Details of bonding type rmsd link_NAG-ASN : bond 0.00723 ( 46) link_NAG-ASN : angle 3.86888 ( 138) link_BETA1-4 : bond 0.00539 ( 18) link_BETA1-4 : angle 1.71430 ( 54) hydrogen bonds : bond 0.12503 ( 1139) hydrogen bonds : angle 6.74011 ( 3204) SS BOND : bond 0.00333 ( 40) SS BOND : angle 1.54774 ( 80) covalent geometry : bond 0.00487 (29241) covalent geometry : angle 0.82118 (39791) *********************** 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 188 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 188 time to evaluate : 3.713 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 1029 MET cc_start: 0.9200 (tpp) cc_final: 0.8974 (tpp) REVERT: C 351 TYR cc_start: 0.8233 (p90) cc_final: 0.7664 (p90) REVERT: C 374 PHE cc_start: 0.7303 (m-80) cc_final: 0.7069 (m-80) REVERT: C 421 TYR cc_start: 0.7677 (m-10) cc_final: 0.6869 (m-80) REVERT: C 571 ASP cc_start: 0.7887 (m-30) cc_final: 0.7218 (p0) REVERT: E 408 MET cc_start: 0.8264 (mmt) cc_final: 0.8017 (mpm) outliers start: 0 outliers final: 0 residues processed: 188 average time/residue: 1.5230 time to fit residues: 334.4590 Evaluate side-chains 89 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 3.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 296 optimal weight: 9.9990 chunk 266 optimal weight: 0.0060 chunk 147 optimal weight: 0.7980 chunk 90 optimal weight: 0.0980 chunk 179 optimal weight: 3.9990 chunk 142 optimal weight: 8.9990 chunk 275 optimal weight: 1.9990 chunk 106 optimal weight: 0.7980 chunk 167 optimal weight: 0.7980 chunk 204 optimal weight: 5.9990 chunk 318 optimal weight: 10.0000 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN A1011 GLN B 115 GLN B 493 GLN ** B 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN C 580 GLN C 613 GLN C 901 GLN E 374 HIS E 472 GLN E 552 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.086433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.052555 restraints weight = 127010.006| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 3.94 r_work: 0.3061 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.1220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 29345 Z= 0.109 Angle : 0.558 11.313 40063 Z= 0.277 Chirality : 0.043 0.356 4657 Planarity : 0.004 0.041 5066 Dihedral : 5.522 53.977 5105 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 0.75 % Allowed : 6.12 % Favored : 93.13 % 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: 0.58 (0.14), residues: 3465 helix: 1.86 (0.16), residues: 1014 sheet: 0.65 (0.19), residues: 678 loop : -0.58 (0.14), residues: 1773 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 165 HIS 0.003 0.001 HIS E 505 PHE 0.019 0.001 PHE A 135 TYR 0.016 0.001 TYR B 369 ARG 0.006 0.000 ARG B 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00534 ( 46) link_NAG-ASN : angle 2.82449 ( 138) link_BETA1-4 : bond 0.00266 ( 18) link_BETA1-4 : angle 0.97309 ( 54) hydrogen bonds : bond 0.04075 ( 1139) hydrogen bonds : angle 5.39665 ( 3204) SS BOND : bond 0.00258 ( 40) SS BOND : angle 1.01433 ( 80) covalent geometry : bond 0.00230 (29241) covalent geometry : angle 0.53110 (39791) *********************** 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 125 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 102 time to evaluate : 3.053 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1029 MET cc_start: 0.9542 (tpp) cc_final: 0.9302 (tpp) REVERT: B 198 ASP cc_start: 0.8824 (m-30) cc_final: 0.8617 (t0) REVERT: C 200 TYR cc_start: 0.8775 (m-80) cc_final: 0.8203 (t80) REVERT: C 237 ARG cc_start: 0.9148 (mtp180) cc_final: 0.8870 (mtm-85) REVERT: C 351 TYR cc_start: 0.8324 (p90) cc_final: 0.8112 (p90) REVERT: C 421 TYR cc_start: 0.8001 (m-10) cc_final: 0.7786 (m-80) REVERT: C 571 ASP cc_start: 0.8454 (m-30) cc_final: 0.7545 (p0) outliers start: 23 outliers final: 11 residues processed: 121 average time/residue: 1.4345 time to fit residues: 206.0522 Evaluate side-chains 90 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 79 time to evaluate : 3.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain E residue 231 GLU Chi-restraints excluded: chain E residue 491 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 261 optimal weight: 2.9990 chunk 73 optimal weight: 0.4980 chunk 245 optimal weight: 6.9990 chunk 44 optimal weight: 1.9990 chunk 132 optimal weight: 0.3980 chunk 29 optimal weight: 10.0000 chunk 172 optimal weight: 4.9990 chunk 123 optimal weight: 8.9990 chunk 180 optimal weight: 0.0470 chunk 329 optimal weight: 8.9990 chunk 148 optimal weight: 2.9990 overall best weight: 1.1882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN C1005 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.085550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.051330 restraints weight = 127593.458| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 3.85 r_work: 0.3020 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.1635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 29345 Z= 0.125 Angle : 0.529 12.249 40063 Z= 0.261 Chirality : 0.043 0.300 4657 Planarity : 0.004 0.040 5066 Dihedral : 4.984 55.111 5105 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 1.00 % Allowed : 7.09 % Favored : 91.90 % 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: 0.81 (0.14), residues: 3465 helix: 2.16 (0.16), residues: 1019 sheet: 0.58 (0.19), residues: 685 loop : -0.43 (0.14), residues: 1761 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 104 HIS 0.003 0.001 HIS E 373 PHE 0.027 0.001 PHE C 342 TYR 0.015 0.001 TYR A1067 ARG 0.004 0.000 ARG C 567 Details of bonding type rmsd link_NAG-ASN : bond 0.00506 ( 46) link_NAG-ASN : angle 2.57624 ( 138) link_BETA1-4 : bond 0.00252 ( 18) link_BETA1-4 : angle 0.97676 ( 54) hydrogen bonds : bond 0.03830 ( 1139) hydrogen bonds : angle 5.09929 ( 3204) SS BOND : bond 0.00190 ( 40) SS BOND : angle 0.89252 ( 80) covalent geometry : bond 0.00275 (29241) covalent geometry : angle 0.50528 (39791) *********************** 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 120 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 89 time to evaluate : 3.076 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 198 ASP cc_start: 0.8911 (m-30) cc_final: 0.8668 (t0) REVERT: C 153 MET cc_start: 0.5005 (pp-130) cc_final: 0.4660 (tmm) REVERT: C 200 TYR cc_start: 0.8946 (m-80) cc_final: 0.8371 (t80) REVERT: C 351 TYR cc_start: 0.8347 (p90) cc_final: 0.8116 (p90) REVERT: C 571 ASP cc_start: 0.8518 (m-30) cc_final: 0.7591 (p0) outliers start: 31 outliers final: 10 residues processed: 113 average time/residue: 1.2727 time to fit residues: 174.4700 Evaluate side-chains 86 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 76 time to evaluate : 3.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain E residue 231 GLU Chi-restraints excluded: chain E residue 491 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 273 optimal weight: 1.9990 chunk 170 optimal weight: 9.9990 chunk 167 optimal weight: 6.9990 chunk 110 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 63 optimal weight: 6.9990 chunk 275 optimal weight: 1.9990 chunk 277 optimal weight: 0.6980 chunk 308 optimal weight: 20.0000 chunk 198 optimal weight: 5.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 957 GLN B 125 ASN B 613 GLN B 907 ASN ** E 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.084477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.050356 restraints weight = 128327.971| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 3.71 r_work: 0.2981 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.2096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 29345 Z= 0.156 Angle : 0.534 11.292 40063 Z= 0.263 Chirality : 0.043 0.286 4657 Planarity : 0.004 0.040 5066 Dihedral : 4.795 56.582 5105 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 1.26 % Allowed : 7.97 % Favored : 90.77 % 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: 0.92 (0.14), residues: 3465 helix: 2.31 (0.16), residues: 1015 sheet: 0.50 (0.20), residues: 652 loop : -0.31 (0.14), residues: 1798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 104 HIS 0.005 0.001 HIS E 373 PHE 0.021 0.001 PHE C 392 TYR 0.017 0.001 TYR A1067 ARG 0.006 0.000 ARG C 214 Details of bonding type rmsd link_NAG-ASN : bond 0.00495 ( 46) link_NAG-ASN : angle 2.46989 ( 138) link_BETA1-4 : bond 0.00201 ( 18) link_BETA1-4 : angle 1.02119 ( 54) hydrogen bonds : bond 0.03811 ( 1139) hydrogen bonds : angle 4.98032 ( 3204) SS BOND : bond 0.00180 ( 40) SS BOND : angle 0.76632 ( 80) covalent geometry : bond 0.00348 (29241) covalent geometry : angle 0.51359 (39791) *********************** 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 123 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 84 time to evaluate : 3.095 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1029 MET cc_start: 0.9487 (OUTLIER) cc_final: 0.9073 (tpp) REVERT: B 198 ASP cc_start: 0.9008 (m-30) cc_final: 0.8720 (t0) REVERT: B 1050 MET cc_start: 0.9284 (ptm) cc_final: 0.9084 (ptm) REVERT: C 153 MET cc_start: 0.4656 (pp-130) cc_final: 0.4435 (tmm) REVERT: C 351 TYR cc_start: 0.8359 (p90) cc_final: 0.8064 (p90) REVERT: C 571 ASP cc_start: 0.8360 (m-30) cc_final: 0.7527 (p0) outliers start: 39 outliers final: 15 residues processed: 113 average time/residue: 1.2784 time to fit residues: 175.6223 Evaluate side-chains 92 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 76 time to evaluate : 3.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 1029 MET Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain E residue 231 GLU Chi-restraints excluded: chain E residue 485 VAL Chi-restraints excluded: chain E residue 491 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 151 optimal weight: 6.9990 chunk 125 optimal weight: 7.9990 chunk 102 optimal weight: 9.9990 chunk 164 optimal weight: 1.9990 chunk 342 optimal weight: 20.0000 chunk 231 optimal weight: 20.0000 chunk 282 optimal weight: 0.3980 chunk 2 optimal weight: 9.9990 chunk 279 optimal weight: 5.9990 chunk 59 optimal weight: 0.7980 chunk 295 optimal weight: 8.9990 overall best weight: 3.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 824 ASN B 824 ASN B 957 GLN ** E 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 540 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.082758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.048453 restraints weight = 127447.631| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 3.73 r_work: 0.2926 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.2745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 29345 Z= 0.261 Angle : 0.607 10.250 40063 Z= 0.299 Chirality : 0.045 0.364 4657 Planarity : 0.004 0.042 5066 Dihedral : 5.139 58.832 5105 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.36 % Allowed : 8.78 % Favored : 89.86 % 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: 0.75 (0.14), residues: 3465 helix: 2.06 (0.16), residues: 1042 sheet: 0.28 (0.20), residues: 618 loop : -0.32 (0.14), residues: 1805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 104 HIS 0.005 0.001 HIS C1064 PHE 0.020 0.002 PHE C 392 TYR 0.018 0.002 TYR B1067 ARG 0.005 0.001 ARG B 509 Details of bonding type rmsd link_NAG-ASN : bond 0.00597 ( 46) link_NAG-ASN : angle 2.57748 ( 138) link_BETA1-4 : bond 0.00168 ( 18) link_BETA1-4 : angle 1.25366 ( 54) hydrogen bonds : bond 0.04245 ( 1139) hydrogen bonds : angle 5.15034 ( 3204) SS BOND : bond 0.00240 ( 40) SS BOND : angle 0.80096 ( 80) covalent geometry : bond 0.00582 (29241) covalent geometry : angle 0.58673 (39791) *********************** 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 122 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 80 time to evaluate : 3.018 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 324 GLU cc_start: 0.8178 (OUTLIER) cc_final: 0.7931 (pp20) REVERT: B 198 ASP cc_start: 0.8905 (m-30) cc_final: 0.8649 (t0) REVERT: C 196 ASN cc_start: 0.9402 (OUTLIER) cc_final: 0.9120 (t160) REVERT: C 351 TYR cc_start: 0.8349 (p90) cc_final: 0.8067 (p90) REVERT: C 571 ASP cc_start: 0.8558 (m-30) cc_final: 0.7741 (p0) REVERT: C 950 ASP cc_start: 0.9245 (OUTLIER) cc_final: 0.8721 (OUTLIER) outliers start: 42 outliers final: 16 residues processed: 114 average time/residue: 1.2630 time to fit residues: 176.8587 Evaluate side-chains 94 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 76 time to evaluate : 2.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain E residue 231 GLU Chi-restraints excluded: chain E residue 323 MET Chi-restraints excluded: chain E residue 485 VAL Chi-restraints excluded: chain E residue 491 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 107 optimal weight: 2.9990 chunk 335 optimal weight: 10.0000 chunk 290 optimal weight: 0.9990 chunk 340 optimal weight: 7.9990 chunk 180 optimal weight: 0.8980 chunk 95 optimal weight: 0.9990 chunk 201 optimal weight: 7.9990 chunk 66 optimal weight: 6.9990 chunk 276 optimal weight: 0.9980 chunk 302 optimal weight: 3.9990 chunk 113 optimal weight: 2.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 535 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.083510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.049478 restraints weight = 127326.515| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 3.71 r_work: 0.2964 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.2790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 29345 Z= 0.134 Angle : 0.524 11.182 40063 Z= 0.257 Chirality : 0.043 0.278 4657 Planarity : 0.003 0.036 5066 Dihedral : 4.865 56.947 5105 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.04 % Allowed : 9.26 % Favored : 89.70 % 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: 0.81 (0.14), residues: 3465 helix: 2.17 (0.16), residues: 1051 sheet: 0.19 (0.21), residues: 591 loop : -0.27 (0.14), residues: 1823 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 104 HIS 0.003 0.001 HIS E 373 PHE 0.022 0.001 PHE C 392 TYR 0.016 0.001 TYR A1067 ARG 0.004 0.000 ARG C 214 Details of bonding type rmsd link_NAG-ASN : bond 0.00478 ( 46) link_NAG-ASN : angle 2.38283 ( 138) link_BETA1-4 : bond 0.00244 ( 18) link_BETA1-4 : angle 0.94959 ( 54) hydrogen bonds : bond 0.03714 ( 1139) hydrogen bonds : angle 4.93169 ( 3204) SS BOND : bond 0.00148 ( 40) SS BOND : angle 0.63934 ( 80) covalent geometry : bond 0.00297 (29241) covalent geometry : angle 0.50496 (39791) *********************** 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 113 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 81 time to evaluate : 3.106 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 740 MET cc_start: 0.9442 (tpt) cc_final: 0.9228 (tpp) REVERT: B 198 ASP cc_start: 0.8948 (m-30) cc_final: 0.8687 (t0) REVERT: C 196 ASN cc_start: 0.9383 (OUTLIER) cc_final: 0.9114 (t160) REVERT: C 351 TYR cc_start: 0.8355 (p90) cc_final: 0.8085 (p90) REVERT: C 571 ASP cc_start: 0.8527 (m-30) cc_final: 0.7749 (p0) outliers start: 32 outliers final: 14 residues processed: 104 average time/residue: 1.4058 time to fit residues: 174.4092 Evaluate side-chains 90 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 75 time to evaluate : 3.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain E residue 231 GLU Chi-restraints excluded: chain E residue 485 VAL Chi-restraints excluded: chain E residue 491 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 193 optimal weight: 1.9990 chunk 39 optimal weight: 0.2980 chunk 314 optimal weight: 30.0000 chunk 91 optimal weight: 8.9990 chunk 320 optimal weight: 8.9990 chunk 82 optimal weight: 0.7980 chunk 36 optimal weight: 7.9990 chunk 328 optimal weight: 20.0000 chunk 229 optimal weight: 10.0000 chunk 323 optimal weight: 30.0000 chunk 37 optimal weight: 1.9990 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 218 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.082669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 97)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.048417 restraints weight = 127406.314| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 3.79 r_work: 0.2923 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.3083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 29345 Z= 0.215 Angle : 0.571 11.276 40063 Z= 0.280 Chirality : 0.043 0.260 4657 Planarity : 0.003 0.040 5066 Dihedral : 4.960 58.817 5105 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.97 % Allowed : 9.49 % Favored : 89.54 % 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: 0.74 (0.14), residues: 3465 helix: 2.11 (0.16), residues: 1049 sheet: -0.02 (0.20), residues: 612 loop : -0.26 (0.14), residues: 1804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 104 HIS 0.005 0.001 HIS E 373 PHE 0.022 0.001 PHE C 392 TYR 0.016 0.001 TYR B1067 ARG 0.003 0.000 ARG C 214 Details of bonding type rmsd link_NAG-ASN : bond 0.00543 ( 46) link_NAG-ASN : angle 2.44603 ( 138) link_BETA1-4 : bond 0.00143 ( 18) link_BETA1-4 : angle 1.15795 ( 54) hydrogen bonds : bond 0.03935 ( 1139) hydrogen bonds : angle 4.99698 ( 3204) SS BOND : bond 0.00185 ( 40) SS BOND : angle 0.67673 ( 80) covalent geometry : bond 0.00482 (29241) covalent geometry : angle 0.55202 (39791) *********************** 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 107 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 77 time to evaluate : 3.078 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 324 GLU cc_start: 0.7855 (OUTLIER) cc_final: 0.7607 (pp20) REVERT: B 198 ASP cc_start: 0.8994 (m-30) cc_final: 0.8744 (t0) REVERT: C 196 ASN cc_start: 0.9361 (OUTLIER) cc_final: 0.9131 (t160) REVERT: C 351 TYR cc_start: 0.8360 (p90) cc_final: 0.8069 (p90) REVERT: C 571 ASP cc_start: 0.8544 (m-30) cc_final: 0.7767 (p0) outliers start: 30 outliers final: 15 residues processed: 100 average time/residue: 1.5901 time to fit residues: 190.7783 Evaluate side-chains 90 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 73 time to evaluate : 3.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain E residue 231 GLU Chi-restraints excluded: chain E residue 485 VAL Chi-restraints excluded: chain E residue 491 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 15 optimal weight: 9.9990 chunk 150 optimal weight: 1.9990 chunk 277 optimal weight: 2.9990 chunk 254 optimal weight: 2.9990 chunk 42 optimal weight: 0.0980 chunk 335 optimal weight: 5.9990 chunk 255 optimal weight: 0.9990 chunk 222 optimal weight: 7.9990 chunk 226 optimal weight: 30.0000 chunk 119 optimal weight: 9.9990 chunk 219 optimal weight: 0.4980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN A 613 GLN ** C 955 ASN ** 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 = 0.4100 r_free = 0.4100 target = 0.083260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.049199 restraints weight = 127921.087| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 3.70 r_work: 0.2957 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.3141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 29345 Z= 0.129 Angle : 0.528 11.598 40063 Z= 0.259 Chirality : 0.043 0.273 4657 Planarity : 0.003 0.039 5066 Dihedral : 4.795 57.497 5105 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 0.94 % Allowed : 9.62 % Favored : 89.44 % 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: 0.83 (0.14), residues: 3465 helix: 2.18 (0.16), residues: 1048 sheet: 0.01 (0.21), residues: 617 loop : -0.18 (0.14), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 104 HIS 0.003 0.001 HIS E 378 PHE 0.021 0.001 PHE C 238 TYR 0.016 0.001 TYR A1067 ARG 0.003 0.000 ARG C 214 Details of bonding type rmsd link_NAG-ASN : bond 0.00456 ( 46) link_NAG-ASN : angle 2.31517 ( 138) link_BETA1-4 : bond 0.00261 ( 18) link_BETA1-4 : angle 0.96274 ( 54) hydrogen bonds : bond 0.03636 ( 1139) hydrogen bonds : angle 4.85145 ( 3204) SS BOND : bond 0.00145 ( 40) SS BOND : angle 0.57867 ( 80) covalent geometry : bond 0.00289 (29241) covalent geometry : angle 0.51026 (39791) *********************** 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 106 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 77 time to evaluate : 3.298 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 198 ASP cc_start: 0.9009 (m-30) cc_final: 0.8759 (t0) REVERT: C 196 ASN cc_start: 0.9328 (OUTLIER) cc_final: 0.9047 (t0) REVERT: C 351 TYR cc_start: 0.8365 (p90) cc_final: 0.8083 (p90) REVERT: C 508 TYR cc_start: 0.8302 (m-80) cc_final: 0.8071 (m-80) REVERT: C 571 ASP cc_start: 0.8498 (m-30) cc_final: 0.7735 (p0) outliers start: 29 outliers final: 15 residues processed: 96 average time/residue: 1.3650 time to fit residues: 157.6166 Evaluate side-chains 90 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 74 time to evaluate : 2.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain E residue 231 GLU Chi-restraints excluded: chain E residue 485 VAL Chi-restraints excluded: chain E residue 491 VAL Chi-restraints excluded: chain E residue 506 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 274 optimal weight: 7.9990 chunk 36 optimal weight: 7.9990 chunk 12 optimal weight: 9.9990 chunk 84 optimal weight: 20.0000 chunk 33 optimal weight: 9.9990 chunk 32 optimal weight: 1.9990 chunk 194 optimal weight: 7.9990 chunk 238 optimal weight: 7.9990 chunk 93 optimal weight: 5.9990 chunk 133 optimal weight: 0.8980 chunk 62 optimal weight: 0.5980 overall best weight: 3.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 498 GLN C 121 ASN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 250 ASN ** E 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.081924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.047528 restraints weight = 127297.253| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 3.82 r_work: 0.2909 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.3575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 29345 Z= 0.274 Angle : 0.628 13.572 40063 Z= 0.307 Chirality : 0.045 0.252 4657 Planarity : 0.004 0.038 5066 Dihedral : 5.195 59.857 5105 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.91 % Allowed : 9.82 % Favored : 89.28 % 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: 0.59 (0.14), residues: 3465 helix: 1.97 (0.16), residues: 1054 sheet: -0.23 (0.20), residues: 667 loop : -0.29 (0.15), residues: 1744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 104 HIS 0.004 0.001 HIS C1064 PHE 0.023 0.002 PHE C 392 TYR 0.018 0.002 TYR B1067 ARG 0.004 0.001 ARG A1107 Details of bonding type rmsd link_NAG-ASN : bond 0.00615 ( 46) link_NAG-ASN : angle 2.57024 ( 138) link_BETA1-4 : bond 0.00180 ( 18) link_BETA1-4 : angle 1.31431 ( 54) hydrogen bonds : bond 0.04208 ( 1139) hydrogen bonds : angle 5.10061 ( 3204) SS BOND : bond 0.00228 ( 40) SS BOND : angle 0.75109 ( 80) covalent geometry : bond 0.00618 (29241) covalent geometry : angle 0.60905 (39791) *********************** 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 106 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 78 time to evaluate : 3.098 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.3669 (OUTLIER) cc_final: 0.3432 (ppp) REVERT: B 198 ASP cc_start: 0.8976 (m-30) cc_final: 0.8743 (t0) REVERT: C 196 ASN cc_start: 0.9313 (OUTLIER) cc_final: 0.8980 (t0) REVERT: C 351 TYR cc_start: 0.8310 (p90) cc_final: 0.8088 (p90) REVERT: E 82 MET cc_start: 0.8267 (pmm) cc_final: 0.8054 (pmm) outliers start: 28 outliers final: 15 residues processed: 96 average time/residue: 1.3886 time to fit residues: 162.3871 Evaluate side-chains 91 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 74 time to evaluate : 3.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain E residue 231 GLU Chi-restraints excluded: chain E residue 376 MET Chi-restraints excluded: chain E residue 491 VAL Chi-restraints excluded: chain E residue 506 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 33 optimal weight: 6.9990 chunk 51 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 chunk 124 optimal weight: 10.0000 chunk 125 optimal weight: 0.1980 chunk 350 optimal weight: 10.0000 chunk 332 optimal weight: 10.0000 chunk 44 optimal weight: 1.9990 chunk 294 optimal weight: 10.0000 chunk 175 optimal weight: 0.6980 chunk 129 optimal weight: 6.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 522 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 = 0.4082 r_free = 0.4082 target = 0.082399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.048124 restraints weight = 126907.949| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 3.78 r_work: 0.2931 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.3629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 29345 Z= 0.180 Angle : 0.571 13.165 40063 Z= 0.279 Chirality : 0.043 0.273 4657 Planarity : 0.003 0.038 5066 Dihedral : 5.064 58.058 5105 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 0.68 % Allowed : 10.20 % Favored : 89.12 % 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: 0.68 (0.14), residues: 3465 helix: 2.04 (0.16), residues: 1054 sheet: -0.13 (0.20), residues: 633 loop : -0.24 (0.15), residues: 1778 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP A 104 HIS 0.004 0.001 HIS E 373 PHE 0.022 0.001 PHE C 238 TYR 0.016 0.001 TYR A1067 ARG 0.003 0.000 ARG C 457 Details of bonding type rmsd link_NAG-ASN : bond 0.00471 ( 46) link_NAG-ASN : angle 2.42300 ( 138) link_BETA1-4 : bond 0.00234 ( 18) link_BETA1-4 : angle 1.06067 ( 54) hydrogen bonds : bond 0.03864 ( 1139) hydrogen bonds : angle 4.99708 ( 3204) SS BOND : bond 0.00163 ( 40) SS BOND : angle 0.63398 ( 80) covalent geometry : bond 0.00405 (29241) covalent geometry : angle 0.55247 (39791) ********************** 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 97 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 76 time to evaluate : 3.134 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 198 ASP cc_start: 0.9046 (m-30) cc_final: 0.8798 (t0) REVERT: C 196 ASN cc_start: 0.9271 (OUTLIER) cc_final: 0.8994 (t0) REVERT: C 351 TYR cc_start: 0.8296 (p90) cc_final: 0.8083 (p90) REVERT: C 508 TYR cc_start: 0.8510 (m-80) cc_final: 0.8245 (m-80) REVERT: E 82 MET cc_start: 0.8302 (pmm) cc_final: 0.8098 (pmm) outliers start: 21 outliers final: 13 residues processed: 89 average time/residue: 1.4512 time to fit residues: 154.5759 Evaluate side-chains 88 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 74 time to evaluate : 3.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain E residue 231 GLU Chi-restraints excluded: chain E residue 376 MET Chi-restraints excluded: chain E residue 491 VAL Chi-restraints excluded: chain E residue 506 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 160 optimal weight: 0.5980 chunk 21 optimal weight: 5.9990 chunk 94 optimal weight: 9.9990 chunk 137 optimal weight: 5.9990 chunk 33 optimal weight: 0.9990 chunk 196 optimal weight: 9.9990 chunk 176 optimal weight: 0.6980 chunk 76 optimal weight: 2.9990 chunk 114 optimal weight: 8.9990 chunk 13 optimal weight: 5.9990 chunk 283 optimal weight: 1.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 498 GLN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.082549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.050090 restraints weight = 128416.954| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 3.88 r_work: 0.2929 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.3668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 29345 Z= 0.141 Angle : 0.545 13.212 40063 Z= 0.266 Chirality : 0.043 0.280 4657 Planarity : 0.003 0.038 5066 Dihedral : 4.835 58.160 5105 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 0.62 % Allowed : 10.30 % Favored : 89.08 % 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: 0.74 (0.14), residues: 3465 helix: 2.13 (0.16), residues: 1043 sheet: -0.20 (0.21), residues: 618 loop : -0.18 (0.15), residues: 1804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP A 104 HIS 0.005 0.001 HIS E 373 PHE 0.025 0.001 PHE C 238 TYR 0.019 0.001 TYR C 421 ARG 0.003 0.000 ARG C 102 Details of bonding type rmsd link_NAG-ASN : bond 0.00447 ( 46) link_NAG-ASN : angle 2.32171 ( 138) link_BETA1-4 : bond 0.00254 ( 18) link_BETA1-4 : angle 1.03620 ( 54) hydrogen bonds : bond 0.03647 ( 1139) hydrogen bonds : angle 4.88296 ( 3204) SS BOND : bond 0.00166 ( 40) SS BOND : angle 0.59614 ( 80) covalent geometry : bond 0.00317 (29241) covalent geometry : angle 0.52796 (39791) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 29933.25 seconds wall clock time: 515 minutes 36.32 seconds (30936.32 seconds total)