Starting phenix.real_space_refine on Tue Jun 24 19:49:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sy1_25513/06_2025/7sy1_25513.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sy1_25513/06_2025/7sy1_25513.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7sy1_25513/06_2025/7sy1_25513.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sy1_25513/06_2025/7sy1_25513.map" model { file = "/net/cci-nas-00/data/ceres_data/7sy1_25513/06_2025/7sy1_25513.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sy1_25513/06_2025/7sy1_25513.cif" } resolution = 2.83 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.039 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 132 5.16 5 C 18201 2.51 5 N 4671 2.21 5 O 5581 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 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: 28585 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: 8136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1040, 8136 Classifications: {'peptide': 1040} Link IDs: {'PTRANS': 56, 'TRANS': 983} Chain breaks: 7 Chain: "C" Number of atoms: 8136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1040, 8136 Classifications: {'peptide': 1040} Link IDs: {'PTRANS': 56, 'TRANS': 983} Chain breaks: 7 Chain: "E" Number of atoms: 4862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 568} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "E" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 17.43, per 1000 atoms: 0.61 Number of scatterers: 28585 At special positions: 0 Unit cell: (141, 157, 236, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 132 16.00 O 5581 8.00 N 4671 7.00 C 18201 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=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.04 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS E 133 " - pdb=" SG CYS E 141 " distance=2.04 Simple disulfide: pdb=" SG CYS E 530 " - pdb=" SG CYS E 542 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 165 " " NAG A1304 " - " ASN A 234 " " NAG A1305 " - " ASN A 282 " " NAG A1306 " - " ASN A 709 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 165 " " NAG B1304 " - " ASN B 234 " " NAG B1305 " - " ASN B 282 " " NAG B1306 " - " ASN B 331 " " NAG B1307 " - " ASN B 343 " " NAG B1308 " - " ASN B 709 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 122 " " NAG C1303 " - " ASN C 165 " " NAG C1304 " - " ASN C 234 " " NAG C1305 " - " ASN C 282 " " NAG C1306 " - " ASN C 331 " " NAG C1307 " - " ASN C 343 " " NAG C1308 " - " ASN C 709 " " NAG D 1 " - " ASN A 17 " " NAG E 701 " - " ASN E 53 " " NAG E 702 " - " ASN E 90 " " NAG E 703 " - " ASN E 103 " " NAG E 704 " - " ASN E 322 " " NAG E 705 " - " ASN E 432 " " NAG E 706 " - " ASN E 546 " " NAG F 1 " - " ASN A 717 " " NAG G 1 " - " ASN A 801 " " NAG H 1 " - " ASN A1074 " " NAG I 1 " - " ASN A1098 " " NAG J 1 " - " ASN A1134 " " NAG K 1 " - " ASN B 17 " " NAG L 1 " - " ASN B 717 " " NAG M 1 " - " ASN B 801 " " NAG N 1 " - " ASN B1074 " " NAG O 1 " - " ASN B1098 " " NAG P 1 " - " ASN B1134 " " NAG Q 1 " - " ASN C 17 " " NAG R 1 " - " ASN C 717 " " NAG S 1 " - " ASN C 801 " " NAG T 1 " - " ASN C1074 " " NAG U 1 " - " ASN C1098 " " NAG V 1 " - " ASN C1134 " Time building additional restraints: 7.61 Conformation dependent library (CDL) restraints added in 3.6 seconds 6930 Ramachandran restraints generated. 3465 Oldfield, 0 Emsley, 3465 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6604 Finding SS restraints... Secondary structure from input PDB file: 92 helices and 42 sheets defined 33.0% alpha, 21.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.89 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 616 through 620 removed outlier: 3.896A 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: 3.641A 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: 3.953A 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: 3.560A 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: 4.305A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1147 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 383 through 387 removed outlier: 3.514A pdb=" N LYS B 386 " --> pdb=" O SER B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.710A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 620 removed outlier: 4.078A 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: 3.563A 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: 3.914A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.038A 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: 3.800A 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 387 removed outlier: 3.741A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 409 removed outlier: 3.886A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 removed outlier: 3.552A pdb=" N ASP C 420 " --> pdb=" O GLY C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 616 through 620 removed outlier: 3.536A pdb=" N GLU C 619 " --> pdb=" O ASN C 616 " (cutoff:3.500A) removed outlier: 4.006A 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: 3.599A 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: 3.537A pdb=" N ALA C 903 " --> pdb=" O PRO C 899 " (cutoff:3.500A) Processing helix chain 'C' and resid 912 through 919 removed outlier: 3.914A 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: 4.079A 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: 3.858A pdb=" N ASP E 38 " --> pdb=" O HIS E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 81 Processing helix chain 'E' and resid 82 through 83 No H-bonds generated for 'chain 'E' and resid 82 through 83' Processing helix chain 'E' and resid 84 through 88 removed outlier: 3.814A 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: 4.069A 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: 3.984A 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: 3.694A 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: 3.742A pdb=" N LEU E 222 " --> pdb=" O SER E 218 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N ILE E 223 " --> pdb=" O ARG E 219 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLU E 224 " --> pdb=" O GLY E 220 " (cutoff:3.500A) removed outlier: 3.802A 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: 3.825A pdb=" N TYR E 279 " --> pdb=" O THR E 276 " (cutoff:3.500A) Processing helix chain 'E' and resid 293 through 300 Processing helix chain 'E' and resid 303 through 318 Processing helix chain 'E' and resid 324 through 331 removed outlier: 3.552A 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: 4.273A pdb=" N HIS E 401 " --> pdb=" O ASN E 397 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N GLU E 402 " --> pdb=" O GLU E 398 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLY E 405 " --> pdb=" O HIS E 401 " (cutoff:3.500A) removed outlier: 3.945A 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: 3.544A pdb=" N GLU E 435 " --> pdb=" O ASP E 431 " (cutoff:3.500A) Processing helix chain 'E' and resid 448 through 465 removed outlier: 4.399A pdb=" N PHE E 452 " --> pdb=" O GLY E 448 " (cutoff:3.500A) Processing helix chain 'E' and resid 469 through 471 No H-bonds generated for 'chain 'E' and resid 469 through 471' Processing helix chain 'E' and resid 472 through 484 Processing helix chain 'E' and resid 499 through 502 removed outlier: 3.779A 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: 4.446A pdb=" N TYR E 516 " --> pdb=" O PHE E 512 " (cutoff:3.500A) removed outlier: 3.577A 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: 3.887A 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: 5.759A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 4.104A pdb=" N ARG C 567 " --> pdb=" O PHE A 43 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 4.194A 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: 3.888A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL A 126 " --> pdb=" O SER A 172 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 154 through 163 removed outlier: 9.490A pdb=" N SER A 155 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 11.395A pdb=" N PHE A 140 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 9.890A pdb=" N PHE A 157 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 11.391A pdb=" N ASP A 138 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N VAL A 159 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.221A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 4.034A 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: 5.152A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.108A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.464A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.433A 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: 6.583A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N LYS B 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.393A 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: 3.925A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.644A 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: 4.331A 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: 5.929A 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: 6.322A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.841A 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: 3.990A 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: 3.849A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N GLU B 132 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N CYS B 166 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 10.146A pdb=" N GLN B 134 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 9.217A pdb=" N ASN B 164 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 8.227A pdb=" N CYS B 136 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 10.216A pdb=" N SER B 162 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 10.159A pdb=" N ASP B 138 " --> pdb=" O TYR B 160 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N TYR B 160 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N GLU B 156 " --> pdb=" O GLY B 142 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N TYR B 144 " --> pdb=" O GLU B 154 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N GLU B 154 " --> pdb=" O TYR B 144 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 154 through 172 current: chain 'B' and resid 259 through 260 Processing sheet with id=AB8, first strand: chain 'B' and resid 311 through 318 removed outlier: 6.729A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 3.862A 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: 5.209A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.443A 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: 4.241A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.951A 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: 6.130A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.732A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.355A 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: 3.829A 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: 3.957A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.658A 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: 4.297A 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: 5.911A 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: 4.130A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 83 through 85 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 83 through 85 current: chain 'C' and resid 116 through 121 removed outlier: 3.526A pdb=" N VAL C 126 " --> pdb=" O SER C 172 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N GLU C 132 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N CYS C 166 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 9.976A pdb=" N GLN C 134 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 9.074A pdb=" N ASN C 164 " --> pdb=" O GLN C 134 " (cutoff:3.500A) removed outlier: 8.348A pdb=" N CYS C 136 " --> pdb=" O SER C 162 " (cutoff:3.500A) removed outlier: 10.322A pdb=" N SER C 162 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 9.977A pdb=" N ASP C 138 " --> pdb=" O TYR C 160 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N TYR C 160 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLU C 156 " --> pdb=" O GLY C 142 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N TYR C 144 " --> pdb=" O GLU C 154 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N GLU C 154 " --> pdb=" O TYR C 144 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 154 through 172 current: chain 'C' and resid 259 through 260 Processing sheet with id=AD4, first strand: chain 'C' and resid 311 through 319 removed outlier: 6.658A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 3.765A 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: 3.997A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.939A 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: 3.597A pdb=" N TYR C 473 " --> pdb=" O TYR C 489 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.064A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.646A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.390A 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: 3.930A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.381A 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: 3.792A pdb=" N LEU E 142 " --> pdb=" O VAL E 132 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 262 through 263 removed outlier: 6.021A 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: 6.347A pdb=" N ASP E 355 " --> pdb=" O LEU E 351 " (cutoff:3.500A) 1154 hydrogen bonds defined for protein. 3255 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: 13.03 Time building geometry restraints manager: 9.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7538 1.33 - 1.46: 8136 1.46 - 1.59: 13391 1.59 - 1.71: 0 1.71 - 1.84: 180 Bond restraints: 29245 Sorted by residual: 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 8.38e+00 bond pdb=" C1 NAG U 1 " pdb=" O5 NAG U 1 " ideal model delta sigma weight residual 1.406 1.464 -0.058 2.00e-02 2.50e+03 8.33e+00 bond pdb=" C1 NAG A1303 " pdb=" O5 NAG A1303 " ideal model delta sigma weight residual 1.406 1.462 -0.056 2.00e-02 2.50e+03 7.81e+00 bond pdb=" C1 NAG I 1 " pdb=" O5 NAG I 1 " ideal model delta sigma weight residual 1.406 1.461 -0.055 2.00e-02 2.50e+03 7.50e+00 bond pdb=" C1 NAG C1303 " pdb=" O5 NAG C1303 " ideal model delta sigma weight residual 1.406 1.461 -0.055 2.00e-02 2.50e+03 7.47e+00 ... (remaining 29240 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.00: 38309 2.00 - 3.99: 1329 3.99 - 5.99: 113 5.99 - 7.99: 33 7.99 - 9.98: 11 Bond angle restraints: 39795 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 110.70 116.37 -5.67 1.22e+00 6.72e-01 2.16e+01 angle pdb=" N PRO C 986 " pdb=" CA PRO C 986 " pdb=" C PRO C 986 " ideal model delta sigma weight residual 110.70 116.30 -5.60 1.22e+00 6.72e-01 2.11e+01 angle pdb=" C SER B 359 " pdb=" N ASN B 360 " pdb=" CA ASN B 360 " ideal model delta sigma weight residual 122.82 129.14 -6.32 1.42e+00 4.96e-01 1.98e+01 angle pdb=" N PRO B 986 " pdb=" CA PRO B 986 " pdb=" C PRO B 986 " ideal model delta sigma weight residual 110.70 115.94 -5.24 1.22e+00 6.72e-01 1.85e+01 angle pdb=" CA GLU C 583 " pdb=" CB GLU C 583 " pdb=" CG GLU C 583 " ideal model delta sigma weight residual 114.10 122.09 -7.99 2.00e+00 2.50e-01 1.60e+01 ... (remaining 39790 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 16787 17.92 - 35.84: 1168 35.84 - 53.77: 197 53.77 - 71.69: 60 71.69 - 89.61: 36 Dihedral angle restraints: 18248 sinusoidal: 8000 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 180.00 154.55 25.45 0 5.00e+00 4.00e-02 2.59e+01 dihedral pdb=" CB CYS E 133 " pdb=" SG CYS E 133 " pdb=" SG CYS E 141 " pdb=" CB CYS E 141 " ideal model delta sinusoidal sigma weight residual -86.00 -46.39 -39.61 1 1.00e+01 1.00e-02 2.20e+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 180.00 157.46 22.54 0 5.00e+00 4.00e-02 2.03e+01 ... (remaining 18245 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 3655 0.067 - 0.134: 871 0.134 - 0.201: 120 0.201 - 0.268: 7 0.268 - 0.335: 2 Chirality restraints: 4655 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 2.81e+00 chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN A 17 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.06 -0.34 2.00e-01 2.50e+01 2.81e+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 -2.14 -0.26 2.00e-01 2.50e+01 1.66e+00 ... (remaining 4652 not shown) Planarity restraints: 5114 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG E 169 " 0.015 2.00e-02 2.50e+03 2.98e-02 8.89e+00 pdb=" C ARG E 169 " -0.052 2.00e-02 2.50e+03 pdb=" O ARG E 169 " 0.019 2.00e-02 2.50e+03 pdb=" N SER E 170 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET A 902 " -0.015 2.00e-02 2.50e+03 2.92e-02 8.53e+00 pdb=" C MET A 902 " 0.051 2.00e-02 2.50e+03 pdb=" O MET A 902 " -0.019 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 " -0.043 5.00e-02 4.00e+02 6.50e-02 6.75e+00 pdb=" N PRO E 590 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO E 590 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO E 590 " -0.037 5.00e-02 4.00e+02 ... (remaining 5111 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 7379 2.80 - 3.33: 24629 3.33 - 3.85: 49164 3.85 - 4.38: 56534 4.38 - 4.90: 97049 Nonbonded interactions: 234755 Sorted by model distance: nonbonded pdb=" OH TYR C 37 " pdb=" O LEU C 54 " model vdw 2.279 3.040 nonbonded pdb=" OH TYR B 37 " pdb=" O LEU B 54 " model vdw 2.279 3.040 nonbonded pdb=" OG1 THR C 323 " pdb=" OE1 GLU C 324 " model vdw 2.283 3.040 nonbonded pdb=" O ASP B 80 " pdb=" OH TYR B 265 " model vdw 2.293 3.040 nonbonded pdb=" O ASP C 80 " pdb=" OH TYR C 265 " model vdw 2.309 3.040 ... (remaining 234750 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: 6.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.280 Check model and map are aligned: 0.220 Set scattering table: 0.280 Process input model: 68.120 Find NCS groups from input model: 0.910 Set up NCS constraints: 0.220 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:15.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 92.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 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 0.062 29349 Z= 0.239 Angle : 0.855 15.110 40067 Z= 0.454 Chirality : 0.057 0.335 4655 Planarity : 0.006 0.065 5068 Dihedral : 12.987 89.609 11524 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 0.03 % Allowed : 2.04 % Favored : 97.93 % 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: -0.15 (0.13), residues: 3465 helix: 0.68 (0.14), residues: 1017 sheet: 0.54 (0.19), residues: 665 loop : -0.79 (0.13), residues: 1783 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 886 HIS 0.006 0.001 HIS E 378 PHE 0.034 0.002 PHE C 238 TYR 0.027 0.002 TYR E 385 ARG 0.011 0.001 ARG C 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00708 ( 46) link_NAG-ASN : angle 3.87301 ( 138) link_BETA1-4 : bond 0.00654 ( 18) link_BETA1-4 : angle 1.80314 ( 54) hydrogen bonds : bond 0.12587 ( 1154) hydrogen bonds : angle 6.83166 ( 3255) SS BOND : bond 0.00292 ( 40) SS BOND : angle 1.57072 ( 80) covalent geometry : bond 0.00487 (29245) covalent geometry : angle 0.82145 (39795) *********************** 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 235 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 234 time to evaluate : 3.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1029 MET cc_start: 0.9216 (tpp) cc_final: 0.9009 (tpp) REVERT: B 153 MET cc_start: 0.4541 (ptt) cc_final: 0.3875 (pp-130) REVERT: C 421 TYR cc_start: 0.8511 (m-10) cc_final: 0.7929 (m-10) REVERT: C 571 ASP cc_start: 0.6973 (m-30) cc_final: 0.6734 (p0) REVERT: E 34 HIS cc_start: 0.8406 (OUTLIER) cc_final: 0.7639 (m90) REVERT: E 292 ASP cc_start: 0.5065 (t70) cc_final: 0.4842 (p0) REVERT: E 323 MET cc_start: 0.7233 (mmp) cc_final: 0.7016 (mmp) REVERT: E 332 MET cc_start: 0.2715 (ttp) cc_final: 0.2135 (tpp) REVERT: E 433 GLU cc_start: 0.7069 (mt-10) cc_final: 0.6710 (pp20) REVERT: E 582 ARG cc_start: 0.7782 (mmm160) cc_final: 0.7070 (tmm-80) REVERT: E 585 LEU cc_start: 0.6777 (mt) cc_final: 0.6463 (tm) outliers start: 1 outliers final: 0 residues processed: 235 average time/residue: 1.4512 time to fit residues: 398.4139 Evaluate side-chains 101 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 100 time to evaluate : 3.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 34 HIS 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: 0.3980 chunk 147 optimal weight: 1.9990 chunk 90 optimal weight: 9.9990 chunk 179 optimal weight: 4.9990 chunk 142 optimal weight: 5.9990 chunk 275 optimal weight: 0.9990 chunk 106 optimal weight: 0.8980 chunk 167 optimal weight: 0.7980 chunk 204 optimal weight: 0.5980 chunk 318 optimal weight: 7.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 125 ASN ** B 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 978 ASN C 901 GLN E 374 HIS E 552 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.095310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.058538 restraints weight = 117079.810| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 4.07 r_work: 0.3101 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.1359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 29349 Z= 0.120 Angle : 0.572 13.135 40067 Z= 0.288 Chirality : 0.043 0.237 4655 Planarity : 0.004 0.051 5068 Dihedral : 5.678 54.797 5107 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 0.84 % Allowed : 6.58 % Favored : 92.58 % 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: 0.52 (0.13), residues: 3465 helix: 1.79 (0.16), residues: 1018 sheet: 0.57 (0.19), residues: 666 loop : -0.58 (0.13), residues: 1781 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 275 HIS 0.003 0.001 HIS E 505 PHE 0.015 0.001 PHE B 194 TYR 0.023 0.001 TYR C 453 ARG 0.010 0.001 ARG A 319 Details of bonding type rmsd link_NAG-ASN : bond 0.00516 ( 46) link_NAG-ASN : angle 2.88414 ( 138) link_BETA1-4 : bond 0.00296 ( 18) link_BETA1-4 : angle 0.97732 ( 54) hydrogen bonds : bond 0.04194 ( 1154) hydrogen bonds : angle 5.48494 ( 3255) SS BOND : bond 0.00343 ( 40) SS BOND : angle 1.04287 ( 80) covalent geometry : bond 0.00259 (29245) covalent geometry : angle 0.54539 (39795) *********************** 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 137 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 111 time to evaluate : 3.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 PHE cc_start: 0.8208 (t80) cc_final: 0.8006 (t80) REVERT: A 780 GLU cc_start: 0.8829 (mm-30) cc_final: 0.8421 (mp0) REVERT: B 54 LEU cc_start: 0.9099 (tp) cc_final: 0.8896 (mm) REVERT: B 173 GLN cc_start: 0.9155 (mm-40) cc_final: 0.8930 (pp30) REVERT: B 740 MET cc_start: 0.9284 (OUTLIER) cc_final: 0.8478 (tmm) REVERT: C 153 MET cc_start: 0.6153 (pmm) cc_final: 0.5851 (pmm) REVERT: C 340 GLU cc_start: 0.8950 (mt-10) cc_final: 0.8663 (pp20) REVERT: C 452 LEU cc_start: 0.8607 (mp) cc_final: 0.8191 (tt) REVERT: C 571 ASP cc_start: 0.8029 (m-30) cc_final: 0.7244 (p0) REVERT: C 646 ARG cc_start: 0.8766 (mtt180) cc_final: 0.8474 (tpt170) REVERT: C 1005 GLN cc_start: 0.9316 (OUTLIER) cc_final: 0.8912 (tt0) REVERT: E 123 MET cc_start: 0.0413 (mtt) cc_final: 0.0061 (ttp) REVERT: E 323 MET cc_start: 0.7293 (mmp) cc_final: 0.6806 (mmp) REVERT: E 332 MET cc_start: 0.3026 (ttp) cc_final: 0.2726 (tpp) REVERT: E 433 GLU cc_start: 0.7316 (mt-10) cc_final: 0.7079 (pp20) REVERT: E 582 ARG cc_start: 0.7388 (mmm160) cc_final: 0.7094 (tmm-80) outliers start: 26 outliers final: 9 residues processed: 126 average time/residue: 1.4623 time to fit residues: 218.3590 Evaluate side-chains 105 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 94 time to evaluate : 3.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 1005 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 132 optimal weight: 7.9990 chunk 29 optimal weight: 10.0000 chunk 172 optimal weight: 0.8980 chunk 123 optimal weight: 9.9990 chunk 180 optimal weight: 3.9990 chunk 329 optimal weight: 30.0000 chunk 148 optimal weight: 3.9990 chunk 168 optimal weight: 0.9990 chunk 32 optimal weight: 10.0000 chunk 306 optimal weight: 30.0000 chunk 182 optimal weight: 0.7980 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 96 GLN E 117 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.093173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.055969 restraints weight = 116265.695| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 3.74 r_work: 0.3004 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.2160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 29349 Z= 0.195 Angle : 0.589 10.772 40067 Z= 0.294 Chirality : 0.044 0.276 4655 Planarity : 0.004 0.036 5068 Dihedral : 5.232 53.267 5105 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.33 % Allowed : 6.80 % Favored : 91.87 % 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: 0.65 (0.14), residues: 3465 helix: 1.96 (0.16), residues: 1021 sheet: 0.36 (0.20), residues: 657 loop : -0.42 (0.14), residues: 1787 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 165 HIS 0.005 0.001 HIS C1083 PHE 0.021 0.002 PHE A 106 TYR 0.028 0.002 TYR E 243 ARG 0.010 0.001 ARG C 214 Details of bonding type rmsd link_NAG-ASN : bond 0.00583 ( 46) link_NAG-ASN : angle 2.69935 ( 138) link_BETA1-4 : bond 0.00199 ( 18) link_BETA1-4 : angle 1.15257 ( 54) hydrogen bonds : bond 0.04230 ( 1154) hydrogen bonds : angle 5.24614 ( 3255) SS BOND : bond 0.00214 ( 40) SS BOND : angle 1.01227 ( 80) covalent geometry : bond 0.00432 (29245) covalent geometry : angle 0.56560 (39795) *********************** 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 144 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 103 time to evaluate : 3.165 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 773 GLU cc_start: 0.8758 (tt0) cc_final: 0.8445 (tt0) REVERT: B 1005 GLN cc_start: 0.8739 (tm-30) cc_final: 0.8315 (tm-30) REVERT: C 153 MET cc_start: 0.6062 (pmm) cc_final: 0.5641 (pmm) REVERT: C 421 TYR cc_start: 0.8847 (m-10) cc_final: 0.8362 (m-10) REVERT: C 434 ILE cc_start: 0.7388 (OUTLIER) cc_final: 0.7109 (pp) REVERT: C 571 ASP cc_start: 0.8248 (m-30) cc_final: 0.7393 (p0) REVERT: C 646 ARG cc_start: 0.8818 (mtt180) cc_final: 0.8533 (tpt170) REVERT: C 990 GLU cc_start: 0.8972 (tm-30) cc_final: 0.8652 (pp20) REVERT: C 1005 GLN cc_start: 0.9366 (OUTLIER) cc_final: 0.8986 (tt0) REVERT: E 115 ARG cc_start: 0.7033 (OUTLIER) cc_final: 0.6757 (ppp80) REVERT: E 123 MET cc_start: 0.0420 (mtt) cc_final: 0.0156 (ttp) REVERT: E 190 MET cc_start: 0.6529 (mmm) cc_final: 0.5834 (tmt) REVERT: E 213 ASP cc_start: 0.8225 (m-30) cc_final: 0.7573 (t70) REVERT: E 332 MET cc_start: 0.3591 (ttp) cc_final: 0.3083 (tpp) REVERT: E 433 GLU cc_start: 0.7224 (mt-10) cc_final: 0.6929 (pp20) REVERT: E 582 ARG cc_start: 0.7823 (mmm160) cc_final: 0.7528 (tmm-80) outliers start: 41 outliers final: 10 residues processed: 138 average time/residue: 1.6405 time to fit residues: 268.6907 Evaluate side-chains 98 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 85 time to evaluate : 3.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1005 GLN Chi-restraints excluded: chain E residue 115 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 277 optimal weight: 2.9990 chunk 308 optimal weight: 6.9990 chunk 198 optimal weight: 8.9990 chunk 50 optimal weight: 3.9990 chunk 118 optimal weight: 6.9990 chunk 254 optimal weight: 1.9990 chunk 255 optimal weight: 0.9980 chunk 259 optimal weight: 0.7980 chunk 151 optimal weight: 2.9990 chunk 320 optimal weight: 9.9990 chunk 346 optimal weight: 20.0000 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 907 ASN B1010 GLN C 762 GLN E 524 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.092572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.055145 restraints weight = 115663.697| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 3.84 r_work: 0.2998 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.2619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 29349 Z= 0.174 Angle : 0.550 10.678 40067 Z= 0.274 Chirality : 0.043 0.271 4655 Planarity : 0.003 0.045 5068 Dihedral : 5.026 53.489 5105 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.13 % Allowed : 8.36 % Favored : 90.51 % 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: 0.71 (0.14), residues: 3465 helix: 2.07 (0.16), residues: 1033 sheet: 0.20 (0.20), residues: 657 loop : -0.36 (0.14), residues: 1775 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 165 HIS 0.003 0.001 HIS A 207 PHE 0.028 0.001 PHE C 168 TYR 0.020 0.001 TYR E 521 ARG 0.009 0.000 ARG C 214 Details of bonding type rmsd link_NAG-ASN : bond 0.00482 ( 46) link_NAG-ASN : angle 2.51961 ( 138) link_BETA1-4 : bond 0.00317 ( 18) link_BETA1-4 : angle 0.99855 ( 54) hydrogen bonds : bond 0.03917 ( 1154) hydrogen bonds : angle 5.08353 ( 3255) SS BOND : bond 0.00182 ( 40) SS BOND : angle 0.83194 ( 80) covalent geometry : bond 0.00388 (29245) covalent geometry : angle 0.52904 (39795) *********************** 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 131 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 96 time to evaluate : 2.930 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 571 ASP cc_start: 0.9103 (m-30) cc_final: 0.8767 (p0) REVERT: B 1005 GLN cc_start: 0.8665 (tm-30) cc_final: 0.8220 (tm-30) REVERT: C 130 VAL cc_start: 0.8583 (t) cc_final: 0.8376 (m) REVERT: C 153 MET cc_start: 0.6135 (pmm) cc_final: 0.5840 (pmm) REVERT: C 369 TYR cc_start: 0.8778 (t80) cc_final: 0.8537 (t80) REVERT: C 421 TYR cc_start: 0.8743 (m-10) cc_final: 0.8454 (m-10) REVERT: C 434 ILE cc_start: 0.7392 (OUTLIER) cc_final: 0.7070 (pp) REVERT: C 571 ASP cc_start: 0.8309 (m-30) cc_final: 0.7471 (p0) REVERT: C 993 ILE cc_start: 0.9245 (OUTLIER) cc_final: 0.9022 (mp) REVERT: C 1005 GLN cc_start: 0.9382 (OUTLIER) cc_final: 0.9001 (tt0) REVERT: C 1145 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.8373 (pt) REVERT: E 115 ARG cc_start: 0.6921 (OUTLIER) cc_final: 0.6595 (ptm-80) REVERT: E 123 MET cc_start: 0.0590 (mtt) cc_final: 0.0177 (ttp) REVERT: E 213 ASP cc_start: 0.8150 (m-30) cc_final: 0.7505 (t70) REVERT: E 323 MET cc_start: 0.5013 (mmp) cc_final: 0.4421 (mmp) REVERT: E 332 MET cc_start: 0.3384 (ttp) cc_final: 0.2884 (tpp) REVERT: E 433 GLU cc_start: 0.7342 (mt-10) cc_final: 0.7052 (pp20) REVERT: E 582 ARG cc_start: 0.7760 (mmm160) cc_final: 0.7424 (tmm-80) outliers start: 35 outliers final: 9 residues processed: 122 average time/residue: 1.3888 time to fit residues: 202.6188 Evaluate side-chains 98 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 84 time to evaluate : 3.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1005 GLN Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain E residue 115 ARG Chi-restraints excluded: chain E residue 607 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 140 optimal weight: 0.9980 chunk 257 optimal weight: 2.9990 chunk 64 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 133 optimal weight: 6.9990 chunk 127 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 69 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 chunk 169 optimal weight: 4.9990 chunk 153 optimal weight: 2.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 824 ASN ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 519 HIS B 824 ASN B1010 GLN C 271 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.091157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.053550 restraints weight = 115229.145| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 3.89 r_work: 0.2947 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.3221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 29349 Z= 0.239 Angle : 0.601 10.612 40067 Z= 0.297 Chirality : 0.045 0.298 4655 Planarity : 0.004 0.050 5068 Dihedral : 5.148 53.588 5105 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.33 % Allowed : 9.01 % Favored : 89.67 % 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: 2.04 (0.16), residues: 1023 sheet: -0.03 (0.19), residues: 670 loop : -0.40 (0.14), residues: 1772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP E 594 HIS 0.007 0.001 HIS B 519 PHE 0.026 0.002 PHE C 464 TYR 0.025 0.002 TYR E 243 ARG 0.009 0.001 ARG C 214 Details of bonding type rmsd link_NAG-ASN : bond 0.00593 ( 46) link_NAG-ASN : angle 2.58717 ( 138) link_BETA1-4 : bond 0.00227 ( 18) link_BETA1-4 : angle 1.22150 ( 54) hydrogen bonds : bond 0.04174 ( 1154) hydrogen bonds : angle 5.15010 ( 3255) SS BOND : bond 0.00212 ( 40) SS BOND : angle 0.73390 ( 80) covalent geometry : bond 0.00537 (29245) covalent geometry : angle 0.58042 (39795) *********************** 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 129 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 88 time to evaluate : 2.989 Fit side-chains revert: symmetry clash REVERT: A 238 PHE cc_start: 0.7655 (OUTLIER) cc_final: 0.6902 (p90) REVERT: A 571 ASP cc_start: 0.9083 (m-30) cc_final: 0.8796 (p0) REVERT: A 773 GLU cc_start: 0.8741 (tt0) cc_final: 0.8472 (tt0) REVERT: C 153 MET cc_start: 0.6360 (pmm) cc_final: 0.5920 (pmm) REVERT: C 351 TYR cc_start: 0.8593 (OUTLIER) cc_final: 0.8216 (p90) REVERT: C 421 TYR cc_start: 0.8825 (m-10) cc_final: 0.8570 (m-10) REVERT: C 434 ILE cc_start: 0.7281 (OUTLIER) cc_final: 0.6956 (pp) REVERT: C 571 ASP cc_start: 0.8402 (m-30) cc_final: 0.7558 (p0) REVERT: E 115 ARG cc_start: 0.6830 (OUTLIER) cc_final: 0.6495 (ptm-80) REVERT: E 123 MET cc_start: 0.0665 (mtt) cc_final: 0.0265 (ttp) REVERT: E 332 MET cc_start: 0.3512 (ttp) cc_final: 0.2995 (tpp) REVERT: E 433 GLU cc_start: 0.7367 (mt-10) cc_final: 0.7077 (pp20) REVERT: E 582 ARG cc_start: 0.7835 (mmm160) cc_final: 0.7506 (tmm-80) outliers start: 41 outliers final: 15 residues processed: 122 average time/residue: 1.2967 time to fit residues: 190.3719 Evaluate side-chains 98 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 79 time to evaluate : 3.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 519 HIS Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain E residue 115 ARG Chi-restraints excluded: chain E residue 283 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 213 optimal weight: 0.8980 chunk 11 optimal weight: 10.0000 chunk 208 optimal weight: 4.9990 chunk 172 optimal weight: 1.9990 chunk 2 optimal weight: 7.9990 chunk 249 optimal weight: 5.9990 chunk 302 optimal weight: 8.9990 chunk 175 optimal weight: 0.8980 chunk 32 optimal weight: 9.9990 chunk 336 optimal weight: 20.0000 chunk 245 optimal weight: 0.3980 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 779 GLN B 519 HIS B1010 GLN B1083 HIS C1005 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.091506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 93)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.054090 restraints weight = 116080.106| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 3.87 r_work: 0.2964 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.3366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 29349 Z= 0.167 Angle : 0.550 10.989 40067 Z= 0.274 Chirality : 0.043 0.291 4655 Planarity : 0.003 0.034 5068 Dihedral : 5.010 55.366 5105 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.10 % Allowed : 9.72 % Favored : 89.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.14), residues: 3465 helix: 2.15 (0.16), residues: 1023 sheet: -0.10 (0.20), residues: 655 loop : -0.33 (0.14), residues: 1787 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP E 594 HIS 0.024 0.001 HIS B 519 PHE 0.020 0.001 PHE A 238 TYR 0.017 0.001 TYR A1067 ARG 0.008 0.000 ARG C 983 Details of bonding type rmsd link_NAG-ASN : bond 0.00490 ( 46) link_NAG-ASN : angle 2.41772 ( 138) link_BETA1-4 : bond 0.00215 ( 18) link_BETA1-4 : angle 1.03950 ( 54) hydrogen bonds : bond 0.03939 ( 1154) hydrogen bonds : angle 5.04496 ( 3255) SS BOND : bond 0.00155 ( 40) SS BOND : angle 0.61996 ( 80) covalent geometry : bond 0.00373 (29245) covalent geometry : angle 0.53101 (39795) *********************** 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 120 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 86 time to evaluate : 2.969 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 571 ASP cc_start: 0.9071 (m-30) cc_final: 0.8785 (p0) REVERT: A 773 GLU cc_start: 0.8649 (tt0) cc_final: 0.8373 (tt0) REVERT: A 786 LYS cc_start: 0.8896 (mmmt) cc_final: 0.8666 (mmmt) REVERT: B 1005 GLN cc_start: 0.8761 (tm-30) cc_final: 0.8271 (tm-30) REVERT: C 153 MET cc_start: 0.6377 (pmm) cc_final: 0.6137 (pmm) REVERT: C 351 TYR cc_start: 0.8638 (OUTLIER) cc_final: 0.8262 (p90) REVERT: C 421 TYR cc_start: 0.8775 (m-10) cc_final: 0.8528 (m-10) REVERT: C 434 ILE cc_start: 0.7230 (OUTLIER) cc_final: 0.6864 (pp) REVERT: C 571 ASP cc_start: 0.8346 (m-30) cc_final: 0.7541 (p0) REVERT: C 993 ILE cc_start: 0.9240 (OUTLIER) cc_final: 0.8997 (mp) REVERT: C 1005 GLN cc_start: 0.9423 (OUTLIER) cc_final: 0.9142 (tp40) REVERT: C 1145 LEU cc_start: 0.8482 (OUTLIER) cc_final: 0.8197 (pt) REVERT: E 115 ARG cc_start: 0.6778 (OUTLIER) cc_final: 0.6572 (ptm-80) REVERT: E 123 MET cc_start: 0.0663 (mtt) cc_final: 0.0267 (ttp) REVERT: E 332 MET cc_start: 0.3467 (ttp) cc_final: 0.3000 (tpp) REVERT: E 433 GLU cc_start: 0.7372 (mt-10) cc_final: 0.7078 (pp20) REVERT: E 582 ARG cc_start: 0.7828 (mmm160) cc_final: 0.7505 (tmm-80) outliers start: 34 outliers final: 14 residues processed: 116 average time/residue: 1.3483 time to fit residues: 187.4089 Evaluate side-chains 100 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 80 time to evaluate : 2.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1005 GLN Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain E residue 115 ARG Chi-restraints excluded: chain E residue 213 ASP Chi-restraints excluded: chain E residue 504 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 321 optimal weight: 10.0000 chunk 38 optimal weight: 6.9990 chunk 156 optimal weight: 0.0570 chunk 13 optimal weight: 6.9990 chunk 85 optimal weight: 0.0570 chunk 22 optimal weight: 4.9990 chunk 216 optimal weight: 0.9980 chunk 169 optimal weight: 2.9990 chunk 308 optimal weight: 8.9990 chunk 70 optimal weight: 0.9980 chunk 103 optimal weight: 1.9990 overall best weight: 0.8218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1010 GLN C1005 GLN ** E 535 HIS ** 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 = 0.4108 r_free = 0.4108 target = 0.092022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.054876 restraints weight = 114630.110| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 3.77 r_work: 0.2986 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.3408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 29349 Z= 0.111 Angle : 0.523 10.357 40067 Z= 0.260 Chirality : 0.043 0.284 4655 Planarity : 0.003 0.034 5068 Dihedral : 4.779 56.237 5105 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.00 % Allowed : 9.91 % 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: 0.76 (0.14), residues: 3465 helix: 2.22 (0.16), residues: 1038 sheet: 0.06 (0.20), residues: 611 loop : -0.32 (0.14), residues: 1816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP E 594 HIS 0.002 0.000 HIS E 505 PHE 0.025 0.001 PHE A 238 TYR 0.027 0.001 TYR E 243 ARG 0.005 0.000 ARG C 983 Details of bonding type rmsd link_NAG-ASN : bond 0.00458 ( 46) link_NAG-ASN : angle 2.28270 ( 138) link_BETA1-4 : bond 0.00298 ( 18) link_BETA1-4 : angle 0.97120 ( 54) hydrogen bonds : bond 0.03698 ( 1154) hydrogen bonds : angle 4.90624 ( 3255) SS BOND : bond 0.00124 ( 40) SS BOND : angle 0.56198 ( 80) covalent geometry : bond 0.00244 (29245) covalent geometry : angle 0.50491 (39795) *********************** 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 117 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 86 time to evaluate : 2.999 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 571 ASP cc_start: 0.9044 (m-30) cc_final: 0.8770 (p0) REVERT: A 773 GLU cc_start: 0.8619 (tt0) cc_final: 0.8311 (tt0) REVERT: A 780 GLU cc_start: 0.8809 (mm-30) cc_final: 0.8390 (mp0) REVERT: A 786 LYS cc_start: 0.8872 (mmmt) cc_final: 0.8602 (mmmt) REVERT: A 900 MET cc_start: 0.9228 (OUTLIER) cc_final: 0.8794 (mtp) REVERT: B 1005 GLN cc_start: 0.8746 (tm-30) cc_final: 0.8227 (tm-30) REVERT: C 47 VAL cc_start: 0.9434 (OUTLIER) cc_final: 0.9169 (m) REVERT: C 153 MET cc_start: 0.6430 (pmm) cc_final: 0.6086 (pmm) REVERT: C 324 GLU cc_start: 0.9173 (OUTLIER) cc_final: 0.8835 (pm20) REVERT: C 351 TYR cc_start: 0.8644 (OUTLIER) cc_final: 0.8240 (p90) REVERT: C 421 TYR cc_start: 0.8838 (m-10) cc_final: 0.8608 (m-10) REVERT: C 434 ILE cc_start: 0.7238 (OUTLIER) cc_final: 0.6871 (pp) REVERT: C 571 ASP cc_start: 0.8372 (m-30) cc_final: 0.7548 (p0) REVERT: C 993 ILE cc_start: 0.9249 (OUTLIER) cc_final: 0.8992 (mp) REVERT: C 1145 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.8140 (pt) REVERT: E 115 ARG cc_start: 0.6843 (OUTLIER) cc_final: 0.6637 (ptm-80) REVERT: E 123 MET cc_start: 0.0661 (mtt) cc_final: 0.0279 (ttp) REVERT: E 332 MET cc_start: 0.3516 (ttp) cc_final: 0.2992 (tpp) REVERT: E 433 GLU cc_start: 0.7361 (mt-10) cc_final: 0.7055 (pp20) REVERT: E 582 ARG cc_start: 0.7833 (mmm160) cc_final: 0.7514 (tmm-80) outliers start: 31 outliers final: 9 residues processed: 111 average time/residue: 1.3775 time to fit residues: 182.2253 Evaluate side-chains 99 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 82 time to evaluate : 3.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 374 PHE Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain E residue 115 ARG Chi-restraints excluded: chain E residue 213 ASP Chi-restraints excluded: chain E residue 557 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 48 optimal weight: 0.9990 chunk 170 optimal weight: 8.9990 chunk 103 optimal weight: 5.9990 chunk 250 optimal weight: 5.9990 chunk 338 optimal weight: 7.9990 chunk 186 optimal weight: 0.8980 chunk 263 optimal weight: 0.0970 chunk 62 optimal weight: 0.9980 chunk 296 optimal weight: 5.9990 chunk 260 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 overall best weight: 1.3982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 519 HIS B1010 GLN C 755 GLN C1005 GLN E 250 ASN ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 493 HIS ** E 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.091569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.054456 restraints weight = 115373.640| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 3.70 r_work: 0.2967 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.3596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 29349 Z= 0.143 Angle : 0.538 11.545 40067 Z= 0.267 Chirality : 0.043 0.286 4655 Planarity : 0.003 0.034 5068 Dihedral : 4.683 56.313 5105 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.94 % Allowed : 10.14 % Favored : 88.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.14), residues: 3465 helix: 2.25 (0.16), residues: 1036 sheet: 0.01 (0.20), residues: 619 loop : -0.29 (0.14), residues: 1810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP E 594 HIS 0.006 0.001 HIS B 519 PHE 0.024 0.001 PHE A 238 TYR 0.025 0.001 TYR E 243 ARG 0.004 0.000 ARG C 983 Details of bonding type rmsd link_NAG-ASN : bond 0.00459 ( 46) link_NAG-ASN : angle 2.28175 ( 138) link_BETA1-4 : bond 0.00231 ( 18) link_BETA1-4 : angle 1.05211 ( 54) hydrogen bonds : bond 0.03726 ( 1154) hydrogen bonds : angle 4.89788 ( 3255) SS BOND : bond 0.00135 ( 40) SS BOND : angle 0.56406 ( 80) covalent geometry : bond 0.00318 (29245) covalent geometry : angle 0.52119 (39795) *********************** 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 119 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 90 time to evaluate : 3.378 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 571 ASP cc_start: 0.9068 (m-30) cc_final: 0.8781 (p0) REVERT: A 773 GLU cc_start: 0.8646 (tt0) cc_final: 0.8355 (tt0) REVERT: A 780 GLU cc_start: 0.8855 (mm-30) cc_final: 0.8420 (mp0) REVERT: A 786 LYS cc_start: 0.8875 (mmmt) cc_final: 0.8623 (mmmt) REVERT: A 900 MET cc_start: 0.9256 (OUTLIER) cc_final: 0.8819 (mtp) REVERT: B 501 TYR cc_start: 0.7940 (OUTLIER) cc_final: 0.7010 (m-10) REVERT: B 1005 GLN cc_start: 0.8740 (tm-30) cc_final: 0.8201 (tm-30) REVERT: C 47 VAL cc_start: 0.9465 (OUTLIER) cc_final: 0.9209 (m) REVERT: C 153 MET cc_start: 0.6330 (pmm) cc_final: 0.5926 (pmm) REVERT: C 324 GLU cc_start: 0.9194 (OUTLIER) cc_final: 0.8850 (pm20) REVERT: C 351 TYR cc_start: 0.8705 (OUTLIER) cc_final: 0.8283 (p90) REVERT: C 421 TYR cc_start: 0.8771 (m-10) cc_final: 0.8516 (m-10) REVERT: C 434 ILE cc_start: 0.7379 (OUTLIER) cc_final: 0.7012 (pp) REVERT: C 462 LYS cc_start: 0.9027 (mppt) cc_final: 0.8719 (ptmm) REVERT: C 571 ASP cc_start: 0.8342 (m-30) cc_final: 0.7574 (p0) REVERT: C 993 ILE cc_start: 0.9263 (OUTLIER) cc_final: 0.9010 (mp) REVERT: C 1145 LEU cc_start: 0.8425 (OUTLIER) cc_final: 0.8150 (pt) REVERT: E 123 MET cc_start: 0.0662 (mtt) cc_final: 0.0273 (ttp) REVERT: E 332 MET cc_start: 0.3422 (ttp) cc_final: 0.2702 (tpp) REVERT: E 433 GLU cc_start: 0.7298 (mt-10) cc_final: 0.6946 (pp20) REVERT: E 455 MET cc_start: 0.6623 (ppp) cc_final: 0.6251 (ppp) REVERT: E 582 ARG cc_start: 0.7844 (mmm160) cc_final: 0.7494 (tmm-80) outliers start: 29 outliers final: 12 residues processed: 113 average time/residue: 1.4374 time to fit residues: 194.5811 Evaluate side-chains 106 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 86 time to evaluate : 2.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain B residue 501 TYR Chi-restraints excluded: chain B residue 519 HIS Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 374 PHE Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain E residue 213 ASP Chi-restraints excluded: chain E residue 557 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 252 optimal weight: 0.9990 chunk 308 optimal weight: 10.0000 chunk 347 optimal weight: 20.0000 chunk 52 optimal weight: 0.6980 chunk 206 optimal weight: 2.9990 chunk 186 optimal weight: 0.9990 chunk 243 optimal weight: 4.9990 chunk 271 optimal weight: 6.9990 chunk 194 optimal weight: 7.9990 chunk 312 optimal weight: 7.9990 chunk 125 optimal weight: 0.9980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 519 HIS B1010 GLN ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 535 HIS ** 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 = 0.4099 r_free = 0.4099 target = 0.091567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.054613 restraints weight = 115541.113| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 3.70 r_work: 0.2976 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.3672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 29349 Z= 0.135 Angle : 0.538 11.033 40067 Z= 0.266 Chirality : 0.043 0.288 4655 Planarity : 0.003 0.034 5068 Dihedral : 4.654 56.645 5105 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.91 % Allowed : 10.59 % Favored : 88.50 % 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: 0.79 (0.14), residues: 3465 helix: 2.26 (0.16), residues: 1035 sheet: 0.01 (0.20), residues: 617 loop : -0.27 (0.14), residues: 1813 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 436 HIS 0.016 0.001 HIS B 519 PHE 0.021 0.001 PHE A 238 TYR 0.014 0.001 TYR A1067 ARG 0.003 0.000 ARG C 355 Details of bonding type rmsd link_NAG-ASN : bond 0.00444 ( 46) link_NAG-ASN : angle 2.24698 ( 138) link_BETA1-4 : bond 0.00247 ( 18) link_BETA1-4 : angle 1.00864 ( 54) hydrogen bonds : bond 0.03695 ( 1154) hydrogen bonds : angle 4.86600 ( 3255) SS BOND : bond 0.00124 ( 40) SS BOND : angle 0.55527 ( 80) covalent geometry : bond 0.00302 (29245) covalent geometry : angle 0.52141 (39795) *********************** 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 116 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 88 time to evaluate : 2.993 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 571 ASP cc_start: 0.9032 (m-30) cc_final: 0.8757 (p0) REVERT: A 773 GLU cc_start: 0.8642 (tt0) cc_final: 0.8330 (tt0) REVERT: A 780 GLU cc_start: 0.8877 (mm-30) cc_final: 0.8443 (mp0) REVERT: A 786 LYS cc_start: 0.8892 (mmmt) cc_final: 0.8650 (mmmt) REVERT: A 900 MET cc_start: 0.9240 (OUTLIER) cc_final: 0.8807 (mtp) REVERT: A 1092 GLU cc_start: 0.8891 (mp0) cc_final: 0.8681 (mp0) REVERT: B 1005 GLN cc_start: 0.8753 (tm-30) cc_final: 0.8214 (tm-30) REVERT: C 47 VAL cc_start: 0.9440 (OUTLIER) cc_final: 0.9181 (m) REVERT: C 153 MET cc_start: 0.6360 (pmm) cc_final: 0.5952 (pmm) REVERT: C 324 GLU cc_start: 0.9197 (OUTLIER) cc_final: 0.8849 (pm20) REVERT: C 351 TYR cc_start: 0.8631 (OUTLIER) cc_final: 0.8284 (p90) REVERT: C 421 TYR cc_start: 0.8787 (m-10) cc_final: 0.8552 (m-10) REVERT: C 434 ILE cc_start: 0.7352 (OUTLIER) cc_final: 0.6975 (pp) REVERT: C 462 LYS cc_start: 0.8977 (mppt) cc_final: 0.8702 (ptmm) REVERT: C 571 ASP cc_start: 0.8325 (m-30) cc_final: 0.7564 (p0) REVERT: C 993 ILE cc_start: 0.9257 (OUTLIER) cc_final: 0.9003 (mp) REVERT: C 1145 LEU cc_start: 0.8475 (OUTLIER) cc_final: 0.8191 (pt) REVERT: E 123 MET cc_start: 0.0723 (mtt) cc_final: 0.0333 (ttp) REVERT: E 332 MET cc_start: 0.3429 (ttp) cc_final: 0.2806 (tpp) REVERT: E 433 GLU cc_start: 0.7282 (mt-10) cc_final: 0.6965 (pp20) REVERT: E 582 ARG cc_start: 0.7804 (mmm160) cc_final: 0.7478 (tmm-80) outliers start: 28 outliers final: 14 residues processed: 109 average time/residue: 1.4046 time to fit residues: 182.9965 Evaluate side-chains 105 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 84 time to evaluate : 3.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 374 PHE Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain E residue 213 ASP Chi-restraints excluded: chain E residue 557 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 104 optimal weight: 10.0000 chunk 93 optimal weight: 4.9990 chunk 32 optimal weight: 7.9990 chunk 106 optimal weight: 5.9990 chunk 34 optimal weight: 0.0000 chunk 27 optimal weight: 0.9980 chunk 119 optimal weight: 9.9990 chunk 298 optimal weight: 0.0370 chunk 95 optimal weight: 2.9990 chunk 108 optimal weight: 0.0980 chunk 284 optimal weight: 1.9990 overall best weight: 0.6264 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1010 GLN ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 535 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.092038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.055414 restraints weight = 114851.476| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 3.60 r_work: 0.2998 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.3698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 29349 Z= 0.103 Angle : 0.533 12.355 40067 Z= 0.263 Chirality : 0.043 0.285 4655 Planarity : 0.003 0.079 5068 Dihedral : 4.535 57.077 5105 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 0.62 % Allowed : 11.14 % Favored : 88.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.14), residues: 3465 helix: 2.25 (0.16), residues: 1036 sheet: 0.13 (0.21), residues: 605 loop : -0.23 (0.14), residues: 1824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 436 HIS 0.006 0.001 HIS E 373 PHE 0.020 0.001 PHE A 238 TYR 0.012 0.001 TYR A1067 ARG 0.018 0.000 ARG B1014 Details of bonding type rmsd link_NAG-ASN : bond 0.00437 ( 46) link_NAG-ASN : angle 2.16983 ( 138) link_BETA1-4 : bond 0.00321 ( 18) link_BETA1-4 : angle 0.95124 ( 54) hydrogen bonds : bond 0.03602 ( 1154) hydrogen bonds : angle 4.80779 ( 3255) SS BOND : bond 0.00108 ( 40) SS BOND : angle 0.54142 ( 80) covalent geometry : bond 0.00225 (29245) covalent geometry : angle 0.51772 (39795) ********************** 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 108 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 89 time to evaluate : 2.899 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 GLN cc_start: 0.9039 (mm-40) cc_final: 0.8228 (pp30) REVERT: A 571 ASP cc_start: 0.9072 (m-30) cc_final: 0.8777 (p0) REVERT: A 773 GLU cc_start: 0.8626 (tt0) cc_final: 0.8320 (tt0) REVERT: A 780 GLU cc_start: 0.8844 (mm-30) cc_final: 0.8449 (mp0) REVERT: A 786 LYS cc_start: 0.8890 (mmmt) cc_final: 0.8663 (mmmt) REVERT: A 900 MET cc_start: 0.9220 (OUTLIER) cc_final: 0.8752 (mtp) REVERT: B 1005 GLN cc_start: 0.8727 (tm-30) cc_final: 0.8180 (tm-30) REVERT: C 47 VAL cc_start: 0.9462 (OUTLIER) cc_final: 0.9207 (m) REVERT: C 153 MET cc_start: 0.6453 (pmm) cc_final: 0.6080 (pmm) REVERT: C 324 GLU cc_start: 0.9221 (OUTLIER) cc_final: 0.8877 (pm20) REVERT: C 351 TYR cc_start: 0.8693 (OUTLIER) cc_final: 0.8300 (p90) REVERT: C 421 TYR cc_start: 0.8816 (m-10) cc_final: 0.8571 (m-10) REVERT: C 462 LYS cc_start: 0.9064 (mppt) cc_final: 0.8733 (ptmm) REVERT: C 571 ASP cc_start: 0.8305 (m-30) cc_final: 0.7531 (p0) REVERT: C 1145 LEU cc_start: 0.8433 (OUTLIER) cc_final: 0.8152 (pt) REVERT: E 62 MET cc_start: 0.6552 (mmm) cc_final: 0.6156 (mmp) REVERT: E 123 MET cc_start: 0.0752 (mtt) cc_final: 0.0365 (ttp) REVERT: E 332 MET cc_start: 0.3574 (ttp) cc_final: 0.2746 (tpp) REVERT: E 433 GLU cc_start: 0.7289 (mt-10) cc_final: 0.6945 (pp20) REVERT: E 455 MET cc_start: 0.6509 (ppp) cc_final: 0.5960 (ppp) REVERT: E 582 ARG cc_start: 0.7777 (mmm160) cc_final: 0.7447 (tmm-80) outliers start: 19 outliers final: 10 residues processed: 103 average time/residue: 1.5522 time to fit residues: 190.0539 Evaluate side-chains 102 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 87 time to evaluate : 3.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain B residue 501 TYR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain E residue 213 ASP Chi-restraints excluded: chain E residue 557 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 333 optimal weight: 5.9990 chunk 280 optimal weight: 3.9990 chunk 258 optimal weight: 0.9990 chunk 34 optimal weight: 5.9990 chunk 156 optimal weight: 0.0470 chunk 301 optimal weight: 6.9990 chunk 342 optimal weight: 1.9990 chunk 204 optimal weight: 4.9990 chunk 310 optimal weight: 20.0000 chunk 64 optimal weight: 5.9990 chunk 263 optimal weight: 0.8980 overall best weight: 1.5884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1010 GLN ** E 374 HIS ** 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 = 0.4095 r_free = 0.4095 target = 0.091336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 102)---------------| | r_work = 0.3307 r_free = 0.3307 target = 0.054044 restraints weight = 115143.594| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 4.03 r_work: 0.2964 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.3860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 29349 Z= 0.152 Angle : 0.558 14.549 40067 Z= 0.276 Chirality : 0.043 0.290 4655 Planarity : 0.004 0.088 5068 Dihedral : 4.594 56.832 5105 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.62 % Allowed : 11.24 % Favored : 88.14 % 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: 2.27 (0.16), residues: 1035 sheet: 0.06 (0.20), residues: 616 loop : -0.24 (0.15), residues: 1814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 594 HIS 0.009 0.001 HIS E 373 PHE 0.021 0.001 PHE A 238 TYR 0.014 0.001 TYR A1067 ARG 0.018 0.000 ARG B1014 Details of bonding type rmsd link_NAG-ASN : bond 0.00442 ( 46) link_NAG-ASN : angle 2.23829 ( 138) link_BETA1-4 : bond 0.00230 ( 18) link_BETA1-4 : angle 1.07069 ( 54) hydrogen bonds : bond 0.03741 ( 1154) hydrogen bonds : angle 4.89051 ( 3255) SS BOND : bond 0.00134 ( 40) SS BOND : angle 0.57434 ( 80) covalent geometry : bond 0.00342 (29245) covalent geometry : angle 0.54239 (39795) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 30721.39 seconds wall clock time: 528 minutes 25.72 seconds (31705.72 seconds total)