Starting phenix.real_space_refine on Mon Jun 23 09:21:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dlm_27506/06_2025/8dlm_27506.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dlm_27506/06_2025/8dlm_27506.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dlm_27506/06_2025/8dlm_27506.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dlm_27506/06_2025/8dlm_27506.map" model { file = "/net/cci-nas-00/data/ceres_data/8dlm_27506/06_2025/8dlm_27506.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dlm_27506/06_2025/8dlm_27506.cif" } resolution = 2.89 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= 0.038 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 124 5.16 5 C 17102 2.51 5 N 4380 2.21 5 O 5246 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 26852 Number of models: 1 Model: "" Number of chains: 26 Chain: "A" Number of atoms: 6523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 837, 6523 Classifications: {'peptide': 837} Link IDs: {'PTRANS': 45, 'TRANS': 791} Chain breaks: 8 Chain: "B" Number of atoms: 8085 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1034, 8085 Classifications: {'peptide': 1034} Link IDs: {'PTRANS': 56, 'TRANS': 977} Chain breaks: 7 Chain: "C" Number of atoms: 6514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 836, 6514 Classifications: {'peptide': 836} Link IDs: {'PTRANS': 45, 'TRANS': 790} Chain breaks: 8 Chain: "E" Number of atoms: 4862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 27, 'TRANS': 568} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "C" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "E" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 16.24, per 1000 atoms: 0.60 Number of scatterers: 26852 At special positions: 0 Unit cell: (140, 158, 237, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 124 16.00 O 5246 8.00 N 4380 7.00 C 17102 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.04 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS E 133 " - pdb=" SG CYS E 141 " distance=2.04 Simple disulfide: pdb=" SG CYS E 530 " - pdb=" SG CYS E 542 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 165 " " NAG A1304 " - " ASN A 234 " " NAG A1305 " - " ASN A 282 " " NAG A1306 " - " ASN A 709 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 165 " " NAG B1304 " - " ASN B 234 " " NAG B1305 " - " ASN B 282 " " NAG B1306 " - " ASN B 331 " " NAG B1307 " - " ASN B 343 " " NAG B1308 " - " ASN B 709 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 122 " " NAG C1303 " - " ASN C 165 " " NAG C1304 " - " ASN C 234 " " NAG C1305 " - " ASN C 282 " " NAG C1306 " - " ASN C 709 " " NAG D 1 " - " ASN A 17 " " NAG E 701 " - " ASN E 53 " " NAG E 702 " - " ASN E 90 " " NAG E 703 " - " ASN E 103 " " NAG E 704 " - " ASN E 322 " " NAG E 705 " - " ASN E 432 " " NAG E 706 " - " ASN E 546 " " NAG F 1 " - " ASN A 717 " " NAG G 1 " - " ASN A 801 " " NAG H 1 " - " ASN A1074 " " NAG I 1 " - " ASN A1098 " " NAG J 1 " - " ASN A1134 " " NAG K 1 " - " ASN B 17 " " NAG L 1 " - " ASN B 717 " " NAG M 1 " - " ASN B 801 " " NAG N 1 " - " ASN B1074 " " NAG O 1 " - " ASN B1098 " " NAG P 1 " - " ASN B1134 " " NAG Q 1 " - " ASN C 17 " " NAG R 1 " - " ASN C 717 " " NAG S 1 " - " ASN C 801 " " NAG T 1 " - " ASN C1074 " " NAG U 1 " - " ASN C1098 " " NAG V 1 " - " ASN C1134 " Time building additional restraints: 7.01 Conformation dependent library (CDL) restraints added in 3.6 seconds 6498 Ramachandran restraints generated. 3249 Oldfield, 0 Emsley, 3249 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6200 Finding SS restraints... Secondary structure from input PDB file: 87 helices and 43 sheets defined 34.2% alpha, 28.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.20 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 616 through 620 removed outlier: 4.099A 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: 3.619A 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: 3.919A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.030A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1147 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 364 through 370 removed outlier: 4.337A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 387 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.662A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 620 removed outlier: 4.096A pdb=" N VAL B 620 " --> pdb=" O CYS B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.608A 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: 3.895A 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 1032 removed outlier: 4.078A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1147 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 616 through 620 removed outlier: 4.087A pdb=" N VAL C 620 " --> pdb=" O CYS C 617 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.611A 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 Processing helix chain 'C' and resid 912 through 919 removed outlier: 3.921A 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: 4.051A 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: 3.671A pdb=" N ASP E 38 " --> pdb=" O HIS E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 81 removed outlier: 3.716A pdb=" N GLN E 81 " --> pdb=" O SER E 77 " (cutoff:3.500A) 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: 3.771A 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: 4.123A 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 147 through 155 Processing helix chain 'E' and resid 157 through 194 Proline residue: E 178 - end of helix removed outlier: 3.693A 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: 3.798A pdb=" N LEU E 222 " --> pdb=" O SER E 218 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N ILE E 223 " --> pdb=" O ARG E 219 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N GLU E 224 " --> pdb=" O GLY E 220 " (cutoff:3.500A) removed outlier: 3.763A 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: 3.835A 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 319 removed outlier: 3.526A pdb=" N GLY E 319 " --> pdb=" O PHE E 315 " (cutoff:3.500A) Processing helix chain 'E' and resid 324 through 331 removed outlier: 3.565A pdb=" N TRP E 328 " --> pdb=" O THR E 324 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 385 removed outlier: 3.676A 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: 4.170A pdb=" N HIS E 401 " --> pdb=" O ASN E 397 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N GLU E 402 " --> pdb=" O GLU E 398 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLY E 405 " --> pdb=" O HIS E 401 " (cutoff:3.500A) removed outlier: 3.942A 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: 3.581A pdb=" N GLU E 435 " --> pdb=" O ASP E 431 " (cutoff:3.500A) Processing helix chain 'E' and resid 448 through 465 removed outlier: 4.327A 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: 3.654A 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: 4.519A pdb=" N TYR E 516 " --> pdb=" O PHE E 512 " (cutoff:3.500A) removed outlier: 3.578A 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: 3.804A 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 removed outlier: 3.536A pdb=" N LEU E 585 " --> pdb=" O VAL E 581 " (cutoff:3.500A) Processing helix chain 'E' and resid 588 through 599 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 Processing sheet with id=AA2, first strand: chain 'A' and resid 27 through 30 removed outlier: 8.130A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 42 through 43 removed outlier: 5.052A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 47 through 55 removed outlier: 4.079A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.824A pdb=" N LEU A 84 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 10.182A pdb=" N GLN A 134 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 9.283A pdb=" N ASN A 164 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 8.317A pdb=" N CYS A 136 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 10.343A pdb=" N SER A 162 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 10.416A pdb=" N ASP A 138 " --> pdb=" O TYR A 160 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N TYR A 160 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLU A 156 " --> pdb=" O GLY A 142 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 6.684A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.157A 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: 4.917A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.072A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.666A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.337A 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: 6.800A pdb=" N VAL A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 8.166A pdb=" N LYS B 790 " --> pdb=" O VAL A 701 " (cutoff:3.500A) removed outlier: 7.796A 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 removed outlier: 6.545A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.545A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.296A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 787 through 790 removed outlier: 3.700A pdb=" N LYS A 790 " --> pdb=" O ASN C 703 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB6, first strand: chain 'B' and resid 27 through 30 Processing sheet with id=AB7, first strand: chain 'B' and resid 27 through 30 removed outlier: 8.110A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.065A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.822A pdb=" N LEU B 84 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N GLU B 132 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N CYS B 166 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 10.143A pdb=" N GLN B 134 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 9.252A pdb=" N ASN B 164 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 8.290A pdb=" N CYS B 136 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 10.348A pdb=" N SER B 162 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 10.379A pdb=" N ASP B 138 " --> pdb=" O TYR B 160 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N TYR B 160 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLU B 156 " --> pdb=" O GLY B 142 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 311 through 318 removed outlier: 6.728A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 325 through 326 removed outlier: 5.145A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.054A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 391 through 392 Processing sheet with id=AC5, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC6, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC7, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.138A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.729A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 701 through 704 removed outlier: 6.777A pdb=" N VAL B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N LYS C 790 " --> pdb=" O VAL B 701 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N ASN B 703 " --> pdb=" O LYS C 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.569A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.569A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.314A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD4, first strand: chain 'C' and resid 27 through 30 Processing sheet with id=AD5, first strand: chain 'C' and resid 27 through 30 removed outlier: 7.984A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 47 through 55 removed outlier: 4.031A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.658A pdb=" N LEU C 84 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N GLU C 132 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N CYS C 166 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 10.156A pdb=" N GLN C 134 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 9.286A pdb=" N ASN C 164 " --> pdb=" O GLN C 134 " (cutoff:3.500A) removed outlier: 8.362A pdb=" N CYS C 136 " --> pdb=" O SER C 162 " (cutoff:3.500A) removed outlier: 10.410A pdb=" N SER C 162 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 10.484A pdb=" N ASP C 138 " --> pdb=" O TYR C 160 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N TYR C 160 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLU C 156 " --> pdb=" O GLY C 142 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 311 through 319 removed outlier: 6.682A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.076A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.650A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.350A 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 removed outlier: 6.524A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.524A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.300A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AE5, first strand: chain 'E' and resid 131 through 132 removed outlier: 3.910A pdb=" N LEU E 142 " --> pdb=" O VAL E 132 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'E' and resid 262 through 263 removed outlier: 6.118A pdb=" N LEU E 262 " --> pdb=" O VAL E 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'E' and resid 347 through 352 removed outlier: 6.379A pdb=" N ASP E 355 " --> pdb=" O LEU E 351 " (cutoff:3.500A) 1299 hydrogen bonds defined for protein. 3648 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: 24.51 Time building geometry restraints manager: 8.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8446 1.34 - 1.47: 6919 1.47 - 1.59: 11928 1.59 - 1.72: 0 1.72 - 1.84: 172 Bond restraints: 27465 Sorted by residual: bond pdb=" C1 NAG E 706 " pdb=" O5 NAG E 706 " ideal model delta sigma weight residual 1.406 1.460 -0.054 2.00e-02 2.50e+03 7.42e+00 bond pdb=" C1 NAG C1303 " pdb=" O5 NAG C1303 " ideal model delta sigma weight residual 1.406 1.459 -0.053 2.00e-02 2.50e+03 7.05e+00 bond pdb=" C1 NAG B1303 " pdb=" O5 NAG B1303 " ideal model delta sigma weight residual 1.406 1.458 -0.052 2.00e-02 2.50e+03 6.88e+00 bond pdb=" C1 NAG A1303 " pdb=" O5 NAG A1303 " ideal model delta sigma weight residual 1.406 1.458 -0.052 2.00e-02 2.50e+03 6.87e+00 bond pdb=" C1 NAG K 1 " pdb=" O5 NAG K 1 " ideal model delta sigma weight residual 1.406 1.457 -0.051 2.00e-02 2.50e+03 6.40e+00 ... (remaining 27460 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.03: 36137 2.03 - 4.06: 1115 4.06 - 6.09: 78 6.09 - 8.12: 30 8.12 - 10.15: 7 Bond angle restraints: 37367 Sorted by residual: angle pdb=" CA TYR B 495 " pdb=" CB TYR B 495 " pdb=" CG TYR B 495 " ideal model delta sigma weight residual 113.90 122.21 -8.31 1.80e+00 3.09e-01 2.13e+01 angle pdb=" N PRO B 986 " pdb=" CA PRO B 986 " pdb=" C PRO B 986 " ideal model delta sigma weight residual 110.70 116.07 -5.37 1.22e+00 6.72e-01 1.94e+01 angle pdb=" N PRO C 986 " pdb=" CA PRO C 986 " pdb=" C PRO C 986 " ideal model delta sigma weight residual 110.70 116.04 -5.34 1.22e+00 6.72e-01 1.91e+01 angle pdb=" N PRO A 986 " pdb=" CA PRO A 986 " pdb=" C PRO A 986 " ideal model delta sigma weight residual 110.70 116.03 -5.33 1.22e+00 6.72e-01 1.91e+01 angle pdb=" C SER B 359 " pdb=" N ASN B 360 " pdb=" CA ASN B 360 " ideal model delta sigma weight residual 122.36 128.20 -5.84 1.42e+00 4.96e-01 1.69e+01 ... (remaining 37362 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 15762 17.73 - 35.46: 1089 35.46 - 53.19: 208 53.19 - 70.92: 67 70.92 - 88.65: 35 Dihedral angle restraints: 17161 sinusoidal: 7548 harmonic: 9613 Sorted by residual: dihedral pdb=" CB CYS E 133 " pdb=" SG CYS E 133 " pdb=" SG CYS E 141 " pdb=" CB CYS E 141 " ideal model delta sinusoidal sigma weight residual -86.00 -49.93 -36.07 1 1.00e+01 1.00e-02 1.84e+01 dihedral pdb=" SG CYS B 391 " pdb=" CB CYS B 525 " pdb=" SG CYS B 525 " pdb=" CA CYS B 525 " ideal model delta sinusoidal sigma weight residual 79.00 17.75 61.25 1 2.00e+01 2.50e-03 1.25e+01 dihedral pdb=" CB GLU C1111 " pdb=" CG GLU C1111 " pdb=" CD GLU C1111 " pdb=" OE1 GLU C1111 " ideal model delta sinusoidal sigma weight residual 0.00 86.82 -86.82 1 3.00e+01 1.11e-03 1.01e+01 ... (remaining 17158 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 3540 0.070 - 0.140: 773 0.140 - 0.210: 67 0.210 - 0.280: 6 0.280 - 0.350: 3 Chirality restraints: 4389 Sorted by residual: 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 -2.05 -0.35 2.00e-01 2.50e+01 3.06e+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 -2.10 -0.30 2.00e-01 2.50e+01 2.24e+00 chirality pdb=" C1 NAG Q 1 " pdb=" ND2 ASN C 17 " pdb=" C2 NAG Q 1 " pdb=" O5 NAG Q 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-01 2.50e+01 2.06e+00 ... (remaining 4386 not shown) Planarity restraints: 4795 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU E 589 " -0.041 5.00e-02 4.00e+02 6.14e-02 6.03e+00 pdb=" N PRO E 590 " 0.106 5.00e-02 4.00e+02 pdb=" CA PRO E 590 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO E 590 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP E 499 " -0.041 5.00e-02 4.00e+02 6.06e-02 5.88e+00 pdb=" N PRO E 500 " 0.105 5.00e-02 4.00e+02 pdb=" CA PRO E 500 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO E 500 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 495 " -0.027 2.00e-02 2.50e+03 1.71e-02 5.86e+00 pdb=" CG TYR B 495 " 0.040 2.00e-02 2.50e+03 pdb=" CD1 TYR B 495 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 TYR B 495 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR B 495 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR B 495 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR B 495 " -0.006 2.00e-02 2.50e+03 pdb=" OH TYR B 495 " -0.004 2.00e-02 2.50e+03 ... (remaining 4792 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 7389 2.81 - 3.34: 23115 3.34 - 3.86: 45975 3.86 - 4.38: 52166 4.38 - 4.90: 90280 Nonbonded interactions: 218925 Sorted by model distance: nonbonded pdb=" OH TYR A 37 " pdb=" O LEU A 54 " model vdw 2.293 3.040 nonbonded pdb=" OH TYR C 37 " pdb=" O LEU C 54 " model vdw 2.302 3.040 nonbonded pdb=" OH TYR A 756 " pdb=" OD1 ASP A 994 " model vdw 2.303 3.040 nonbonded pdb=" OH TYR B 37 " pdb=" O LEU B 54 " model vdw 2.307 3.040 nonbonded pdb=" OH TYR C 756 " pdb=" OD1 ASP C 994 " model vdw 2.313 3.040 ... (remaining 218920 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 528 or resid 530 through 1147 or resid 1301 thr \ ough 1306)) 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: 0.010 Normalize map: mean=0, sd=1: 4.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.140 Check model and map are aligned: 0.200 Set scattering table: 0.240 Process input model: 77.740 Find NCS groups from input model: 1.930 Set up NCS constraints: 0.310 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: 0.020 Load rotamer database and sin/cos tables:89.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 174.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 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 0.055 27563 Z= 0.238 Angle : 0.826 16.070 37625 Z= 0.441 Chirality : 0.056 0.350 4389 Planarity : 0.006 0.061 4751 Dihedral : 13.167 88.650 10853 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.03 % Allowed : 2.83 % Favored : 97.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.41 (0.13), residues: 3249 helix: 1.48 (0.14), residues: 994 sheet: 0.94 (0.20), residues: 586 loop : -0.73 (0.14), residues: 1669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP E 69 HIS 0.008 0.001 HIS E 34 PHE 0.024 0.002 PHE A 275 TYR 0.040 0.002 TYR B 495 ARG 0.008 0.001 ARG E 460 Details of bonding type rmsd link_NAG-ASN : bond 0.00729 ( 44) link_NAG-ASN : angle 3.79374 ( 132) link_BETA1-4 : bond 0.00627 ( 18) link_BETA1-4 : angle 1.30548 ( 54) hydrogen bonds : bond 0.12039 ( 1251) hydrogen bonds : angle 6.89331 ( 3648) SS BOND : bond 0.00274 ( 36) SS BOND : angle 1.49651 ( 72) covalent geometry : bond 0.00476 (27465) covalent geometry : angle 0.79369 (37367) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6498 Ramachandran restraints generated. 3249 Oldfield, 0 Emsley, 3249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6498 Ramachandran restraints generated. 3249 Oldfield, 0 Emsley, 3249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 312 time to evaluate : 3.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 PHE cc_start: 0.8590 (m-80) cc_final: 0.8197 (m-10) REVERT: A 90 VAL cc_start: 0.7311 (t) cc_final: 0.7056 (p) REVERT: A 106 PHE cc_start: 0.8677 (m-80) cc_final: 0.8123 (m-10) REVERT: A 168 PHE cc_start: 0.8028 (t80) cc_final: 0.7768 (t80) REVERT: A 194 PHE cc_start: 0.8753 (m-80) cc_final: 0.7757 (m-80) REVERT: A 284 THR cc_start: 0.8875 (m) cc_final: 0.8625 (p) REVERT: A 740 MET cc_start: 0.8104 (ttt) cc_final: 0.7800 (ttp) REVERT: B 337 PRO cc_start: 0.8811 (Cg_exo) cc_final: 0.8536 (Cg_endo) REVERT: B 532 ASN cc_start: 0.8495 (m-40) cc_final: 0.8278 (p0) REVERT: C 170 TYR cc_start: 0.8356 (t80) cc_final: 0.8150 (t80) REVERT: C 197 ILE cc_start: 0.8196 (mp) cc_final: 0.7903 (mm) REVERT: C 238 PHE cc_start: 0.7716 (p90) cc_final: 0.7078 (p90) REVERT: C 269 TYR cc_start: 0.6714 (m-80) cc_final: 0.6412 (m-80) REVERT: E 82 MET cc_start: 0.7868 (mtp) cc_final: 0.7635 (mpt) REVERT: E 134 ASN cc_start: 0.7235 (t0) cc_final: 0.6859 (p0) REVERT: E 292 ASP cc_start: 0.5134 (t70) cc_final: 0.4031 (m-30) REVERT: E 323 MET cc_start: 0.6582 (mmp) cc_final: 0.6113 (mpm) REVERT: E 474 MET cc_start: -0.0590 (mmt) cc_final: -0.1007 (mmt) REVERT: E 564 GLU cc_start: 0.3784 (mm-30) cc_final: 0.2991 (pm20) outliers start: 1 outliers final: 1 residues processed: 313 average time/residue: 1.4609 time to fit residues: 532.3004 Evaluate side-chains 130 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 129 time to evaluate : 2.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 983 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 276 optimal weight: 4.9990 chunk 248 optimal weight: 3.9990 chunk 137 optimal weight: 3.9990 chunk 84 optimal weight: 6.9990 chunk 167 optimal weight: 2.9990 chunk 132 optimal weight: 3.9990 chunk 257 optimal weight: 1.9990 chunk 99 optimal weight: 0.8980 chunk 156 optimal weight: 3.9990 chunk 191 optimal weight: 10.0000 chunk 297 optimal weight: 20.0000 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 GLN A 872 GLN B 856 ASN C 762 GLN C 907 ASN C 955 ASN ** C 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 552 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.101719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.062795 restraints weight = 98619.961| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 3.62 r_work: 0.3117 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 27563 Z= 0.247 Angle : 0.688 17.961 37625 Z= 0.339 Chirality : 0.046 0.287 4389 Planarity : 0.005 0.059 4751 Dihedral : 6.574 57.260 4824 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 1.86 % Allowed : 7.83 % Favored : 90.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3249 helix: 2.23 (0.15), residues: 1006 sheet: 0.79 (0.21), residues: 535 loop : -0.57 (0.14), residues: 1708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 104 HIS 0.005 0.001 HIS C1064 PHE 0.016 0.002 PHE C 86 TYR 0.021 0.002 TYR B1067 ARG 0.017 0.001 ARG A 983 Details of bonding type rmsd link_NAG-ASN : bond 0.01165 ( 44) link_NAG-ASN : angle 3.74573 ( 132) link_BETA1-4 : bond 0.00259 ( 18) link_BETA1-4 : angle 1.19833 ( 54) hydrogen bonds : bond 0.04563 ( 1251) hydrogen bonds : angle 5.62316 ( 3648) SS BOND : bond 0.00307 ( 36) SS BOND : angle 1.25542 ( 72) covalent geometry : bond 0.00545 (27465) covalent geometry : angle 0.65008 (37367) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6498 Ramachandran restraints generated. 3249 Oldfield, 0 Emsley, 3249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6498 Ramachandran restraints generated. 3249 Oldfield, 0 Emsley, 3249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 144 time to evaluate : 3.157 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 90 VAL cc_start: 0.7031 (t) cc_final: 0.6807 (p) REVERT: A 104 TRP cc_start: 0.8214 (m-90) cc_final: 0.7782 (m-10) REVERT: A 106 PHE cc_start: 0.8983 (m-80) cc_final: 0.8601 (m-10) REVERT: A 168 PHE cc_start: 0.7915 (t80) cc_final: 0.7620 (t80) REVERT: A 194 PHE cc_start: 0.8478 (m-80) cc_final: 0.8022 (m-80) REVERT: A 197 ILE cc_start: 0.8783 (OUTLIER) cc_final: 0.8556 (mp) REVERT: A 740 MET cc_start: 0.9018 (ttt) cc_final: 0.8662 (ttp) REVERT: A 983 ARG cc_start: 0.8534 (OUTLIER) cc_final: 0.8162 (OUTLIER) REVERT: B 175 PHE cc_start: 0.5783 (m-10) cc_final: 0.5064 (m-10) REVERT: B 380 TYR cc_start: 0.7827 (m-80) cc_final: 0.7545 (m-80) REVERT: B 517 LEU cc_start: 0.9162 (mm) cc_final: 0.8525 (mm) REVERT: B 532 ASN cc_start: 0.9317 (m-40) cc_final: 0.8857 (t0) REVERT: B 764 ASN cc_start: 0.9200 (m110) cc_final: 0.8991 (m-40) REVERT: C 53 ASP cc_start: 0.8084 (t0) cc_final: 0.7703 (t0) REVERT: C 170 TYR cc_start: 0.8698 (t80) cc_final: 0.7854 (t80) REVERT: C 197 ILE cc_start: 0.8374 (mp) cc_final: 0.8091 (mm) REVERT: C 238 PHE cc_start: 0.7371 (p90) cc_final: 0.6710 (p90) REVERT: E 134 ASN cc_start: 0.7205 (t0) cc_final: 0.6712 (p0) REVERT: E 564 GLU cc_start: 0.3687 (mm-30) cc_final: 0.2887 (pm20) outliers start: 54 outliers final: 17 residues processed: 177 average time/residue: 1.2094 time to fit residues: 258.0090 Evaluate side-chains 137 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 119 time to evaluate : 2.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 983 ARG Chi-restraints excluded: chain A residue 1055 SER Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 79 PHE Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 1029 MET Chi-restraints excluded: chain C residue 1118 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 156 optimal weight: 3.9990 chunk 250 optimal weight: 4.9990 chunk 275 optimal weight: 10.0000 chunk 168 optimal weight: 4.9990 chunk 82 optimal weight: 3.9990 chunk 128 optimal weight: 9.9990 chunk 211 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 234 optimal weight: 0.9980 chunk 311 optimal weight: 10.0000 chunk 112 optimal weight: 6.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 824 ASN B 856 ASN ** B 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 824 ASN C 978 ASN E 96 GLN ** E 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 417 HIS E 524 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.099491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.060056 restraints weight = 98082.869| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 3.63 r_work: 0.3057 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.2891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 27563 Z= 0.287 Angle : 0.687 11.033 37625 Z= 0.343 Chirality : 0.047 0.302 4389 Planarity : 0.005 0.076 4751 Dihedral : 6.425 56.909 4824 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.24 % Allowed : 9.10 % Favored : 88.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3249 helix: 2.21 (0.16), residues: 1007 sheet: 0.51 (0.21), residues: 525 loop : -0.69 (0.14), residues: 1717 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 104 HIS 0.006 0.002 HIS A1064 PHE 0.019 0.002 PHE C 898 TYR 0.023 0.002 TYR A1067 ARG 0.006 0.001 ARG C1014 Details of bonding type rmsd link_NAG-ASN : bond 0.00884 ( 44) link_NAG-ASN : angle 3.20483 ( 132) link_BETA1-4 : bond 0.00206 ( 18) link_BETA1-4 : angle 1.22727 ( 54) hydrogen bonds : bond 0.04556 ( 1251) hydrogen bonds : angle 5.57252 ( 3648) SS BOND : bond 0.00318 ( 36) SS BOND : angle 1.72124 ( 72) covalent geometry : bond 0.00638 (27465) covalent geometry : angle 0.65674 (37367) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6498 Ramachandran restraints generated. 3249 Oldfield, 0 Emsley, 3249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6498 Ramachandran restraints generated. 3249 Oldfield, 0 Emsley, 3249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 114 time to evaluate : 9.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.8051 (m-90) cc_final: 0.7770 (m-10) REVERT: A 168 PHE cc_start: 0.7894 (t80) cc_final: 0.7568 (t80) REVERT: A 194 PHE cc_start: 0.8159 (m-80) cc_final: 0.7470 (m-80) REVERT: A 740 MET cc_start: 0.8902 (ttt) cc_final: 0.8573 (ttp) REVERT: B 309 GLU cc_start: 0.9015 (mp0) cc_final: 0.8713 (pm20) REVERT: B 365 TYR cc_start: 0.9123 (m-80) cc_final: 0.8892 (m-80) REVERT: B 380 TYR cc_start: 0.8158 (m-80) cc_final: 0.7943 (m-80) REVERT: B 532 ASN cc_start: 0.9448 (m-40) cc_final: 0.8897 (t0) REVERT: B 764 ASN cc_start: 0.9236 (m110) cc_final: 0.8910 (m110) REVERT: C 197 ILE cc_start: 0.8516 (mp) cc_final: 0.8281 (mm) REVERT: E 62 MET cc_start: 0.7760 (ttp) cc_final: 0.7507 (mtp) REVERT: E 134 ASN cc_start: 0.7258 (t0) cc_final: 0.6736 (p0) REVERT: E 267 LEU cc_start: 0.4323 (OUTLIER) cc_final: 0.3589 (tp) REVERT: E 557 MET cc_start: 0.5829 (tmm) cc_final: 0.5570 (tmt) outliers start: 65 outliers final: 22 residues processed: 162 average time/residue: 1.1870 time to fit residues: 237.8738 Evaluate side-chains 122 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 99 time to evaluate : 2.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 923 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1055 SER Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 1029 MET Chi-restraints excluded: chain C residue 1118 ASP Chi-restraints excluded: chain E residue 267 LEU Chi-restraints excluded: chain E residue 485 VAL Chi-restraints excluded: chain E residue 559 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 69 optimal weight: 0.7980 chunk 160 optimal weight: 0.9980 chunk 6 optimal weight: 9.9990 chunk 102 optimal weight: 5.9990 chunk 268 optimal weight: 3.9990 chunk 260 optimal weight: 0.9980 chunk 158 optimal weight: 0.8980 chunk 317 optimal weight: 20.0000 chunk 104 optimal weight: 6.9990 chunk 92 optimal weight: 8.9990 chunk 189 optimal weight: 8.9990 overall best weight: 1.5382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 856 ASN ** B 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 ASN C 115 GLN ** E 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 250 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.100554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.061271 restraints weight = 98356.830| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 3.70 r_work: 0.3089 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.2965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 27563 Z= 0.151 Angle : 0.584 11.899 37625 Z= 0.287 Chirality : 0.044 0.281 4389 Planarity : 0.004 0.071 4751 Dihedral : 5.816 56.042 4820 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 1.83 % Allowed : 10.38 % Favored : 87.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.14), residues: 3249 helix: 2.41 (0.16), residues: 1004 sheet: 0.49 (0.21), residues: 557 loop : -0.60 (0.14), residues: 1688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 104 HIS 0.004 0.001 HIS E 34 PHE 0.024 0.001 PHE C 541 TYR 0.021 0.001 TYR A1067 ARG 0.004 0.000 ARG C 995 Details of bonding type rmsd link_NAG-ASN : bond 0.00665 ( 44) link_NAG-ASN : angle 3.04831 ( 132) link_BETA1-4 : bond 0.00224 ( 18) link_BETA1-4 : angle 1.02466 ( 54) hydrogen bonds : bond 0.03943 ( 1251) hydrogen bonds : angle 5.26251 ( 3648) SS BOND : bond 0.00194 ( 36) SS BOND : angle 1.88932 ( 72) covalent geometry : bond 0.00328 (27465) covalent geometry : angle 0.54919 (37367) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6498 Ramachandran restraints generated. 3249 Oldfield, 0 Emsley, 3249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6498 Ramachandran restraints generated. 3249 Oldfield, 0 Emsley, 3249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 117 time to evaluate : 3.074 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 PHE cc_start: 0.8664 (m-80) cc_final: 0.8169 (m-10) REVERT: A 168 PHE cc_start: 0.7939 (t80) cc_final: 0.7638 (t80) REVERT: A 194 PHE cc_start: 0.8172 (m-80) cc_final: 0.7854 (m-80) REVERT: B 316 SER cc_start: 0.9206 (t) cc_final: 0.8994 (p) REVERT: B 365 TYR cc_start: 0.9075 (m-80) cc_final: 0.8816 (m-80) REVERT: B 380 TYR cc_start: 0.8109 (m-80) cc_final: 0.7807 (m-80) REVERT: B 532 ASN cc_start: 0.9426 (m-40) cc_final: 0.8873 (t0) REVERT: B 764 ASN cc_start: 0.9257 (m110) cc_final: 0.9002 (m-40) REVERT: C 197 ILE cc_start: 0.8527 (mp) cc_final: 0.8278 (mm) REVERT: C 269 TYR cc_start: 0.6959 (m-80) cc_final: 0.6671 (m-80) REVERT: E 62 MET cc_start: 0.7764 (ttp) cc_final: 0.7488 (mtp) REVERT: E 134 ASN cc_start: 0.7267 (t0) cc_final: 0.6730 (p0) REVERT: E 267 LEU cc_start: 0.4553 (OUTLIER) cc_final: 0.3610 (tp) REVERT: E 557 MET cc_start: 0.6145 (tmm) cc_final: 0.5835 (tmt) outliers start: 53 outliers final: 17 residues processed: 155 average time/residue: 1.1669 time to fit residues: 218.6866 Evaluate side-chains 121 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 103 time to evaluate : 2.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 923 ILE Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 1118 ASP Chi-restraints excluded: chain E residue 267 LEU Chi-restraints excluded: chain E residue 376 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 315 optimal weight: 6.9990 chunk 91 optimal weight: 8.9990 chunk 310 optimal weight: 8.9990 chunk 241 optimal weight: 3.9990 chunk 319 optimal weight: 7.9990 chunk 314 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 261 optimal weight: 2.9990 chunk 254 optimal weight: 6.9990 chunk 129 optimal weight: 4.9990 chunk 317 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS B 856 ASN ** B 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 305 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.098820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.059439 restraints weight = 98226.044| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 3.64 r_work: 0.3047 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.3483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 27563 Z= 0.261 Angle : 0.657 11.835 37625 Z= 0.324 Chirality : 0.046 0.310 4389 Planarity : 0.004 0.074 4751 Dihedral : 5.826 57.805 4820 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.24 % Allowed : 11.28 % Favored : 86.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.63 (0.14), residues: 3249 helix: 2.22 (0.16), residues: 1024 sheet: 0.32 (0.21), residues: 548 loop : -0.70 (0.14), residues: 1677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 104 HIS 0.004 0.001 HIS E 34 PHE 0.018 0.002 PHE C 106 TYR 0.021 0.002 TYR B1067 ARG 0.005 0.001 ARG B1107 Details of bonding type rmsd link_NAG-ASN : bond 0.00783 ( 44) link_NAG-ASN : angle 3.10570 ( 132) link_BETA1-4 : bond 0.00180 ( 18) link_BETA1-4 : angle 1.29770 ( 54) hydrogen bonds : bond 0.04311 ( 1251) hydrogen bonds : angle 5.39508 ( 3648) SS BOND : bond 0.00332 ( 36) SS BOND : angle 1.86361 ( 72) covalent geometry : bond 0.00581 (27465) covalent geometry : angle 0.62544 (37367) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6498 Ramachandran restraints generated. 3249 Oldfield, 0 Emsley, 3249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6498 Ramachandran restraints generated. 3249 Oldfield, 0 Emsley, 3249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 114 time to evaluate : 3.037 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.8121 (m-10) cc_final: 0.7839 (m-10) REVERT: A 168 PHE cc_start: 0.7819 (t80) cc_final: 0.7551 (t80) REVERT: A 740 MET cc_start: 0.8876 (ttp) cc_final: 0.8651 (ttp) REVERT: B 269 TYR cc_start: 0.7727 (m-10) cc_final: 0.7462 (m-80) REVERT: B 309 GLU cc_start: 0.9052 (mp0) cc_final: 0.8796 (pm20) REVERT: B 380 TYR cc_start: 0.8080 (m-80) cc_final: 0.7742 (m-80) REVERT: B 532 ASN cc_start: 0.9420 (m-40) cc_final: 0.8979 (t0) REVERT: B 764 ASN cc_start: 0.9273 (m110) cc_final: 0.8994 (m-40) REVERT: B 856 ASN cc_start: 0.6772 (OUTLIER) cc_final: 0.5737 (p0) REVERT: C 104 TRP cc_start: 0.7567 (m-90) cc_final: 0.7288 (m-90) REVERT: C 197 ILE cc_start: 0.8611 (mp) cc_final: 0.8386 (mm) REVERT: C 269 TYR cc_start: 0.7192 (m-80) cc_final: 0.6906 (m-80) REVERT: E 62 MET cc_start: 0.7758 (ttp) cc_final: 0.7473 (mtp) REVERT: E 134 ASN cc_start: 0.6912 (t0) cc_final: 0.6441 (p0) REVERT: E 267 LEU cc_start: 0.4565 (OUTLIER) cc_final: 0.3482 (tp) REVERT: E 557 MET cc_start: 0.6274 (tmm) cc_final: 0.6008 (tmt) outliers start: 65 outliers final: 26 residues processed: 165 average time/residue: 1.2683 time to fit residues: 253.8455 Evaluate side-chains 130 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 102 time to evaluate : 2.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 1029 MET Chi-restraints excluded: chain C residue 1118 ASP Chi-restraints excluded: chain E residue 267 LEU Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 376 MET Chi-restraints excluded: chain E residue 485 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 193 optimal weight: 5.9990 chunk 150 optimal weight: 0.5980 chunk 104 optimal weight: 4.9990 chunk 243 optimal weight: 0.9990 chunk 230 optimal weight: 0.9990 chunk 251 optimal weight: 4.9990 chunk 321 optimal weight: 6.9990 chunk 266 optimal weight: 0.9980 chunk 68 optimal weight: 0.9980 chunk 3 optimal weight: 7.9990 chunk 320 optimal weight: 9.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 907 ASN ** B 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 137 ASN ** E 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.100155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.061097 restraints weight = 97912.008| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 3.71 r_work: 0.3087 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.3476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 27563 Z= 0.122 Angle : 0.575 12.158 37625 Z= 0.284 Chirality : 0.044 0.287 4389 Planarity : 0.004 0.073 4751 Dihedral : 5.395 56.813 4820 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.79 % Allowed : 12.31 % Favored : 85.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.84 (0.14), residues: 3249 helix: 2.35 (0.16), residues: 1012 sheet: 0.52 (0.20), residues: 579 loop : -0.56 (0.15), residues: 1658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 104 HIS 0.003 0.001 HIS E 34 PHE 0.016 0.001 PHE C 541 TYR 0.020 0.001 TYR A1067 ARG 0.003 0.000 ARG C 102 Details of bonding type rmsd link_NAG-ASN : bond 0.00616 ( 44) link_NAG-ASN : angle 2.90943 ( 132) link_BETA1-4 : bond 0.00273 ( 18) link_BETA1-4 : angle 0.99652 ( 54) hydrogen bonds : bond 0.03812 ( 1251) hydrogen bonds : angle 5.20169 ( 3648) SS BOND : bond 0.00237 ( 36) SS BOND : angle 1.81931 ( 72) covalent geometry : bond 0.00265 (27465) covalent geometry : angle 0.54370 (37367) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6498 Ramachandran restraints generated. 3249 Oldfield, 0 Emsley, 3249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6498 Ramachandran restraints generated. 3249 Oldfield, 0 Emsley, 3249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 110 time to evaluate : 3.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 VAL cc_start: 0.7274 (t) cc_final: 0.6850 (m) REVERT: A 104 TRP cc_start: 0.8163 (m-10) cc_final: 0.7906 (m-10) REVERT: A 106 PHE cc_start: 0.8842 (m-10) cc_final: 0.8452 (m-10) REVERT: A 168 PHE cc_start: 0.7877 (t80) cc_final: 0.7614 (t80) REVERT: A 194 PHE cc_start: 0.8530 (m-10) cc_final: 0.8293 (m-10) REVERT: A 900 MET cc_start: 0.9196 (mtp) cc_final: 0.8953 (mtm) REVERT: B 269 TYR cc_start: 0.7723 (m-10) cc_final: 0.7468 (m-80) REVERT: B 309 GLU cc_start: 0.9042 (mp0) cc_final: 0.8726 (pm20) REVERT: B 532 ASN cc_start: 0.9427 (m-40) cc_final: 0.9003 (t0) REVERT: B 764 ASN cc_start: 0.9262 (m110) cc_final: 0.9011 (m-40) REVERT: B 873 TYR cc_start: 0.9427 (OUTLIER) cc_final: 0.8329 (m-80) REVERT: C 197 ILE cc_start: 0.8727 (mp) cc_final: 0.8519 (mm) REVERT: C 269 TYR cc_start: 0.7174 (m-80) cc_final: 0.6861 (m-80) REVERT: E 62 MET cc_start: 0.7755 (ttp) cc_final: 0.7296 (tpp) REVERT: E 134 ASN cc_start: 0.6926 (t0) cc_final: 0.6446 (p0) REVERT: E 267 LEU cc_start: 0.4494 (OUTLIER) cc_final: 0.3068 (tp) REVERT: E 332 MET cc_start: 0.4924 (ppp) cc_final: 0.4674 (ptp) REVERT: E 366 MET cc_start: 0.2016 (mmm) cc_final: 0.1707 (tpp) REVERT: E 557 MET cc_start: 0.6255 (tmm) cc_final: 0.5289 (ttt) outliers start: 52 outliers final: 21 residues processed: 150 average time/residue: 1.7235 time to fit residues: 312.2588 Evaluate side-chains 124 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 101 time to evaluate : 4.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 923 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 1118 ASP Chi-restraints excluded: chain E residue 267 LEU Chi-restraints excluded: chain E residue 376 MET Chi-restraints excluded: chain E residue 474 MET Chi-restraints excluded: chain E residue 485 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 250 optimal weight: 4.9990 chunk 246 optimal weight: 0.7980 chunk 9 optimal weight: 10.0000 chunk 233 optimal weight: 2.9990 chunk 303 optimal weight: 0.5980 chunk 92 optimal weight: 8.9990 chunk 296 optimal weight: 0.8980 chunk 276 optimal weight: 5.9990 chunk 29 optimal weight: 10.0000 chunk 245 optimal weight: 0.5980 chunk 45 optimal weight: 6.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 856 ASN ** B 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.100129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.060926 restraints weight = 97980.887| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 3.68 r_work: 0.3087 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.3560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 27563 Z= 0.134 Angle : 0.574 12.293 37625 Z= 0.282 Chirality : 0.044 0.295 4389 Planarity : 0.004 0.073 4751 Dihedral : 5.099 57.419 4820 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.55 % Allowed : 12.90 % Favored : 85.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.14), residues: 3249 helix: 2.42 (0.16), residues: 1000 sheet: 0.57 (0.21), residues: 547 loop : -0.48 (0.15), residues: 1702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 104 HIS 0.003 0.001 HIS E 34 PHE 0.025 0.001 PHE B 175 TYR 0.021 0.001 TYR A 170 ARG 0.003 0.000 ARG C 102 Details of bonding type rmsd link_NAG-ASN : bond 0.00623 ( 44) link_NAG-ASN : angle 2.87172 ( 132) link_BETA1-4 : bond 0.00281 ( 18) link_BETA1-4 : angle 1.05781 ( 54) hydrogen bonds : bond 0.03742 ( 1251) hydrogen bonds : angle 5.10566 ( 3648) SS BOND : bond 0.00419 ( 36) SS BOND : angle 1.78321 ( 72) covalent geometry : bond 0.00295 (27465) covalent geometry : angle 0.54291 (37367) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6498 Ramachandran restraints generated. 3249 Oldfield, 0 Emsley, 3249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6498 Ramachandran restraints generated. 3249 Oldfield, 0 Emsley, 3249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 109 time to evaluate : 2.826 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 104 TRP cc_start: 0.8129 (m-10) cc_final: 0.7911 (m-10) REVERT: A 106 PHE cc_start: 0.8904 (m-80) cc_final: 0.8517 (m-10) REVERT: A 168 PHE cc_start: 0.7858 (t80) cc_final: 0.7612 (t80) REVERT: A 194 PHE cc_start: 0.8491 (m-80) cc_final: 0.8250 (m-10) REVERT: A 900 MET cc_start: 0.9185 (mtp) cc_final: 0.8934 (mtm) REVERT: B 309 GLU cc_start: 0.9034 (mp0) cc_final: 0.8726 (pm20) REVERT: B 532 ASN cc_start: 0.9445 (m-40) cc_final: 0.9022 (t0) REVERT: B 764 ASN cc_start: 0.9281 (m110) cc_final: 0.9017 (m-40) REVERT: B 856 ASN cc_start: 0.7000 (OUTLIER) cc_final: 0.6132 (p0) REVERT: B 873 TYR cc_start: 0.9452 (OUTLIER) cc_final: 0.8414 (m-80) REVERT: C 133 PHE cc_start: 0.7616 (m-80) cc_final: 0.7150 (m-80) REVERT: C 197 ILE cc_start: 0.8786 (mp) cc_final: 0.8547 (mm) REVERT: C 269 TYR cc_start: 0.7236 (m-80) cc_final: 0.6936 (m-80) REVERT: C 314 GLN cc_start: 0.8872 (OUTLIER) cc_final: 0.8600 (tm-30) REVERT: E 62 MET cc_start: 0.7739 (ttp) cc_final: 0.7291 (tpp) REVERT: E 134 ASN cc_start: 0.6954 (t0) cc_final: 0.6487 (p0) REVERT: E 267 LEU cc_start: 0.4227 (OUTLIER) cc_final: 0.3111 (tp) REVERT: E 366 MET cc_start: 0.1834 (mmm) cc_final: 0.1630 (tpp) REVERT: E 557 MET cc_start: 0.6297 (tmm) cc_final: 0.5379 (ttt) outliers start: 45 outliers final: 19 residues processed: 142 average time/residue: 1.2119 time to fit residues: 208.6850 Evaluate side-chains 123 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 100 time to evaluate : 2.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 1118 ASP Chi-restraints excluded: chain E residue 267 LEU Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 474 MET Chi-restraints excluded: chain E residue 485 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 14 optimal weight: 6.9990 chunk 40 optimal weight: 10.0000 chunk 272 optimal weight: 5.9990 chunk 231 optimal weight: 3.9990 chunk 225 optimal weight: 0.3980 chunk 114 optimal weight: 4.9990 chunk 205 optimal weight: 0.8980 chunk 34 optimal weight: 0.5980 chunk 165 optimal weight: 3.9990 chunk 215 optimal weight: 4.9990 chunk 233 optimal weight: 4.9990 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 856 ASN ** B 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 586 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.099419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 101)---------------| | r_work = 0.3413 r_free = 0.3413 target = 0.060094 restraints weight = 97820.214| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 3.73 r_work: 0.3062 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.3754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 27563 Z= 0.181 Angle : 0.597 12.272 37625 Z= 0.295 Chirality : 0.044 0.301 4389 Planarity : 0.004 0.073 4751 Dihedral : 5.143 57.738 4820 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.41 % Allowed : 12.97 % Favored : 85.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.89 (0.14), residues: 3249 helix: 2.37 (0.16), residues: 1007 sheet: 0.50 (0.21), residues: 556 loop : -0.49 (0.15), residues: 1686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 104 HIS 0.004 0.001 HIS E 34 PHE 0.017 0.001 PHE B 175 TYR 0.019 0.001 TYR A1067 ARG 0.003 0.000 ARG B 815 Details of bonding type rmsd link_NAG-ASN : bond 0.00652 ( 44) link_NAG-ASN : angle 2.88392 ( 132) link_BETA1-4 : bond 0.00197 ( 18) link_BETA1-4 : angle 1.07806 ( 54) hydrogen bonds : bond 0.03908 ( 1251) hydrogen bonds : angle 5.13674 ( 3648) SS BOND : bond 0.00260 ( 36) SS BOND : angle 1.67527 ( 72) covalent geometry : bond 0.00403 (27465) covalent geometry : angle 0.56830 (37367) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6498 Ramachandran restraints generated. 3249 Oldfield, 0 Emsley, 3249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6498 Ramachandran restraints generated. 3249 Oldfield, 0 Emsley, 3249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 104 time to evaluate : 2.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.8051 (m-90) cc_final: 0.7792 (m-10) REVERT: A 106 PHE cc_start: 0.8925 (m-80) cc_final: 0.8602 (m-10) REVERT: A 168 PHE cc_start: 0.7809 (t80) cc_final: 0.7555 (t80) REVERT: A 194 PHE cc_start: 0.8515 (m-80) cc_final: 0.8286 (m-10) REVERT: A 900 MET cc_start: 0.9202 (OUTLIER) cc_final: 0.8942 (mtm) REVERT: B 269 TYR cc_start: 0.7737 (m-10) cc_final: 0.7441 (m-80) REVERT: B 309 GLU cc_start: 0.9055 (mp0) cc_final: 0.8717 (pm20) REVERT: B 408 ARG cc_start: 0.7576 (ppt170) cc_final: 0.7288 (ppt170) REVERT: B 532 ASN cc_start: 0.9473 (m-40) cc_final: 0.9092 (t0) REVERT: B 764 ASN cc_start: 0.9259 (m110) cc_final: 0.9002 (m-40) REVERT: B 873 TYR cc_start: 0.9462 (OUTLIER) cc_final: 0.8436 (m-80) REVERT: C 197 ILE cc_start: 0.8813 (mp) cc_final: 0.8581 (mm) REVERT: C 269 TYR cc_start: 0.7165 (m-80) cc_final: 0.6819 (m-80) REVERT: C 314 GLN cc_start: 0.8902 (OUTLIER) cc_final: 0.8628 (tm-30) REVERT: E 62 MET cc_start: 0.7729 (ttp) cc_final: 0.7260 (tpp) REVERT: E 134 ASN cc_start: 0.7023 (t0) cc_final: 0.6529 (p0) REVERT: E 267 LEU cc_start: 0.4358 (OUTLIER) cc_final: 0.3132 (tp) REVERT: E 332 MET cc_start: 0.4783 (ppp) cc_final: 0.4523 (ptt) REVERT: E 366 MET cc_start: 0.1715 (mmm) cc_final: 0.1505 (tpp) REVERT: E 408 MET cc_start: 0.6801 (mpp) cc_final: 0.6593 (mmt) REVERT: E 557 MET cc_start: 0.6440 (tmm) cc_final: 0.5568 (ttt) outliers start: 41 outliers final: 18 residues processed: 135 average time/residue: 1.3000 time to fit residues: 208.6530 Evaluate side-chains 120 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 98 time to evaluate : 3.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 923 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 1118 ASP Chi-restraints excluded: chain E residue 267 LEU Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 474 MET Chi-restraints excluded: chain E residue 485 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 87 optimal weight: 3.9990 chunk 203 optimal weight: 2.9990 chunk 222 optimal weight: 1.9990 chunk 148 optimal weight: 0.9990 chunk 317 optimal weight: 2.9990 chunk 40 optimal weight: 9.9990 chunk 78 optimal weight: 0.9980 chunk 28 optimal weight: 3.9990 chunk 56 optimal weight: 0.6980 chunk 4 optimal weight: 6.9990 chunk 112 optimal weight: 10.0000 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN ** B 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 305 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.099683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.060598 restraints weight = 97918.233| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 3.75 r_work: 0.3074 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.3854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 27563 Z= 0.154 Angle : 0.590 12.307 37625 Z= 0.292 Chirality : 0.044 0.299 4389 Planarity : 0.004 0.073 4751 Dihedral : 5.060 57.297 4820 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.41 % Allowed : 13.17 % Favored : 85.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.90 (0.14), residues: 3249 helix: 2.39 (0.16), residues: 1000 sheet: 0.50 (0.21), residues: 561 loop : -0.47 (0.15), residues: 1688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP B 104 HIS 0.003 0.001 HIS E 34 PHE 0.019 0.001 PHE C 106 TYR 0.022 0.001 TYR A 170 ARG 0.018 0.000 ARG C 319 Details of bonding type rmsd link_NAG-ASN : bond 0.00615 ( 44) link_NAG-ASN : angle 2.83865 ( 132) link_BETA1-4 : bond 0.00226 ( 18) link_BETA1-4 : angle 1.01743 ( 54) hydrogen bonds : bond 0.03815 ( 1251) hydrogen bonds : angle 5.07424 ( 3648) SS BOND : bond 0.00220 ( 36) SS BOND : angle 1.52432 ( 72) covalent geometry : bond 0.00340 (27465) covalent geometry : angle 0.56225 (37367) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6498 Ramachandran restraints generated. 3249 Oldfield, 0 Emsley, 3249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6498 Ramachandran restraints generated. 3249 Oldfield, 0 Emsley, 3249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 100 time to evaluate : 2.967 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.7955 (m-90) cc_final: 0.7690 (m-10) REVERT: A 106 PHE cc_start: 0.8962 (m-80) cc_final: 0.8660 (m-10) REVERT: A 168 PHE cc_start: 0.7752 (t80) cc_final: 0.7506 (t80) REVERT: A 194 PHE cc_start: 0.8500 (m-80) cc_final: 0.8270 (m-10) REVERT: A 900 MET cc_start: 0.9181 (OUTLIER) cc_final: 0.8906 (mtm) REVERT: B 309 GLU cc_start: 0.9043 (mp0) cc_final: 0.8698 (pm20) REVERT: B 408 ARG cc_start: 0.7571 (ppt170) cc_final: 0.7286 (ppt170) REVERT: B 532 ASN cc_start: 0.9472 (m-40) cc_final: 0.9104 (t0) REVERT: B 764 ASN cc_start: 0.9294 (m110) cc_final: 0.9024 (m-40) REVERT: B 873 TYR cc_start: 0.9461 (OUTLIER) cc_final: 0.8447 (m-80) REVERT: B 934 ILE cc_start: 0.9049 (mm) cc_final: 0.8832 (mp) REVERT: C 133 PHE cc_start: 0.7558 (m-80) cc_final: 0.7087 (m-80) REVERT: C 197 ILE cc_start: 0.8855 (mp) cc_final: 0.8629 (mm) REVERT: C 314 GLN cc_start: 0.8885 (OUTLIER) cc_final: 0.8610 (tm-30) REVERT: E 62 MET cc_start: 0.7714 (ttp) cc_final: 0.7248 (tpp) REVERT: E 134 ASN cc_start: 0.7019 (t0) cc_final: 0.6548 (p0) REVERT: E 267 LEU cc_start: 0.4499 (OUTLIER) cc_final: 0.3370 (tp) REVERT: E 332 MET cc_start: 0.4702 (ppp) cc_final: 0.4496 (ptt) REVERT: E 366 MET cc_start: 0.1832 (mmm) cc_final: 0.1610 (tpp) outliers start: 41 outliers final: 19 residues processed: 131 average time/residue: 1.2599 time to fit residues: 200.3895 Evaluate side-chains 118 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 95 time to evaluate : 3.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 923 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 1118 ASP Chi-restraints excluded: chain E residue 267 LEU Chi-restraints excluded: chain E residue 474 MET Chi-restraints excluded: chain E residue 485 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 194 optimal weight: 10.0000 chunk 46 optimal weight: 0.9990 chunk 124 optimal weight: 9.9990 chunk 115 optimal weight: 10.0000 chunk 230 optimal weight: 2.9990 chunk 294 optimal weight: 6.9990 chunk 210 optimal weight: 1.9990 chunk 216 optimal weight: 7.9990 chunk 147 optimal weight: 0.7980 chunk 242 optimal weight: 0.6980 chunk 301 optimal weight: 6.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 954 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.099558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.060497 restraints weight = 97385.506| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 3.60 r_work: 0.3074 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.3961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 27563 Z= 0.152 Angle : 0.599 12.702 37625 Z= 0.294 Chirality : 0.044 0.301 4389 Planarity : 0.004 0.073 4751 Dihedral : 5.009 57.329 4820 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.07 % Allowed : 13.69 % Favored : 85.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.94 (0.15), residues: 3249 helix: 2.39 (0.16), residues: 1005 sheet: 0.53 (0.21), residues: 557 loop : -0.43 (0.15), residues: 1687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP B 104 HIS 0.004 0.001 HIS E 378 PHE 0.014 0.001 PHE C 135 TYR 0.020 0.001 TYR A1067 ARG 0.016 0.000 ARG C 319 Details of bonding type rmsd link_NAG-ASN : bond 0.00615 ( 44) link_NAG-ASN : angle 2.82034 ( 132) link_BETA1-4 : bond 0.00199 ( 18) link_BETA1-4 : angle 1.03645 ( 54) hydrogen bonds : bond 0.03784 ( 1251) hydrogen bonds : angle 5.05723 ( 3648) SS BOND : bond 0.00208 ( 36) SS BOND : angle 1.51188 ( 72) covalent geometry : bond 0.00337 (27465) covalent geometry : angle 0.57221 (37367) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6498 Ramachandran restraints generated. 3249 Oldfield, 0 Emsley, 3249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6498 Ramachandran restraints generated. 3249 Oldfield, 0 Emsley, 3249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 104 time to evaluate : 3.111 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.7945 (m-90) cc_final: 0.7707 (m-10) REVERT: A 106 PHE cc_start: 0.8976 (m-80) cc_final: 0.8675 (m-10) REVERT: A 168 PHE cc_start: 0.7814 (t80) cc_final: 0.7569 (t80) REVERT: A 194 PHE cc_start: 0.8492 (m-80) cc_final: 0.8255 (m-10) REVERT: A 900 MET cc_start: 0.9187 (OUTLIER) cc_final: 0.8912 (mtm) REVERT: B 309 GLU cc_start: 0.9053 (mp0) cc_final: 0.8705 (pm20) REVERT: B 532 ASN cc_start: 0.9453 (m-40) cc_final: 0.9086 (t0) REVERT: B 764 ASN cc_start: 0.9267 (m110) cc_final: 0.9008 (m-40) REVERT: B 873 TYR cc_start: 0.9461 (OUTLIER) cc_final: 0.8458 (m-80) REVERT: B 934 ILE cc_start: 0.9005 (mm) cc_final: 0.8795 (mp) REVERT: C 104 TRP cc_start: 0.7399 (m-90) cc_final: 0.7170 (m-90) REVERT: C 133 PHE cc_start: 0.7737 (m-80) cc_final: 0.7123 (m-80) REVERT: C 314 GLN cc_start: 0.8881 (OUTLIER) cc_final: 0.8604 (tm-30) REVERT: E 62 MET cc_start: 0.7674 (ttp) cc_final: 0.7188 (tpp) REVERT: E 134 ASN cc_start: 0.6990 (t0) cc_final: 0.6532 (p0) REVERT: E 267 LEU cc_start: 0.4111 (OUTLIER) cc_final: 0.3118 (tp) REVERT: E 557 MET cc_start: 0.6218 (tmm) cc_final: 0.5847 (tmt) outliers start: 31 outliers final: 20 residues processed: 128 average time/residue: 1.2264 time to fit residues: 191.6097 Evaluate side-chains 120 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 96 time to evaluate : 4.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 923 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 1118 ASP Chi-restraints excluded: chain E residue 267 LEU Chi-restraints excluded: chain E residue 474 MET Chi-restraints excluded: chain E residue 485 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 272 optimal weight: 6.9990 chunk 136 optimal weight: 2.9990 chunk 246 optimal weight: 0.0870 chunk 59 optimal weight: 2.9990 chunk 159 optimal weight: 0.5980 chunk 113 optimal weight: 0.0570 chunk 187 optimal weight: 0.9990 chunk 294 optimal weight: 9.9990 chunk 134 optimal weight: 5.9990 chunk 152 optimal weight: 0.6980 chunk 197 optimal weight: 10.0000 overall best weight: 0.4878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1005 GLN ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 388 ASN B 872 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 755 GLN ** E 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.100577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.061852 restraints weight = 98084.342| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 3.74 r_work: 0.3112 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.3939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 27563 Z= 0.106 Angle : 0.585 12.676 37625 Z= 0.287 Chirality : 0.043 0.295 4389 Planarity : 0.004 0.072 4751 Dihedral : 4.762 56.709 4820 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.00 % Allowed : 13.83 % Favored : 85.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.15), residues: 3249 helix: 2.43 (0.16), residues: 998 sheet: 0.76 (0.21), residues: 573 loop : -0.40 (0.15), residues: 1678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 104 HIS 0.003 0.001 HIS E 374 PHE 0.023 0.001 PHE C 192 TYR 0.024 0.001 TYR A 170 ARG 0.014 0.000 ARG C 319 Details of bonding type rmsd link_NAG-ASN : bond 0.00579 ( 44) link_NAG-ASN : angle 2.73113 ( 132) link_BETA1-4 : bond 0.00308 ( 18) link_BETA1-4 : angle 0.92690 ( 54) hydrogen bonds : bond 0.03534 ( 1251) hydrogen bonds : angle 4.91711 ( 3648) SS BOND : bond 0.00168 ( 36) SS BOND : angle 1.33763 ( 72) covalent geometry : bond 0.00226 (27465) covalent geometry : angle 0.56040 (37367) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 28504.60 seconds wall clock time: 500 minutes 2.51 seconds (30002.51 seconds total)