Starting phenix.real_space_refine on Thu Jun 26 07:38:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wwi_32866/06_2025/7wwi_32866.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wwi_32866/06_2025/7wwi_32866.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wwi_32866/06_2025/7wwi_32866.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wwi_32866/06_2025/7wwi_32866.map" model { file = "/net/cci-nas-00/data/ceres_data/7wwi_32866/06_2025/7wwi_32866.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wwi_32866/06_2025/7wwi_32866.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.039 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 132 5.16 5 C 19271 2.51 5 N 4986 2.21 5 O 5848 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 2.27s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 30237 Number of models: 1 Model: "" Number of chains: 26 Chain: "A" Number of atoms: 8121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1034, 8121 Classifications: {'peptide': 1034} Link IDs: {'PTRANS': 57, 'TRANS': 976} Chain breaks: 8 Chain: "B" Number of atoms: 8126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1035, 8126 Classifications: {'peptide': 1035} Link IDs: {'PTRANS': 57, 'TRANS': 977} Chain breaks: 8 Chain: "C" Number of atoms: 8126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1035, 8126 Classifications: {'peptide': 1035} Link IDs: {'PTRANS': 57, 'TRANS': 977} Chain breaks: 8 Chain: "D" Number of atoms: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 834 Classifications: {'peptide': 108} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 102} Chain: "E" Number of atoms: 922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 922 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "F" Number of atoms: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 828 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 102} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 922 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "H" Number of atoms: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 834 Classifications: {'peptide': 108} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 102} Chain: "I" Number of atoms: 922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 922 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} 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: "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: "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: "W" 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: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 20.36, per 1000 atoms: 0.67 Number of scatterers: 30237 At special positions: 0 Unit cell: (145.14, 156.62, 222.22, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 132 16.00 O 5848 8.00 N 4986 7.00 C 19271 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=48, 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 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 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=2.04 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=2.04 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.04 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 D 23 " - pdb=" SG CYS D 88 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.04 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " 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 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 W 1 " - " NAG W 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 234 " " NAG A1303 " - " ASN A 282 " " NAG A1304 " - " ASN A 331 " " NAG A1305 " - " ASN A 709 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 234 " " NAG B1303 " - " ASN B 282 " " NAG B1304 " - " ASN B 331 " " NAG B1305 " - " ASN B 709 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 234 " " NAG C1303 " - " ASN C 282 " " NAG C1304 " - " ASN C 331 " " NAG C1305 " - " ASN C 709 " " NAG J 1 " - " ASN C 801 " " NAG K 1 " - " ASN C1074 " " NAG L 1 " - " ASN C1098 " " NAG M 1 " - " ASN C1134 " " NAG N 1 " - " ASN B 717 " " NAG O 1 " - " ASN C 717 " " NAG P 1 " - " ASN B 801 " " NAG Q 1 " - " ASN B1074 " " NAG R 1 " - " ASN B1098 " " NAG S 1 " - " ASN B1134 " " NAG T 1 " - " ASN A 717 " " NAG U 1 " - " ASN A 801 " " NAG V 1 " - " ASN A1098 " " NAG W 1 " - " ASN A1134 " Time building additional restraints: 8.17 Conformation dependent library (CDL) restraints added in 4.9 seconds 7450 Ramachandran restraints generated. 3725 Oldfield, 0 Emsley, 3725 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7084 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 59 sheets defined 21.1% alpha, 30.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.51 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 366 through 371 Processing helix chain 'A' and resid 383 through 387 removed outlier: 3.514A pdb=" N LYS A 386 " --> pdb=" O SER A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.259A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 737 through 743 removed outlier: 3.583A pdb=" N TYR A 741 " --> pdb=" O ASP A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 755 removed outlier: 4.045A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 891 removed outlier: 4.117A pdb=" N GLY A 891 " --> pdb=" O PHE A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 941 removed outlier: 4.423A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N LYS A 921 " --> pdb=" O TYR A 917 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N LEU A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 966 removed outlier: 3.833A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU A 966 " --> pdb=" O LEU A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.056A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL A1033 " --> pdb=" O MET A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 4.154A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) 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 371 removed outlier: 3.779A pdb=" N VAL B 367 " --> pdb=" O ASP B 364 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N LEU B 371 " --> pdb=" O LEU B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 387 Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.387A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'B' and resid 737 through 743 removed outlier: 3.548A pdb=" N CYS B 743 " --> pdb=" O THR B 739 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.705A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.550A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.575A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.188A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.691A pdb=" N GLN B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.472A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL B1033 " --> pdb=" O MET B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 3.862A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 366 through 371 removed outlier: 3.887A pdb=" N LEU C 371 " --> pdb=" O LEU C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.064A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 616 through 620 removed outlier: 3.657A pdb=" N VAL C 620 " --> pdb=" O CYS C 617 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 747 through 754 Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.812A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.146A 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 966 removed outlier: 3.714A pdb=" N GLN C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU C 966 " --> pdb=" O LEU C 962 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 982 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.046A 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 'D' and resid 79 through 83 Processing helix chain 'E' and resid 28 through 30 No H-bonds generated for 'chain 'E' and resid 28 through 30' Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.897A pdb=" N THR E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 79 through 83 removed outlier: 3.795A pdb=" N PHE F 83 " --> pdb=" O PRO F 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 62 through 65 removed outlier: 4.090A pdb=" N GLN G 65 " --> pdb=" O GLN G 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 62 through 65' Processing helix chain 'G' and resid 87 through 91 removed outlier: 3.623A pdb=" N THR G 91 " --> pdb=" O SER G 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 79 through 83 removed outlier: 3.949A pdb=" N PHE H 83 " --> pdb=" O PRO H 80 " (cutoff:3.500A) Processing helix chain 'I' and resid 62 through 65 Processing helix chain 'I' and resid 87 through 91 removed outlier: 3.533A pdb=" N THR I 91 " --> pdb=" O SER I 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 8.465A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 5.374A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.801A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.588A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 133 through 142 removed outlier: 8.302A pdb=" N CYS A 136 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 10.358A pdb=" N SER A 162 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 10.371A pdb=" N ASP A 138 " --> pdb=" O TYR A 160 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N TYR A 160 " --> pdb=" O ASP A 138 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 7.328A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 324 through 325 removed outlier: 7.247A pdb=" N GLU A 324 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 8.859A pdb=" N ASN A 542 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 356 through 358 removed outlier: 3.896A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.082A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.604A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 701 through 704 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.946A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 734 through 735 Processing sheet with id=AB6, first strand: chain 'A' and resid 787 through 790 removed outlier: 3.710A pdb=" N LYS A 790 " --> pdb=" O ASN B 703 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB8, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AB9, first strand: chain 'B' and resid 27 through 30 removed outlier: 8.223A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 42 through 43 Processing sheet with id=AC2, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.055A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 removed outlier: 5.987A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N VAL B 126 " --> pdb=" O VAL B 171 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N VAL B 171 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ILE B 128 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N GLU B 169 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N VAL B 130 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N ASN B 165 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N GLN B 134 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ALA B 163 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 8.529A pdb=" N CYS B 136 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N SER B 161 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N ASP B 138 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N VAL B 159 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N PHE B 140 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N PHE B 157 " --> pdb=" O PHE B 140 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 319 removed outlier: 7.485A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 356 through 358 Processing sheet with id=AC6, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC7, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC8, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.101A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.748A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.709A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.514A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 787 through 788 Processing sheet with id=AD3, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD4, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AD5, first strand: chain 'C' and resid 27 through 30 removed outlier: 8.001A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.767A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.732A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.892A 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: 3.508A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N VAL C 126 " --> pdb=" O VAL C 171 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N VAL C 171 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N ILE C 128 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N GLU C 169 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N VAL C 130 " --> pdb=" O THR C 167 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N ASN C 165 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N GLN C 134 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N ALA C 163 " --> pdb=" O GLN C 134 " (cutoff:3.500A) removed outlier: 8.970A pdb=" N CYS C 136 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 8.203A pdb=" N SER C 161 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ASP C 138 " --> pdb=" O VAL C 159 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N VAL C 159 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N PHE C 140 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N PHE C 157 " --> pdb=" O PHE C 140 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.390A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 325 through 328 Processing sheet with id=AE1, first strand: chain 'C' and resid 356 through 358 removed outlier: 3.501A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE3, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE4, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.187A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.622A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.701A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.701A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 734 through 735 Processing sheet with id=AE8, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AE9, first strand: chain 'D' and resid 4 through 7 Processing sheet with id=AF1, first strand: chain 'D' and resid 10 through 13 removed outlier: 4.115A pdb=" N ALA D 13 " --> pdb=" O GLU D 105 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'E' and resid 3 through 6 Processing sheet with id=AF3, first strand: chain 'E' and resid 10 through 12 removed outlier: 8.600A pdb=" N TYR E 32 " --> pdb=" O ILE E 52 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N ILE E 52 " --> pdb=" O TYR E 32 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N PHE E 34 " --> pdb=" O ARG E 50 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N ARG E 50 " --> pdb=" O PHE E 34 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N TRP E 36 " --> pdb=" O MET E 48 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'E' and resid 10 through 12 Processing sheet with id=AF5, first strand: chain 'F' and resid 4 through 7 Processing sheet with id=AF6, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.651A pdb=" N LEU F 11 " --> pdb=" O GLU F 105 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N LEU F 33 " --> pdb=" O TYR F 49 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N TYR F 49 " --> pdb=" O LEU F 33 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'G' and resid 3 through 6 Processing sheet with id=AF8, first strand: chain 'G' and resid 10 through 12 removed outlier: 8.695A pdb=" N TYR G 32 " --> pdb=" O ILE G 52 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N ILE G 52 " --> pdb=" O TYR G 32 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N PHE G 34 " --> pdb=" O ARG G 50 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ARG G 50 " --> pdb=" O PHE G 34 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N TRP G 36 " --> pdb=" O MET G 48 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'G' and resid 10 through 12 removed outlier: 3.503A pdb=" N ASP G 110 " --> pdb=" O ARG G 98 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'H' and resid 4 through 7 Processing sheet with id=AG2, first strand: chain 'H' and resid 10 through 13 removed outlier: 6.730A pdb=" N TRP H 35 " --> pdb=" O LEU H 47 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'I' and resid 3 through 6 Processing sheet with id=AG4, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.365A pdb=" N GLU I 10 " --> pdb=" O THR I 118 " (cutoff:3.500A) removed outlier: 8.580A pdb=" N TYR I 32 " --> pdb=" O ILE I 52 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N ILE I 52 " --> pdb=" O TYR I 32 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N PHE I 34 " --> pdb=" O ARG I 50 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N ARG I 50 " --> pdb=" O PHE I 34 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N TRP I 36 " --> pdb=" O MET I 48 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.365A pdb=" N GLU I 10 " --> pdb=" O THR I 118 " (cutoff:3.500A) 1245 hydrogen bonds defined for protein. 3285 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: 14.66 Time building geometry restraints manager: 9.70 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: 9580 1.34 - 1.46: 7726 1.46 - 1.59: 13453 1.59 - 1.71: 0 1.71 - 1.83: 168 Bond restraints: 30927 Sorted by residual: bond pdb=" N THR C 19 " pdb=" CA THR C 19 " ideal model delta sigma weight residual 1.459 1.488 -0.029 9.10e-03 1.21e+04 1.01e+01 bond pdb=" N VAL B 736 " pdb=" CA VAL B 736 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.18e-02 7.18e+03 9.52e+00 bond pdb=" N THR A 20 " pdb=" CA THR A 20 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.18e-02 7.18e+03 7.79e+00 bond pdb=" N LEU C 18 " pdb=" CA LEU C 18 " ideal model delta sigma weight residual 1.455 1.488 -0.032 1.21e-02 6.83e+03 7.13e+00 bond pdb=" N VAL C 16 " pdb=" CA VAL C 16 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.29e-02 6.01e+03 7.00e+00 ... (remaining 30922 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.76: 41042 1.76 - 3.53: 900 3.53 - 5.29: 83 5.29 - 7.05: 9 7.05 - 8.82: 4 Bond angle restraints: 42038 Sorted by residual: angle pdb=" CA GLY A 89 " pdb=" C GLY A 89 " pdb=" N VAL A 90 " ideal model delta sigma weight residual 114.86 118.38 -3.52 1.01e+00 9.80e-01 1.21e+01 angle pdb=" N MET B 740 " pdb=" CA MET B 740 " pdb=" C MET B 740 " ideal model delta sigma weight residual 113.23 109.07 4.16 1.24e+00 6.50e-01 1.12e+01 angle pdb=" N LYS A 528 " pdb=" CA LYS A 528 " pdb=" C LYS A 528 " ideal model delta sigma weight residual 113.89 108.64 5.25 1.58e+00 4.01e-01 1.10e+01 angle pdb=" N THR C 20 " pdb=" CA THR C 20 " pdb=" C THR C 20 " ideal model delta sigma weight residual 112.87 109.00 3.87 1.20e+00 6.94e-01 1.04e+01 angle pdb=" N PRO C 986 " pdb=" CA PRO C 986 " pdb=" C PRO C 986 " ideal model delta sigma weight residual 110.70 114.53 -3.83 1.22e+00 6.72e-01 9.85e+00 ... (remaining 42033 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.56: 17325 17.56 - 35.11: 1319 35.11 - 52.67: 276 52.67 - 70.23: 55 70.23 - 87.78: 37 Dihedral angle restraints: 19012 sinusoidal: 7993 harmonic: 11019 Sorted by residual: dihedral pdb=" CB CYS B1082 " pdb=" SG CYS B1082 " pdb=" SG CYS B1126 " pdb=" CB CYS B1126 " ideal model delta sinusoidal sigma weight residual -86.00 -6.19 -79.81 1 1.00e+01 1.00e-02 7.90e+01 dihedral pdb=" CB CYS D 23 " pdb=" SG CYS D 23 " pdb=" SG CYS D 88 " pdb=" CB CYS D 88 " ideal model delta sinusoidal sigma weight residual 93.00 162.58 -69.58 1 1.00e+01 1.00e-02 6.25e+01 dihedral pdb=" CB CYS F 23 " pdb=" SG CYS F 23 " pdb=" SG CYS F 88 " pdb=" CB CYS F 88 " ideal model delta sinusoidal sigma weight residual 93.00 156.62 -63.62 1 1.00e+01 1.00e-02 5.33e+01 ... (remaining 19009 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 4412 0.087 - 0.174: 440 0.174 - 0.260: 8 0.260 - 0.347: 0 0.347 - 0.434: 1 Chirality restraints: 4861 Sorted by residual: chirality pdb=" C1 NAG A1305 " pdb=" ND2 ASN A 709 " pdb=" C2 NAG A1305 " pdb=" O5 NAG A1305 " both_signs ideal model delta sigma weight residual False -2.40 -1.97 -0.43 2.00e-01 2.50e+01 4.71e+00 chirality pdb=" C1 NAG B1301 " pdb=" ND2 ASN B 61 " pdb=" C2 NAG B1301 " pdb=" O5 NAG B1301 " both_signs ideal model delta sigma weight residual False -2.40 -2.15 -0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" C1 NAG B1303 " pdb=" ND2 ASN B 282 " pdb=" C2 NAG B1303 " pdb=" O5 NAG B1303 " both_signs ideal model delta sigma weight residual False -2.40 -2.17 -0.23 2.00e-01 2.50e+01 1.27e+00 ... (remaining 4858 not shown) Planarity restraints: 5383 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO C 986 " -0.038 5.00e-02 4.00e+02 5.72e-02 5.24e+00 pdb=" N PRO C 987 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO C 987 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 987 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER F 7 " 0.036 5.00e-02 4.00e+02 5.45e-02 4.74e+00 pdb=" N PRO F 8 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO F 8 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO F 8 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE G 52 " 0.035 5.00e-02 4.00e+02 5.31e-02 4.51e+00 pdb=" N PRO G 53 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO G 53 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO G 53 " 0.030 5.00e-02 4.00e+02 ... (remaining 5380 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 494 2.67 - 3.22: 27802 3.22 - 3.78: 44920 3.78 - 4.34: 60548 4.34 - 4.90: 101865 Nonbonded interactions: 235629 Sorted by model distance: nonbonded pdb=" OG SER F 26 " pdb=" OE1 GLN F 27 " model vdw 2.107 3.040 nonbonded pdb=" OG1 THR C 109 " pdb=" OD1 ASP C 111 " model vdw 2.226 3.040 nonbonded pdb=" OG1 THR A 323 " pdb=" OE1 GLU A 324 " model vdw 2.234 3.040 nonbonded pdb=" OE2 GLU B 156 " pdb=" NH1 ARG B 158 " model vdw 2.249 3.120 nonbonded pdb=" OH TYR H 94 " pdb=" OD1 ASN I 59 " model vdw 2.251 3.040 ... (remaining 235624 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 15 through 827 or resid 853 through 1147 or resid 1301 thr \ ough 1305)) selection = (chain 'C' and (resid 15 through 827 or resid 853 through 1147 or resid 1301 thr \ ough 1305)) } ncs_group { reference = (chain 'D' and (resid 1 through 17 or (resid 18 and (name N or name CA or name C \ or name O or name CB )) or resid 19 through 108)) selection = chain 'F' selection = (chain 'H' and (resid 1 through 17 or (resid 18 and (name N or name CA or name C \ or name O or name CB )) or resid 19 through 108)) } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'I' } ncs_group { reference = 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' selection = chain 'W' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 14.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.350 Check model and map are aligned: 0.220 Set scattering table: 0.290 Process input model: 75.100 Find NCS groups from input model: 1.970 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 96.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 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 : 0.003 0.051 31018 Z= 0.174 Angle : 0.619 10.494 42263 Z= 0.334 Chirality : 0.046 0.434 4861 Planarity : 0.004 0.057 5354 Dihedral : 13.202 87.783 11784 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.14), residues: 3725 helix: 2.20 (0.21), residues: 660 sheet: 0.65 (0.16), residues: 1032 loop : -0.96 (0.13), residues: 2033 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 111 HIS 0.003 0.000 HIS C 954 PHE 0.021 0.001 PHE A 515 TYR 0.025 0.001 TYR C 904 ARG 0.007 0.000 ARG B 466 Details of bonding type rmsd link_NAG-ASN : bond 0.00600 ( 29) link_NAG-ASN : angle 3.04029 ( 87) link_BETA1-4 : bond 0.00454 ( 14) link_BETA1-4 : angle 0.94352 ( 42) hydrogen bonds : bond 0.12987 ( 1215) hydrogen bonds : angle 6.30111 ( 3285) SS BOND : bond 0.00303 ( 48) SS BOND : angle 0.95726 ( 96) covalent geometry : bond 0.00319 (30927) covalent geometry : angle 0.60303 (42038) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7450 Ramachandran restraints generated. 3725 Oldfield, 0 Emsley, 3725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7450 Ramachandran restraints generated. 3725 Oldfield, 0 Emsley, 3725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 3306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 289 time to evaluate : 3.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 456 PHE cc_start: 0.8721 (m-80) cc_final: 0.8390 (m-80) REVERT: B 740 MET cc_start: 0.8636 (tmm) cc_final: 0.8358 (tmm) REVERT: D 45 LYS cc_start: 0.7807 (mmtm) cc_final: 0.7560 (mmtm) REVERT: E 110 ASP cc_start: 0.7369 (t70) cc_final: 0.7145 (t0) REVERT: F 55 GLU cc_start: 0.8508 (tp30) cc_final: 0.8058 (tp30) REVERT: F 103 LYS cc_start: 0.9151 (tptt) cc_final: 0.8884 (tptp) REVERT: G 101 GLU cc_start: 0.8549 (tm-30) cc_final: 0.8297 (tm-30) REVERT: I 74 LYS cc_start: 0.8416 (tppt) cc_final: 0.8020 (tptt) outliers start: 0 outliers final: 0 residues processed: 289 average time/residue: 0.4260 time to fit residues: 196.5779 Evaluate side-chains 200 residues out of total 3306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 200 time to evaluate : 3.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 316 optimal weight: 7.9990 chunk 284 optimal weight: 1.9990 chunk 157 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 chunk 191 optimal weight: 2.9990 chunk 151 optimal weight: 6.9990 chunk 293 optimal weight: 4.9990 chunk 113 optimal weight: 8.9990 chunk 178 optimal weight: 0.0870 chunk 218 optimal weight: 3.9990 chunk 340 optimal weight: 0.0000 overall best weight: 1.6168 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN A 115 GLN A 188 ASN A 487 ASN A 762 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 804 GLN C 935 GLN C1010 GLN D 37 GLN ** D 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.080463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.052596 restraints weight = 104889.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.054702 restraints weight = 49053.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.056049 restraints weight = 31123.264| |-----------------------------------------------------------------------------| r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.0977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 31018 Z= 0.150 Angle : 0.571 10.511 42263 Z= 0.291 Chirality : 0.045 0.417 4861 Planarity : 0.004 0.070 5354 Dihedral : 6.264 58.103 4975 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 0.61 % Allowed : 6.63 % Favored : 92.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.14), residues: 3725 helix: 2.12 (0.21), residues: 667 sheet: 0.60 (0.16), residues: 1031 loop : -0.91 (0.13), residues: 2027 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP G 36 HIS 0.004 0.001 HIS B1058 PHE 0.022 0.001 PHE C 559 TYR 0.022 0.001 TYR F 49 ARG 0.005 0.000 ARG C 815 Details of bonding type rmsd link_NAG-ASN : bond 0.00451 ( 29) link_NAG-ASN : angle 2.78731 ( 87) link_BETA1-4 : bond 0.00332 ( 14) link_BETA1-4 : angle 1.04562 ( 42) hydrogen bonds : bond 0.04661 ( 1215) hydrogen bonds : angle 5.26748 ( 3285) SS BOND : bond 0.00351 ( 48) SS BOND : angle 0.92199 ( 96) covalent geometry : bond 0.00345 (30927) covalent geometry : angle 0.55581 (42038) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7450 Ramachandran restraints generated. 3725 Oldfield, 0 Emsley, 3725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7450 Ramachandran restraints generated. 3725 Oldfield, 0 Emsley, 3725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 3306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 215 time to evaluate : 3.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 740 MET cc_start: 0.8918 (tmm) cc_final: 0.8463 (tmm) REVERT: C 269 TYR cc_start: 0.7607 (m-80) cc_final: 0.7335 (m-80) REVERT: F 103 LYS cc_start: 0.9171 (tptt) cc_final: 0.8909 (tptp) REVERT: G 101 GLU cc_start: 0.8673 (tm-30) cc_final: 0.8438 (tm-30) REVERT: H 70 GLU cc_start: 0.8293 (tp30) cc_final: 0.7977 (tp30) REVERT: H 82 ASP cc_start: 0.7851 (m-30) cc_final: 0.7443 (m-30) REVERT: H 104 LEU cc_start: 0.8157 (OUTLIER) cc_final: 0.7940 (mt) REVERT: I 74 LYS cc_start: 0.8413 (tppt) cc_final: 0.8026 (tptt) REVERT: I 98 ARG cc_start: 0.8106 (ttp80) cc_final: 0.7188 (ttp80) outliers start: 20 outliers final: 12 residues processed: 228 average time/residue: 0.3965 time to fit residues: 148.0798 Evaluate side-chains 201 residues out of total 3306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 188 time to evaluate : 3.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain H residue 104 LEU Chi-restraints excluded: chain I residue 57 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 260 optimal weight: 2.9990 chunk 110 optimal weight: 9.9990 chunk 189 optimal weight: 4.9990 chunk 261 optimal weight: 0.8980 chunk 31 optimal weight: 8.9990 chunk 42 optimal weight: 20.0000 chunk 72 optimal weight: 6.9990 chunk 168 optimal weight: 4.9990 chunk 93 optimal weight: 2.9990 chunk 155 optimal weight: 5.9990 chunk 43 optimal weight: 1.9990 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 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 GLN ** B 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN B 762 GLN ** D 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 90 GLN ** D 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 6 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.079141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.051570 restraints weight = 106536.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.053562 restraints weight = 52501.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.054839 restraints weight = 34243.497| |-----------------------------------------------------------------------------| r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.1456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 31018 Z= 0.220 Angle : 0.600 11.718 42263 Z= 0.308 Chirality : 0.046 0.461 4861 Planarity : 0.004 0.068 5354 Dihedral : 5.907 56.447 4975 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.06 % Allowed : 9.65 % Favored : 89.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.14), residues: 3725 helix: 1.98 (0.21), residues: 666 sheet: 0.56 (0.16), residues: 982 loop : -1.03 (0.13), residues: 2077 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP G 36 HIS 0.006 0.001 HIS B1058 PHE 0.031 0.002 PHE C 559 TYR 0.027 0.001 TYR G 32 ARG 0.005 0.000 ARG C 815 Details of bonding type rmsd link_NAG-ASN : bond 0.00467 ( 29) link_NAG-ASN : angle 2.82706 ( 87) link_BETA1-4 : bond 0.00271 ( 14) link_BETA1-4 : angle 1.15691 ( 42) hydrogen bonds : bond 0.05216 ( 1215) hydrogen bonds : angle 5.21637 ( 3285) SS BOND : bond 0.00371 ( 48) SS BOND : angle 1.07517 ( 96) covalent geometry : bond 0.00512 (30927) covalent geometry : angle 0.58383 (42038) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7450 Ramachandran restraints generated. 3725 Oldfield, 0 Emsley, 3725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7450 Ramachandran restraints generated. 3725 Oldfield, 0 Emsley, 3725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 3306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 209 time to evaluate : 3.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 456 PHE cc_start: 0.8671 (m-80) cc_final: 0.8231 (m-80) REVERT: B 740 MET cc_start: 0.8911 (tmm) cc_final: 0.8332 (tmm) REVERT: B 752 LEU cc_start: 0.9507 (mp) cc_final: 0.9244 (tt) REVERT: C 170 TYR cc_start: 0.8455 (t80) cc_final: 0.8108 (t80) REVERT: C 375 PHE cc_start: 0.8515 (OUTLIER) cc_final: 0.8217 (p90) REVERT: C 740 MET cc_start: 0.9328 (tpp) cc_final: 0.9070 (tpp) REVERT: F 42 LYS cc_start: 0.9458 (mtpp) cc_final: 0.9123 (mmmt) REVERT: F 103 LYS cc_start: 0.9199 (tptt) cc_final: 0.8903 (tppt) REVERT: G 101 GLU cc_start: 0.8755 (tm-30) cc_final: 0.8426 (tm-30) REVERT: H 70 GLU cc_start: 0.8398 (tp30) cc_final: 0.8129 (tp30) REVERT: H 103 LYS cc_start: 0.8848 (tptp) cc_final: 0.8604 (tptp) REVERT: I 74 LYS cc_start: 0.8350 (tppt) cc_final: 0.7943 (tptt) REVERT: I 98 ARG cc_start: 0.8177 (ttp80) cc_final: 0.7216 (ttp80) outliers start: 35 outliers final: 20 residues processed: 232 average time/residue: 0.4316 time to fit residues: 163.2348 Evaluate side-chains 205 residues out of total 3306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 184 time to evaluate : 3.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain I residue 57 ILE Chi-restraints excluded: chain I residue 71 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 268 optimal weight: 0.0770 chunk 362 optimal weight: 3.9990 chunk 198 optimal weight: 2.9990 chunk 350 optimal weight: 6.9990 chunk 201 optimal weight: 0.7980 chunk 302 optimal weight: 0.6980 chunk 79 optimal weight: 2.9990 chunk 212 optimal weight: 6.9990 chunk 12 optimal weight: 9.9990 chunk 322 optimal weight: 20.0000 chunk 31 optimal weight: 10.0000 overall best weight: 1.5142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 ASN C 450 ASN ** D 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 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 = 0.3593 r_free = 0.3593 target = 0.079456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.051492 restraints weight = 106643.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.053606 restraints weight = 49865.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.054964 restraints weight = 31705.316| |-----------------------------------------------------------------------------| r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.1550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 31018 Z= 0.140 Angle : 0.547 11.018 42263 Z= 0.281 Chirality : 0.045 0.441 4861 Planarity : 0.004 0.064 5354 Dihedral : 5.476 56.402 4975 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.18 % Allowed : 10.44 % Favored : 88.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.14), residues: 3725 helix: 2.12 (0.21), residues: 671 sheet: 0.62 (0.16), residues: 986 loop : -0.99 (0.13), residues: 2068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 36 HIS 0.003 0.001 HIS B1058 PHE 0.024 0.001 PHE C 559 TYR 0.021 0.001 TYR F 49 ARG 0.004 0.000 ARG C 815 Details of bonding type rmsd link_NAG-ASN : bond 0.00395 ( 29) link_NAG-ASN : angle 2.58823 ( 87) link_BETA1-4 : bond 0.00313 ( 14) link_BETA1-4 : angle 0.96314 ( 42) hydrogen bonds : bond 0.04624 ( 1215) hydrogen bonds : angle 5.00723 ( 3285) SS BOND : bond 0.00335 ( 48) SS BOND : angle 0.91167 ( 96) covalent geometry : bond 0.00321 (30927) covalent geometry : angle 0.53354 (42038) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7450 Ramachandran restraints generated. 3725 Oldfield, 0 Emsley, 3725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7450 Ramachandran restraints generated. 3725 Oldfield, 0 Emsley, 3725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 3306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 204 time to evaluate : 3.093 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 456 PHE cc_start: 0.8689 (m-80) cc_final: 0.8239 (m-80) REVERT: B 752 LEU cc_start: 0.9531 (mp) cc_final: 0.9269 (tt) REVERT: C 170 TYR cc_start: 0.8477 (t80) cc_final: 0.8168 (t80) REVERT: C 740 MET cc_start: 0.9350 (tpp) cc_final: 0.9094 (tpp) REVERT: F 103 LYS cc_start: 0.9238 (tptt) cc_final: 0.8928 (tppt) REVERT: G 101 GLU cc_start: 0.8721 (tm-30) cc_final: 0.8384 (tm-30) REVERT: H 70 GLU cc_start: 0.8406 (tp30) cc_final: 0.8094 (tp30) REVERT: H 82 ASP cc_start: 0.8090 (m-30) cc_final: 0.7803 (m-30) REVERT: I 50 ARG cc_start: 0.9279 (ttp-110) cc_final: 0.9039 (ttp80) REVERT: I 74 LYS cc_start: 0.8312 (tppt) cc_final: 0.7927 (tptt) REVERT: I 98 ARG cc_start: 0.8118 (ttp80) cc_final: 0.7148 (ttp80) outliers start: 39 outliers final: 27 residues processed: 234 average time/residue: 0.4090 time to fit residues: 156.8334 Evaluate side-chains 215 residues out of total 3306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 188 time to evaluate : 3.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain I residue 57 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 161 optimal weight: 1.9990 chunk 107 optimal weight: 4.9990 chunk 226 optimal weight: 20.0000 chunk 126 optimal weight: 6.9990 chunk 122 optimal weight: 6.9990 chunk 189 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 chunk 313 optimal weight: 0.0770 chunk 297 optimal weight: 3.9990 chunk 223 optimal weight: 9.9990 chunk 76 optimal weight: 3.9990 overall best weight: 2.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN B 907 ASN ** D 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 38 GLN ** D 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.078356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.050463 restraints weight = 105947.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.052536 restraints weight = 49390.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.053863 restraints weight = 31392.879| |-----------------------------------------------------------------------------| r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.1808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 31018 Z= 0.198 Angle : 0.576 11.596 42263 Z= 0.296 Chirality : 0.045 0.460 4861 Planarity : 0.004 0.063 5354 Dihedral : 5.337 55.999 4975 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 1.82 % Allowed : 11.16 % Favored : 87.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.14), residues: 3725 helix: 2.05 (0.21), residues: 669 sheet: 0.64 (0.16), residues: 979 loop : -1.05 (0.13), residues: 2077 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 36 HIS 0.004 0.001 HIS C1058 PHE 0.028 0.001 PHE C 559 TYR 0.020 0.001 TYR A1067 ARG 0.004 0.000 ARG C 815 Details of bonding type rmsd link_NAG-ASN : bond 0.00433 ( 29) link_NAG-ASN : angle 2.67076 ( 87) link_BETA1-4 : bond 0.00304 ( 14) link_BETA1-4 : angle 1.11148 ( 42) hydrogen bonds : bond 0.04956 ( 1215) hydrogen bonds : angle 5.03990 ( 3285) SS BOND : bond 0.00340 ( 48) SS BOND : angle 0.98051 ( 96) covalent geometry : bond 0.00460 (30927) covalent geometry : angle 0.56174 (42038) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7450 Ramachandran restraints generated. 3725 Oldfield, 0 Emsley, 3725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7450 Ramachandran restraints generated. 3725 Oldfield, 0 Emsley, 3725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 3306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 200 time to evaluate : 3.452 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: B 456 PHE cc_start: 0.8736 (m-80) cc_final: 0.8292 (m-80) REVERT: B 752 LEU cc_start: 0.9556 (mp) cc_final: 0.9309 (tt) REVERT: C 170 TYR cc_start: 0.8597 (t80) cc_final: 0.8336 (t80) REVERT: C 740 MET cc_start: 0.9363 (tpp) cc_final: 0.9131 (tpp) REVERT: G 62 GLN cc_start: 0.8826 (tp40) cc_final: 0.8589 (tp40) REVERT: G 101 GLU cc_start: 0.8785 (tm-30) cc_final: 0.8417 (tm-30) REVERT: H 70 GLU cc_start: 0.8421 (tp30) cc_final: 0.8021 (tp30) REVERT: I 50 ARG cc_start: 0.9294 (ttp-110) cc_final: 0.9014 (ttp80) REVERT: I 98 ARG cc_start: 0.8162 (ttp80) cc_final: 0.7174 (ttp80) outliers start: 60 outliers final: 45 residues processed: 246 average time/residue: 0.4260 time to fit residues: 171.2036 Evaluate side-chains 231 residues out of total 3306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 186 time to evaluate : 3.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 82 GLU Chi-restraints excluded: chain H residue 58 VAL Chi-restraints excluded: chain I residue 57 ILE Chi-restraints excluded: chain I residue 71 THR Chi-restraints excluded: chain I residue 96 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 261 optimal weight: 4.9990 chunk 331 optimal weight: 6.9990 chunk 120 optimal weight: 6.9990 chunk 211 optimal weight: 4.9990 chunk 334 optimal weight: 10.0000 chunk 337 optimal weight: 9.9990 chunk 276 optimal weight: 0.5980 chunk 216 optimal weight: 7.9990 chunk 50 optimal weight: 3.9990 chunk 314 optimal weight: 20.0000 chunk 235 optimal weight: 1.9990 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 603 ASN A 613 GLN ** A 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 ASN ** D 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 39 GLN ** G 65 GLN ** 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 = 0.3554 r_free = 0.3554 target = 0.077529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.049555 restraints weight = 106173.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.051580 restraints weight = 49433.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.052893 restraints weight = 31544.049| |-----------------------------------------------------------------------------| r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 31018 Z= 0.260 Angle : 0.624 12.066 42263 Z= 0.320 Chirality : 0.046 0.478 4861 Planarity : 0.004 0.063 5354 Dihedral : 5.466 59.882 4975 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 1.75 % Allowed : 12.16 % Favored : 86.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.14), residues: 3725 helix: 2.00 (0.21), residues: 659 sheet: 0.52 (0.16), residues: 983 loop : -1.11 (0.13), residues: 2083 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP G 36 HIS 0.005 0.001 HIS C1058 PHE 0.031 0.002 PHE C 559 TYR 0.022 0.002 TYR A 904 ARG 0.005 0.000 ARG C 995 Details of bonding type rmsd link_NAG-ASN : bond 0.00487 ( 29) link_NAG-ASN : angle 2.81491 ( 87) link_BETA1-4 : bond 0.00291 ( 14) link_BETA1-4 : angle 1.13894 ( 42) hydrogen bonds : bond 0.05359 ( 1215) hydrogen bonds : angle 5.15910 ( 3285) SS BOND : bond 0.00385 ( 48) SS BOND : angle 1.09791 ( 96) covalent geometry : bond 0.00606 (30927) covalent geometry : angle 0.60935 (42038) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7450 Ramachandran restraints generated. 3725 Oldfield, 0 Emsley, 3725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7450 Ramachandran restraints generated. 3725 Oldfield, 0 Emsley, 3725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 3306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 191 time to evaluate : 3.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 423 TYR cc_start: 0.5881 (t80) cc_final: 0.5659 (t80) REVERT: A 448 ASN cc_start: 0.8614 (t0) cc_final: 0.7763 (p0) REVERT: B 456 PHE cc_start: 0.8715 (m-80) cc_final: 0.8258 (m-80) REVERT: B 752 LEU cc_start: 0.9559 (mp) cc_final: 0.9326 (tt) REVERT: C 170 TYR cc_start: 0.8622 (t80) cc_final: 0.8418 (t80) REVERT: F 42 LYS cc_start: 0.9465 (mtpp) cc_final: 0.9098 (ptpp) REVERT: G 62 GLN cc_start: 0.8864 (tp40) cc_final: 0.8601 (tp40) REVERT: G 101 GLU cc_start: 0.8816 (tm-30) cc_final: 0.8415 (tm-30) REVERT: I 46 GLU cc_start: 0.7987 (mt-10) cc_final: 0.7688 (pt0) outliers start: 58 outliers final: 49 residues processed: 233 average time/residue: 0.4145 time to fit residues: 157.2779 Evaluate side-chains 229 residues out of total 3306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 180 time to evaluate : 3.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 907 ASN Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain E residue 48 MET Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain H residue 10 THR Chi-restraints excluded: chain H residue 58 VAL Chi-restraints excluded: chain I residue 57 ILE Chi-restraints excluded: chain I residue 96 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 62 optimal weight: 0.9990 chunk 307 optimal weight: 4.9990 chunk 48 optimal weight: 0.7980 chunk 11 optimal weight: 7.9990 chunk 189 optimal weight: 0.9980 chunk 356 optimal weight: 6.9990 chunk 342 optimal weight: 5.9990 chunk 225 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 187 optimal weight: 0.8980 chunk 242 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 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 = 0.3589 r_free = 0.3589 target = 0.079257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.051416 restraints weight = 106132.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.053558 restraints weight = 49090.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.054902 restraints weight = 31026.049| |-----------------------------------------------------------------------------| r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 31018 Z= 0.113 Angle : 0.550 10.880 42263 Z= 0.280 Chirality : 0.044 0.430 4861 Planarity : 0.004 0.062 5354 Dihedral : 5.113 58.445 4975 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.36 % Allowed : 13.07 % Favored : 85.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.14), residues: 3725 helix: 2.16 (0.21), residues: 667 sheet: 0.62 (0.16), residues: 982 loop : -1.02 (0.13), residues: 2076 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 436 HIS 0.004 0.001 HIS A 954 PHE 0.022 0.001 PHE B 565 TYR 0.021 0.001 TYR F 49 ARG 0.007 0.000 ARG I 98 Details of bonding type rmsd link_NAG-ASN : bond 0.00402 ( 29) link_NAG-ASN : angle 2.45339 ( 87) link_BETA1-4 : bond 0.00363 ( 14) link_BETA1-4 : angle 0.87341 ( 42) hydrogen bonds : bond 0.04456 ( 1215) hydrogen bonds : angle 4.89921 ( 3285) SS BOND : bond 0.00340 ( 48) SS BOND : angle 0.90412 ( 96) covalent geometry : bond 0.00256 (30927) covalent geometry : angle 0.53786 (42038) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7450 Ramachandran restraints generated. 3725 Oldfield, 0 Emsley, 3725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7450 Ramachandran restraints generated. 3725 Oldfield, 0 Emsley, 3725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 3306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 211 time to evaluate : 5.010 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 TYR cc_start: 0.8340 (t80) cc_final: 0.8103 (t80) REVERT: A 448 ASN cc_start: 0.8630 (t0) cc_final: 0.7827 (p0) REVERT: B 456 PHE cc_start: 0.8742 (m-80) cc_final: 0.8315 (m-80) REVERT: B 752 LEU cc_start: 0.9543 (mp) cc_final: 0.9317 (tt) REVERT: F 42 LYS cc_start: 0.9485 (mtpp) cc_final: 0.9125 (ptpp) REVERT: F 103 LYS cc_start: 0.9278 (tptt) cc_final: 0.8961 (tppt) REVERT: G 62 GLN cc_start: 0.8904 (tp40) cc_final: 0.8692 (tp40) REVERT: G 101 GLU cc_start: 0.8771 (tm-30) cc_final: 0.8395 (tm-30) REVERT: I 46 GLU cc_start: 0.7972 (mt-10) cc_final: 0.7642 (pt0) REVERT: I 87 ARG cc_start: 0.9197 (ttm-80) cc_final: 0.8928 (ttm-80) outliers start: 45 outliers final: 31 residues processed: 246 average time/residue: 0.4823 time to fit residues: 196.5738 Evaluate side-chains 227 residues out of total 3306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 196 time to evaluate : 3.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain E residue 48 MET Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain H residue 10 THR Chi-restraints excluded: chain H residue 58 VAL Chi-restraints excluded: chain I residue 57 ILE Chi-restraints excluded: chain I residue 96 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 169 optimal weight: 4.9990 chunk 212 optimal weight: 4.9990 chunk 202 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 84 optimal weight: 5.9990 chunk 89 optimal weight: 3.9990 chunk 114 optimal weight: 9.9990 chunk 359 optimal weight: 0.9990 chunk 302 optimal weight: 0.6980 chunk 23 optimal weight: 7.9990 chunk 197 optimal weight: 0.9980 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 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 = 0.3591 r_free = 0.3591 target = 0.079283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.051472 restraints weight = 106401.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.053601 restraints weight = 49178.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.054955 restraints weight = 31142.682| |-----------------------------------------------------------------------------| r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.2085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 31018 Z= 0.122 Angle : 0.556 10.822 42263 Z= 0.284 Chirality : 0.044 0.428 4861 Planarity : 0.004 0.061 5354 Dihedral : 4.973 59.389 4975 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.33 % Allowed : 13.65 % Favored : 85.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.14), residues: 3725 helix: 2.19 (0.21), residues: 667 sheet: 0.60 (0.16), residues: 975 loop : -0.96 (0.13), residues: 2083 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 436 HIS 0.002 0.001 HIS C1058 PHE 0.020 0.001 PHE C 559 TYR 0.020 0.001 TYR F 49 ARG 0.013 0.000 ARG E 67 Details of bonding type rmsd link_NAG-ASN : bond 0.00372 ( 29) link_NAG-ASN : angle 2.41036 ( 87) link_BETA1-4 : bond 0.00314 ( 14) link_BETA1-4 : angle 0.95237 ( 42) hydrogen bonds : bond 0.04321 ( 1215) hydrogen bonds : angle 4.84148 ( 3285) SS BOND : bond 0.00324 ( 48) SS BOND : angle 0.91054 ( 96) covalent geometry : bond 0.00281 (30927) covalent geometry : angle 0.54441 (42038) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7450 Ramachandran restraints generated. 3725 Oldfield, 0 Emsley, 3725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7450 Ramachandran restraints generated. 3725 Oldfield, 0 Emsley, 3725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 3306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 206 time to evaluate : 3.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 TYR cc_start: 0.8348 (t80) cc_final: 0.8097 (t80) REVERT: A 448 ASN cc_start: 0.8660 (t0) cc_final: 0.7860 (p0) REVERT: B 456 PHE cc_start: 0.8741 (m-80) cc_final: 0.8315 (m-80) REVERT: B 752 LEU cc_start: 0.9530 (mp) cc_final: 0.9303 (tt) REVERT: E 110 ASP cc_start: 0.7630 (t70) cc_final: 0.7395 (t0) REVERT: F 42 LYS cc_start: 0.9484 (mtpp) cc_final: 0.9118 (ptpp) REVERT: G 101 GLU cc_start: 0.8798 (tm-30) cc_final: 0.8423 (tm-30) REVERT: I 46 GLU cc_start: 0.7978 (mt-10) cc_final: 0.7687 (pt0) REVERT: I 87 ARG cc_start: 0.9171 (ttm-80) cc_final: 0.8945 (ttm-80) REVERT: I 96 CYS cc_start: 0.8679 (OUTLIER) cc_final: 0.8435 (p) outliers start: 44 outliers final: 33 residues processed: 240 average time/residue: 0.4202 time to fit residues: 165.8662 Evaluate side-chains 226 residues out of total 3306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 192 time to evaluate : 3.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain E residue 48 MET Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain H residue 10 THR Chi-restraints excluded: chain H residue 58 VAL Chi-restraints excluded: chain I residue 57 ILE Chi-restraints excluded: chain I residue 96 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 162 optimal weight: 4.9990 chunk 293 optimal weight: 1.9990 chunk 363 optimal weight: 6.9990 chunk 284 optimal weight: 1.9990 chunk 215 optimal weight: 10.0000 chunk 126 optimal weight: 10.0000 chunk 32 optimal weight: 3.9990 chunk 230 optimal weight: 3.9990 chunk 84 optimal weight: 5.9990 chunk 326 optimal weight: 20.0000 chunk 360 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 ASN ** D 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 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 = 0.3551 r_free = 0.3551 target = 0.077398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.049762 restraints weight = 107137.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.051690 restraints weight = 53307.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.052907 restraints weight = 34972.171| |-----------------------------------------------------------------------------| r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.2313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 31018 Z= 0.253 Angle : 0.636 11.919 42263 Z= 0.326 Chirality : 0.046 0.473 4861 Planarity : 0.004 0.061 5354 Dihedral : 5.238 56.374 4975 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 1.48 % Allowed : 13.92 % Favored : 84.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.14), residues: 3725 helix: 1.99 (0.21), residues: 664 sheet: 0.49 (0.16), residues: 969 loop : -1.11 (0.13), residues: 2092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 258 HIS 0.005 0.001 HIS A1058 PHE 0.030 0.002 PHE C 559 TYR 0.021 0.002 TYR A1067 ARG 0.012 0.001 ARG E 67 Details of bonding type rmsd link_NAG-ASN : bond 0.00475 ( 29) link_NAG-ASN : angle 2.75350 ( 87) link_BETA1-4 : bond 0.00264 ( 14) link_BETA1-4 : angle 1.17565 ( 42) hydrogen bonds : bond 0.05274 ( 1215) hydrogen bonds : angle 5.08834 ( 3285) SS BOND : bond 0.00373 ( 48) SS BOND : angle 1.08274 ( 96) covalent geometry : bond 0.00588 (30927) covalent geometry : angle 0.62180 (42038) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7450 Ramachandran restraints generated. 3725 Oldfield, 0 Emsley, 3725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7450 Ramachandran restraints generated. 3725 Oldfield, 0 Emsley, 3725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 3306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 185 time to evaluate : 3.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 448 ASN cc_start: 0.8688 (t0) cc_final: 0.7831 (p0) REVERT: B 456 PHE cc_start: 0.8752 (m-80) cc_final: 0.8338 (m-80) REVERT: B 752 LEU cc_start: 0.9516 (mp) cc_final: 0.9300 (tt) REVERT: C 1002 GLN cc_start: 0.8745 (OUTLIER) cc_final: 0.7926 (tm-30) REVERT: E 110 ASP cc_start: 0.7638 (t70) cc_final: 0.7393 (t0) REVERT: G 101 GLU cc_start: 0.8866 (tm-30) cc_final: 0.8451 (tm-30) outliers start: 49 outliers final: 42 residues processed: 219 average time/residue: 0.4228 time to fit residues: 155.5494 Evaluate side-chains 221 residues out of total 3306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 178 time to evaluate : 3.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 981 PHE Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 742 ILE Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain E residue 48 MET Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 55 LEU Chi-restraints excluded: chain H residue 58 VAL Chi-restraints excluded: chain I residue 57 ILE Chi-restraints excluded: chain I residue 96 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 311 optimal weight: 7.9990 chunk 197 optimal weight: 0.0870 chunk 359 optimal weight: 7.9990 chunk 94 optimal weight: 0.9990 chunk 319 optimal weight: 8.9990 chunk 330 optimal weight: 9.9990 chunk 275 optimal weight: 0.6980 chunk 134 optimal weight: 0.7980 chunk 123 optimal weight: 10.0000 chunk 227 optimal weight: 3.9990 chunk 177 optimal weight: 0.6980 overall best weight: 0.6560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN B 907 ASN ** D 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.078561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.050813 restraints weight = 105687.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.052878 restraints weight = 49254.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.054192 restraints weight = 31291.120| |-----------------------------------------------------------------------------| r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.2236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 31018 Z= 0.109 Angle : 0.567 10.624 42263 Z= 0.289 Chirality : 0.045 0.414 4861 Planarity : 0.004 0.061 5354 Dihedral : 4.934 55.756 4975 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.12 % Allowed : 14.89 % Favored : 83.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.14), residues: 3725 helix: 2.19 (0.21), residues: 669 sheet: 0.67 (0.17), residues: 952 loop : -1.04 (0.13), residues: 2104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 436 HIS 0.003 0.000 HIS B1048 PHE 0.018 0.001 PHE C 559 TYR 0.037 0.001 TYR A 423 ARG 0.012 0.000 ARG E 67 Details of bonding type rmsd link_NAG-ASN : bond 0.00409 ( 29) link_NAG-ASN : angle 2.34816 ( 87) link_BETA1-4 : bond 0.00359 ( 14) link_BETA1-4 : angle 0.86340 ( 42) hydrogen bonds : bond 0.04278 ( 1215) hydrogen bonds : angle 4.81400 ( 3285) SS BOND : bond 0.00330 ( 48) SS BOND : angle 0.88101 ( 96) covalent geometry : bond 0.00244 (30927) covalent geometry : angle 0.55649 (42038) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7450 Ramachandran restraints generated. 3725 Oldfield, 0 Emsley, 3725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7450 Ramachandran restraints generated. 3725 Oldfield, 0 Emsley, 3725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 3306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 209 time to evaluate : 3.344 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 170 TYR cc_start: 0.8337 (t80) cc_final: 0.8103 (t80) REVERT: A 448 ASN cc_start: 0.8637 (t0) cc_final: 0.7840 (p0) REVERT: B 752 LEU cc_start: 0.9532 (mp) cc_final: 0.9319 (tt) REVERT: E 110 ASP cc_start: 0.7614 (t70) cc_final: 0.7366 (t0) REVERT: F 103 LYS cc_start: 0.9244 (tptt) cc_final: 0.8963 (tptp) REVERT: G 38 ARG cc_start: 0.7500 (tpp80) cc_final: 0.7154 (tpt170) REVERT: G 101 GLU cc_start: 0.8794 (tm-30) cc_final: 0.8409 (tm-30) REVERT: I 12 LYS cc_start: 0.8833 (mtpp) cc_final: 0.8503 (mtpp) REVERT: I 46 GLU cc_start: 0.7852 (mt-10) cc_final: 0.7601 (pt0) REVERT: I 96 CYS cc_start: 0.8749 (OUTLIER) cc_final: 0.8508 (p) REVERT: I 98 ARG cc_start: 0.8060 (ttp80) cc_final: 0.7165 (ttp80) outliers start: 37 outliers final: 32 residues processed: 237 average time/residue: 0.4407 time to fit residues: 171.3675 Evaluate side-chains 231 residues out of total 3306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 198 time to evaluate : 3.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 981 PHE Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 742 ILE Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain E residue 48 MET Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain H residue 58 VAL Chi-restraints excluded: chain I residue 57 ILE Chi-restraints excluded: chain I residue 96 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 314 optimal weight: 6.9990 chunk 154 optimal weight: 0.7980 chunk 33 optimal weight: 0.1980 chunk 241 optimal weight: 1.9990 chunk 101 optimal weight: 0.1980 chunk 99 optimal weight: 1.9990 chunk 248 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 chunk 200 optimal weight: 0.9980 chunk 107 optimal weight: 4.9990 chunk 153 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 ASN ** D 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 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 = 0.3569 r_free = 0.3569 target = 0.078817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.050905 restraints weight = 106422.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.052985 restraints weight = 49944.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.054313 restraints weight = 31843.706| |-----------------------------------------------------------------------------| r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.2263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 31018 Z= 0.113 Angle : 0.563 10.531 42263 Z= 0.286 Chirality : 0.044 0.414 4861 Planarity : 0.004 0.060 5354 Dihedral : 4.752 55.588 4975 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.44 % Favored : 96.54 % Rotamer: Outliers : 1.15 % Allowed : 14.77 % Favored : 84.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.14), residues: 3725 helix: 2.21 (0.21), residues: 664 sheet: 0.72 (0.17), residues: 963 loop : -1.01 (0.13), residues: 2098 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 436 HIS 0.002 0.000 HIS B 66 PHE 0.050 0.001 PHE G 29 TYR 0.020 0.001 TYR F 49 ARG 0.011 0.000 ARG E 67 Details of bonding type rmsd link_NAG-ASN : bond 0.00374 ( 29) link_NAG-ASN : angle 2.30340 ( 87) link_BETA1-4 : bond 0.00352 ( 14) link_BETA1-4 : angle 0.94898 ( 42) hydrogen bonds : bond 0.04123 ( 1215) hydrogen bonds : angle 4.75464 ( 3285) SS BOND : bond 0.00388 ( 48) SS BOND : angle 1.02946 ( 96) covalent geometry : bond 0.00259 (30927) covalent geometry : angle 0.55155 (42038) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12584.65 seconds wall clock time: 219 minutes 40.35 seconds (13180.35 seconds total)