Starting phenix.real_space_refine on Mon Sep 14 04:21:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7cac_30326/09_2026/7cac_30326.cif Found real_map, /net/cci-nas-00/data/ceres_data/7cac_30326/09_2026/7cac_30326.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7cac_30326/09_2026/7cac_30326.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7cac_30326/09_2026/7cac_30326.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7cac_30326/09_2026/7cac_30326.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7cac_30326/09_2026/7cac_30326.map" model { file = "/net/cci-nas-00/data/ceres_data/7cac_30326/09_2026/7cac_30326.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7cac_30326/09_2026/7cac_30326.cif" } resolution = 3.55 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.000 sd= 0.001 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 118 5.16 5 C 17890 2.51 5 N 4589 2.21 5 O 5525 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 28122 Number of models: 1 Model: "" Number of chains: 23 Chain: "A" Number of atoms: 8018 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1026, 8018 Classifications: {'peptide': 1026} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 50, 'TRANS': 975} Chain breaks: 7 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLU:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "B" Number of atoms: 8021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1026, 8021 Classifications: {'peptide': 1026} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 50, 'TRANS': 975} Chain breaks: 7 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 8024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1026, 8024 Classifications: {'peptide': 1026} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 50, 'TRANS': 975} Chain breaks: 7 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 1611 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 207, 1605 Classifications: {'peptide': 207} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 196} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Conformer: "B" Number of residues, atoms: 207, 1605 Classifications: {'peptide': 207} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 196} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 bond proxies already assigned to first conformer: 1635 Chain: "E" Number of atoms: 1608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1608 Classifications: {'peptide': 214} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 200} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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 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 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 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 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 chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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 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 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 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 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 chiralities: 2 Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ASER D 114 " occ=0.52 ... (10 atoms not shown) pdb=" OG BSER D 114 " occ=0.48 Time building chain proxies: 6.29, per 1000 atoms: 0.22 Number of scatterers: 28122 At special positions: 0 Unit cell: (146.64, 173.68, 187.2, 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 118 16.00 O 5525 8.00 N 4589 7.00 C 17890 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=37, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.02 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 480 " - pdb=" SG CYS A 488 " 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=2.02 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.02 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.04 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " 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=2.02 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.00 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.02 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=2.00 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.00 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.02 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " 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=2.02 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.02 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.04 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 87 " distance=2.03 Simple disulfide: pdb=" SG CYS D 134 " - pdb=" SG CYS D 193 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 203 " 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=4, symmetry=0 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 282 " " NAG A1304 " - " ASN A 331 " " NAG A1305 " - " ASN A 343 " " NAG A1306 " - " ASN A 603 " " NAG A1307 " - " ASN A 616 " " NAG A1308 " - " ASN A 657 " " NAG A1309 " - " ASN A 709 " " NAG A1310 " - " ASN A1074 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 282 " " NAG B1304 " - " ASN B 331 " " NAG B1305 " - " ASN B 343 " " NAG B1306 " - " ASN B 603 " " NAG B1307 " - " ASN B 616 " " NAG B1308 " - " ASN B 657 " " NAG B1309 " - " ASN B 709 " " NAG B1310 " - " ASN B1074 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 122 " " NAG C1303 " - " ASN C 282 " " NAG C1304 " - " ASN C 331 " " NAG C1305 " - " ASN C 343 " " NAG C1306 " - " ASN C 603 " " NAG C1307 " - " ASN C 616 " " NAG C1308 " - " ASN C 657 " " NAG C1309 " - " ASN C 709 " " NAG C1310 " - " ASN C1074 " " NAG F 1 " - " ASN A 234 " " NAG G 1 " - " ASN A 717 " " NAG H 1 " - " ASN A 801 " " NAG I 1 " - " ASN A1098 " " NAG J 1 " - " ASN A1134 " " NAG L 1 " - " ASN B 717 " " NAG M 1 " - " ASN B 801 " " NAG N 1 " - " ASN B1098 " " NAG O 1 " - " ASN B1134 " " NAG P 1 " - " ASN C 234 " " NAG Q 1 " - " ASN C 717 " " NAG R 1 " - " ASN C 801 " " NAG S 1 " - " ASN C1098 " " NAG T 1 " - " ASN C1134 " Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.72 Conformation dependent library (CDL) restraints added in 1.5 seconds 6896 Ramachandran restraints generated. 3448 Oldfield, 0 Emsley, 3448 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6572 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 64 sheets defined 22.2% alpha, 26.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.82 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 removed outlier: 3.628A pdb=" N CYS A 301 " --> pdb=" O SER A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 364 through 369 removed outlier: 3.652A pdb=" N TYR A 369 " --> pdb=" O SER A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 390 removed outlier: 3.591A pdb=" N ASP A 389 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 407 removed outlier: 3.535A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 421 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.504A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.641A pdb=" N ASN A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.501A pdb=" N ASP A 820 " --> pdb=" O SER A 816 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU A 821 " --> pdb=" O PHE A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 852 through 857 removed outlier: 4.142A pdb=" N ASN A 856 " --> pdb=" O ALA A 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.548A pdb=" N LEU A 878 " --> pdb=" O THR A 874 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLY A 885 " --> pdb=" O THR A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 910 removed outlier: 3.545A pdb=" N ALA A 903 " --> pdb=" O ALA A 899 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N TYR A 904 " --> pdb=" O MET A 900 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 940 removed outlier: 3.527A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU A 918 " --> pdb=" O ASN A 914 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N LYS A 921 " --> pdb=" O TYR A 917 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N LEU A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYS A 933 " --> pdb=" O SER A 929 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.612A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU A 981 " --> pdb=" O LEU A 977 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1032 removed outlier: 4.543A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 1116 through 1118 No H-bonds generated for 'chain 'A' and resid 1116 through 1118' Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 4.039A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ASP A1146 " --> pdb=" O GLN A1142 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 removed outlier: 3.505A pdb=" N THR B 299 " --> pdb=" O PRO B 295 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS B 300 " --> pdb=" O LEU B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 366 through 370 removed outlier: 3.654A pdb=" N TYR B 369 " --> pdb=" O SER B 366 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASN B 370 " --> pdb=" O VAL B 367 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 366 through 370' Processing helix chain 'B' and resid 385 through 389 Processing helix chain 'B' and resid 403 through 407 removed outlier: 3.506A pdb=" N VAL B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 421 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.981A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.723A pdb=" N LEU B 763 " --> pdb=" O PHE B 759 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ASN B 764 " --> pdb=" O CYS B 760 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLU B 773 " --> pdb=" O GLY B 769 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS B 776 " --> pdb=" O VAL B 772 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.634A pdb=" N LEU B 821 " --> pdb=" O PHE B 817 " (cutoff:3.500A) Processing helix chain 'B' and resid 852 through 857 Processing helix chain 'B' and resid 866 through 885 removed outlier: 3.707A pdb=" N LEU B 878 " --> pdb=" O THR B 874 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N THR B 883 " --> pdb=" O ALA B 879 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLY B 885 " --> pdb=" O THR B 881 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.882A pdb=" N ALA B 903 " --> pdb=" O ALA B 899 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ASN B 907 " --> pdb=" O ALA B 903 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 941 removed outlier: 3.647A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLU B 918 " --> pdb=" O ASN B 914 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N LYS B 921 " --> pdb=" O TYR B 917 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N LEU B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 982 removed outlier: 3.540A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU B 981 " --> pdb=" O LEU B 977 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1032 removed outlier: 3.619A pdb=" N ALA B 989 " --> pdb=" O ASP B 985 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ASP B 994 " --> pdb=" O GLU B 990 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 3.920A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASP B1146 " --> pdb=" O GLN B1142 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 removed outlier: 3.630A pdb=" N CYS C 301 " --> pdb=" O SER C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 364 through 369 removed outlier: 3.651A pdb=" N TYR C 369 " --> pdb=" O SER C 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 390 removed outlier: 3.590A pdb=" N ASP C 389 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 407 removed outlier: 3.535A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 421 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.504A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU C 754 " --> pdb=" O SER C 750 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.641A pdb=" N ASN C 764 " --> pdb=" O CYS C 760 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.501A pdb=" N ASP C 820 " --> pdb=" O SER C 816 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU C 821 " --> pdb=" O PHE C 817 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 removed outlier: 3.548A pdb=" N LEU C 878 " --> pdb=" O THR C 874 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLY C 885 " --> pdb=" O THR C 881 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 910 removed outlier: 3.546A pdb=" N ALA C 903 " --> pdb=" O ALA C 899 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N TYR C 904 " --> pdb=" O MET C 900 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 940 removed outlier: 3.527A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU C 918 " --> pdb=" O ASN C 914 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N LYS C 921 " --> pdb=" O TYR C 917 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N LEU C 922 " --> pdb=" O GLU C 918 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYS C 933 " --> pdb=" O SER C 929 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.612A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU C 981 " --> pdb=" O LEU C 977 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1032 removed outlier: 4.543A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) Processing helix chain 'C' and resid 1116 through 1118 No H-bonds generated for 'chain 'C' and resid 1116 through 1118' Processing helix chain 'C' and resid 1140 through 1146 removed outlier: 4.039A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ASP C1146 " --> pdb=" O GLN C1142 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 188 removed outlier: 3.601A pdb=" N HIS D 188 " --> pdb=" O ASP D 184 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.521A pdb=" N THR E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 163 through 165 No H-bonds generated for 'chain 'E' and resid 163 through 165' Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 3.811A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 36 through 37 removed outlier: 7.056A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 10.841A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N GLU A 224 " --> pdb=" O SER A 205 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LYS A 195 " --> pdb=" O LYS A 202 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 36 through 37 removed outlier: 7.056A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 10.841A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N GLU A 224 " --> pdb=" O SER A 205 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA A 93 " --> pdb=" O TYR A 266 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 48 through 52 removed outlier: 7.363A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA6, first strand: chain 'A' and resid 84 through 85 removed outlier: 7.252A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ILE A 128 " --> pdb=" O TYR A 170 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N TYR A 170 " --> pdb=" O ILE A 128 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 318 removed outlier: 3.842A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.848A pdb=" N ILE A 326 " --> pdb=" O ASN A 542 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N THR A 553 " --> pdb=" O ASP A 586 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.587A pdb=" N PHE A 400 " --> pdb=" O VAL A 510 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.674A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 453 through 454 Processing sheet with id=AB3, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB4, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.388A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.815A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.450A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.846A pdb=" N ILE A 714 " --> pdb=" O LYS A1073 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 718 through 728 removed outlier: 7.168A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 734 through 735 Processing sheet with id=AB9, first strand: chain 'A' and resid 787 through 789 removed outlier: 5.660A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'A' and resid 1120 through 1123 removed outlier: 3.768A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 47 through 52 removed outlier: 3.986A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 63 through 64 removed outlier: 3.563A pdb=" N LYS B 195 " --> pdb=" O LYS B 202 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLU B 224 " --> pdb=" O SER B 205 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.595A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 84 through 85 removed outlier: 7.348A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 133 through 135 removed outlier: 7.045A pdb=" N GLN B 134 " --> pdb=" O SER B 161 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 311 through 317 removed outlier: 3.933A pdb=" N THR B 599 " --> pdb=" O GLY B 311 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 326 through 328 removed outlier: 5.803A pdb=" N ILE B 326 " --> pdb=" O ASN B 542 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.505A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD2, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD3, first strand: chain 'B' and resid 553 through 554 removed outlier: 3.840A pdb=" N THR B 553 " --> pdb=" O ASP B 586 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.348A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.879A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N SER B 673 " --> pdb=" O ILE B 693 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 701 through 702 removed outlier: 6.504A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.871A pdb=" N ILE B 714 " --> pdb=" O LYS B1073 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LYS B1073 " --> pdb=" O ILE B 714 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 718 through 728 removed outlier: 7.234A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 735 through 736 Processing sheet with id=AD9, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AE1, first strand: chain 'C' and resid 27 through 30 removed outlier: 3.810A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 36 through 37 removed outlier: 7.056A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 10.842A pdb=" N ALA C 222 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N HIS C 207 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N GLU C 224 " --> pdb=" O SER C 205 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LYS C 195 " --> pdb=" O LYS C 202 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 36 through 37 removed outlier: 7.056A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 10.842A pdb=" N ALA C 222 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N HIS C 207 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N GLU C 224 " --> pdb=" O SER C 205 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA C 93 " --> pdb=" O TYR C 266 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 48 through 52 removed outlier: 7.363A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AE6, first strand: chain 'C' and resid 84 through 85 removed outlier: 7.252A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ILE C 128 " --> pdb=" O TYR C 170 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N TYR C 170 " --> pdb=" O ILE C 128 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 311 through 318 removed outlier: 3.842A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 325 through 328 removed outlier: 5.848A pdb=" N ILE C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N THR C 553 " --> pdb=" O ASP C 586 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.587A pdb=" N PHE C 400 " --> pdb=" O VAL C 510 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.674A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF1 Processing sheet with id=AF2, first strand: chain 'C' and resid 453 through 454 Processing sheet with id=AF3, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AF4, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.388A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.816A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.846A pdb=" N ILE C 714 " --> pdb=" O LYS C1073 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 718 through 728 removed outlier: 7.168A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 734 through 735 Processing sheet with id=AF8, first strand: chain 'C' and resid 1120 through 1123 removed outlier: 3.769A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'D' and resid 4 through 6 Processing sheet with id=AG1, first strand: chain 'D' and resid 9 through 12 Processing sheet with id=AG2, first strand: chain 'D' and resid 114 through 118 removed outlier: 5.634A pdb=" N TYR D 172 " --> pdb=" O ASN D 138 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'D' and resid 114 through 118 removed outlier: 5.634A pdb=" N TYR D 172 " --> pdb=" O ASN D 138 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N SER D 173 " --> pdb=" O GLN D 165 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N GLN D 165 " --> pdb=" O SER D 173 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'D' and resid 153 through 154 removed outlier: 3.613A pdb=" N LYS D 145 " --> pdb=" O THR D 196 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'D' and resid 153 through 154 removed outlier: 3.613A pdb=" N LYS D 145 " --> pdb=" O THR D 196 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N TYR D 191 " --> pdb=" O PHE D 206 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'E' and resid 3 through 6 removed outlier: 3.527A pdb=" N GLU E 82 " --> pdb=" O THR E 69 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N THR E 69 " --> pdb=" O GLU E 82 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'E' and resid 10 through 12 removed outlier: 3.643A pdb=" N GLU E 10 " --> pdb=" O THR E 115 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N ILE E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N TYR E 50 " --> pdb=" O ILE E 34 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N TRP E 36 " --> pdb=" O ILE E 48 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N TYR E 50 " --> pdb=" O SER E 59 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N SER E 59 " --> pdb=" O TYR E 50 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'E' and resid 127 through 131 removed outlier: 3.627A pdb=" N SER E 187 " --> pdb=" O CYS E 147 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N TYR E 183 " --> pdb=" O ASP E 151 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL E 188 " --> pdb=" O HIS E 171 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'E' and resid 127 through 131 removed outlier: 3.627A pdb=" N SER E 187 " --> pdb=" O CYS E 147 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N TYR E 183 " --> pdb=" O ASP E 151 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'E' and resid 157 through 161 removed outlier: 4.326A pdb=" N TYR E 201 " --> pdb=" O VAL E 218 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N CYS E 203 " --> pdb=" O LYS E 216 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LYS E 216 " --> pdb=" O CYS E 203 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N VAL E 214 " --> pdb=" O VAL E 205 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N HIS E 207 " --> pdb=" O THR E 212 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N THR E 212 " --> pdb=" O HIS E 207 " (cutoff:3.500A) 1018 hydrogen bonds defined for protein. 2712 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: 8.03 Time building geometry restraints manager: 3.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 8514 1.33 - 1.46: 7040 1.46 - 1.58: 13058 1.58 - 1.71: 0 1.71 - 1.83: 147 Bond restraints: 28759 Sorted by residual: bond pdb=" C CYS A 336 " pdb=" N PRO A 337 " ideal model delta sigma weight residual 1.334 1.213 0.121 2.34e-02 1.83e+03 2.66e+01 bond pdb=" C CYS C 336 " pdb=" N PRO C 337 " ideal model delta sigma weight residual 1.334 1.214 0.120 2.34e-02 1.83e+03 2.64e+01 bond pdb=" C1 NAG P 1 " pdb=" O5 NAG P 1 " ideal model delta sigma weight residual 1.406 1.337 0.069 2.00e-02 2.50e+03 1.20e+01 bond pdb=" C1 NAG F 1 " pdb=" O5 NAG F 1 " ideal model delta sigma weight residual 1.406 1.338 0.068 2.00e-02 2.50e+03 1.15e+01 bond pdb=" N VAL C 227 " pdb=" CA VAL C 227 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.15e-02 7.56e+03 1.04e+01 ... (remaining 28754 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.49: 38194 2.49 - 4.99: 857 4.99 - 7.48: 81 7.48 - 9.97: 7 9.97 - 12.47: 3 Bond angle restraints: 39142 Sorted by residual: angle pdb=" C SER B 810 " pdb=" N LYS B 811 " pdb=" CA LYS B 811 " ideal model delta sigma weight residual 121.48 109.01 12.47 2.04e+00 2.40e-01 3.73e+01 angle pdb=" C THR D 90 " pdb=" N ASN D 91 " pdb=" CA ASN D 91 " ideal model delta sigma weight residual 121.54 130.59 -9.05 1.91e+00 2.74e-01 2.25e+01 angle pdb=" C ASN C 87 " pdb=" CA ASN C 87 " pdb=" CB ASN C 87 " ideal model delta sigma weight residual 116.34 109.72 6.62 1.40e+00 5.10e-01 2.24e+01 angle pdb=" C ASN A 87 " pdb=" CA ASN A 87 " pdb=" CB ASN A 87 " ideal model delta sigma weight residual 116.34 109.78 6.56 1.40e+00 5.10e-01 2.20e+01 angle pdb=" N THR C 236 " pdb=" CA THR C 236 " pdb=" C THR C 236 " ideal model delta sigma weight residual 114.31 108.74 5.57 1.29e+00 6.01e-01 1.87e+01 ... (remaining 39137 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.85: 15968 16.85 - 33.69: 519 33.69 - 50.54: 79 50.54 - 67.39: 41 67.39 - 84.24: 15 Dihedral angle restraints: 16622 sinusoidal: 6413 harmonic: 10209 Sorted by residual: dihedral pdb=" CA ARG C 158 " pdb=" C ARG C 158 " pdb=" N VAL C 159 " pdb=" CA VAL C 159 " ideal model delta harmonic sigma weight residual 180.00 136.74 43.26 0 5.00e+00 4.00e-02 7.48e+01 dihedral pdb=" CA ARG A 158 " pdb=" C ARG A 158 " pdb=" N VAL A 159 " pdb=" CA VAL A 159 " ideal model delta harmonic sigma weight residual 180.00 136.83 43.17 0 5.00e+00 4.00e-02 7.46e+01 dihedral pdb=" CB CYS A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1126 " pdb=" CB CYS A1126 " ideal model delta sinusoidal sigma weight residual -86.00 -158.97 72.97 1 1.00e+01 1.00e-02 6.79e+01 ... (remaining 16619 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.279: 4602 0.279 - 0.558: 7 0.558 - 0.837: 0 0.837 - 1.116: 1 1.116 - 1.395: 1 Chirality restraints: 4611 Sorted by residual: chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN A 234 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.01 -1.39 2.00e-01 2.50e+01 4.86e+01 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 -1.38 -1.02 2.00e-01 2.50e+01 2.62e+01 chirality pdb=" C1 NAG C1306 " pdb=" ND2 ASN C 603 " pdb=" C2 NAG C1306 " pdb=" O5 NAG C1306 " both_signs ideal model delta sigma weight residual False -2.40 -1.94 -0.46 2.00e-01 2.50e+01 5.22e+00 ... (remaining 4608 not shown) Planarity restraints: 5019 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 234 " 0.013 2.00e-02 2.50e+03 3.32e-01 1.38e+03 pdb=" CG ASN A 234 " 0.078 2.00e-02 2.50e+03 pdb=" OD1 ASN A 234 " -0.315 2.00e-02 2.50e+03 pdb=" ND2 ASN A 234 " 0.571 2.00e-02 2.50e+03 pdb=" C1 NAG F 1 " -0.347 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 234 " -0.068 2.00e-02 2.50e+03 7.39e-02 6.83e+01 pdb=" CG ASN C 234 " 0.024 2.00e-02 2.50e+03 pdb=" OD1 ASN C 234 " 0.012 2.00e-02 2.50e+03 pdb=" ND2 ASN C 234 " 0.119 2.00e-02 2.50e+03 pdb=" C1 NAG P 1 " -0.088 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 154 " -0.012 2.00e-02 2.50e+03 2.34e-02 5.49e+00 pdb=" C GLU B 154 " 0.041 2.00e-02 2.50e+03 pdb=" O GLU B 154 " -0.015 2.00e-02 2.50e+03 pdb=" N SER B 155 " -0.014 2.00e-02 2.50e+03 ... (remaining 5016 not shown) Histogram of nonbonded interaction distances: 1.08 - 1.84: 9 1.84 - 2.61: 531 2.61 - 3.37: 38186 3.37 - 4.14: 69677 4.14 - 4.90: 123729 Nonbonded interactions: 232132 Sorted by model distance: nonbonded pdb=" CG PRO A 589 " pdb=" CD1 PHE B 855 " model vdw 1.078 3.740 nonbonded pdb=" OE1 GLN B 414 " pdb=" OH TYR E 101 " model vdw 1.590 3.040 nonbonded pdb=" CG PRO A 589 " pdb=" CE1 PHE B 855 " model vdw 1.718 3.740 nonbonded pdb=" N PRO A 589 " pdb=" CZ PHE B 855 " model vdw 1.738 3.420 nonbonded pdb=" O PRO A 589 " pdb=" CE1 PHE B 855 " model vdw 1.764 3.340 ... (remaining 232127 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 25 through 698 or (resid 699 and (name N or name CA or nam \ e C or name O or name CB )) or resid 700 through 1310)) selection = (chain 'B' and (resid 25 through 485 or (resid 486 and (name N or name CA or nam \ e C or name O or name CB )) or resid 487 through 1310)) selection = (chain 'C' and (resid 25 through 485 or (resid 486 and (name N or name CA or nam \ e C or name O or name CB )) or resid 487 through 698 or (resid 699 and (name N o \ r name CA or name C or name O or name CB )) or resid 700 through 1310)) } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' } 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=0.48 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: 5.710 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: 0.010 Extract box with map and model: 0.510 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 29.620 Find NCS groups from input model: 0.680 Set up NCS constraints: 0.080 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:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6541 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 : 0.009 0.409 28859 Z= 0.473 Angle : 0.943 28.418 39393 Z= 0.499 Chirality : 0.061 1.395 4611 Planarity : 0.005 0.050 4975 Dihedral : 9.662 84.237 9939 Min Nonbonded Distance : 1.078 Molprobity Statistics. All-atom Clashscore : 25.85 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.46 % Favored : 94.28 % Rotamer: Outliers : 1.02 % Allowed : 0.79 % Favored : 98.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.36 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.22 (0.11), residues: 3448 helix: -3.58 (0.13), residues: 632 sheet: -1.82 (0.15), residues: 783 loop : -1.77 (0.11), residues: 2033 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 815 TYR 0.033 0.003 TYR B 495 PHE 0.037 0.003 PHE B 135 TRP 0.040 0.003 TRP B 64 HIS 0.012 0.002 HIS D 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00835 / 0.40 (28759) covalent geometry : angle 0.88539 / 0.49 (39142) SS BOND : bond 0.00934 / 0.66 ( 37) SS BOND : angle 1.40570 / 0.99 ( 74) hydrogen bonds : bond 0.28121 / 18.78 ( 960) hydrogen bonds : angle 11.49684 / 7.95 ( 2712) Misc. bond : bond 0.18550 / 11.61 ( 4) link_BETA1-4 : bond 0.00585 / 0.40 ( 15) link_BETA1-4 : angle 2.36305 / 1.60 ( 45) link_NAG-ASN : bond 0.06313 / 3.02 ( 44) link_NAG-ASN : angle 5.47856 / 3.89 ( 132) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6896 Ramachandran restraints generated. 3448 Oldfield, 0 Emsley, 3448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6896 Ramachandran restraints generated. 3448 Oldfield, 0 Emsley, 3448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 3064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 272 time to evaluate : 0.856 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 856 ASN cc_start: 0.6627 (OUTLIER) cc_final: 0.6204 (t0) REVERT: B 861 LEU cc_start: 0.8240 (OUTLIER) cc_final: 0.7893 (mt) REVERT: B 1029 MET cc_start: 0.7891 (tpp) cc_final: 0.7680 (tpp) REVERT: C 853 TYR cc_start: 0.4148 (OUTLIER) cc_final: 0.3451 (m-10) REVERT: D 160 GLU cc_start: 0.3333 (OUTLIER) cc_final: 0.2758 (mm-30) outliers start: 31 outliers final: 17 residues processed: 298 average time/residue: 0.2072 time to fit residues: 94.4672 Evaluate side-chains 148 residues out of total 3064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 127 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 853 TYR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 853 TYR Chi-restraints excluded: chain C residue 854 ARG Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 160 GLU Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain E residue 99 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 347 random chunks: chunk 197 optimal weight: 0.5980 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 0.2980 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 30.0000 chunk 183 optimal weight: 0.3980 chunk 298 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 196 ASN A 317 ASN A 437 ASN A 501 ASN A 779 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 317 ASN B 437 ASN B 655 HIS ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 913 GLN B1010 GLN C 239 GLN C 317 ASN C 437 ASN C 501 ASN C 779 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN ** D 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.109307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.079872 restraints weight = 153536.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.082970 restraints weight = 76372.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.083549 restraints weight = 42103.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.083549 restraints weight = 32880.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.083549 restraints weight = 32880.346| |-----------------------------------------------------------------------------| r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3599 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3599 r_free = 0.3599 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3599 r_free = 0.3599 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (5 function evaluations) r_final: 0.3599 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.2152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.099 28859 Z= 0.169 Angle : 0.751 17.289 39393 Z= 0.387 Chirality : 0.051 0.664 4611 Planarity : 0.005 0.058 4975 Dihedral : 6.989 56.603 3783 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 14.21 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.02 % Favored : 96.89 % Rotamer: Outliers : 1.31 % Allowed : 4.00 % Favored : 94.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.87 (0.13), residues: 3448 helix: -0.90 (0.18), residues: 659 sheet: -1.29 (0.16), residues: 811 loop : -1.31 (0.12), residues: 1978 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 854 TYR 0.033 0.002 TYR D 35 PHE 0.041 0.002 PHE B 855 TRP 0.027 0.002 TRP C 64 HIS 0.010 0.002 HIS D 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.17 (28759) covalent geometry : angle 0.71618 / 0.38 (39142) SS BOND : bond 0.00363 / 0.24 ( 37) SS BOND : angle 1.46278 / 1.01 ( 74) hydrogen bonds : bond 0.05341 / 3.54 ( 960) hydrogen bonds : angle 7.64569 / 5.28 ( 2712) Misc. bond : bond 0.00298 / 0.19 ( 4) link_BETA1-4 : bond 0.00689 / 0.49 ( 15) link_BETA1-4 : angle 1.09278 / 0.73 ( 45) link_NAG-ASN : bond 0.00534 / 0.28 ( 44) link_NAG-ASN : angle 3.80413 / 2.68 ( 132) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6896 Ramachandran restraints generated. 3448 Oldfield, 0 Emsley, 3448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6896 Ramachandran restraints generated. 3448 Oldfield, 0 Emsley, 3448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 3064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 170 time to evaluate : 0.980 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 105 ILE cc_start: 0.8219 (OUTLIER) cc_final: 0.7893 (tt) REVERT: B 115 GLN cc_start: 0.5353 (mp10) cc_final: 0.5142 (tt0) REVERT: B 556 ASN cc_start: 0.7331 (p0) cc_final: 0.7071 (t0) REVERT: C 190 ARG cc_start: 0.3389 (mtt-85) cc_final: 0.3054 (mtt180) REVERT: C 556 ASN cc_start: 0.8190 (p0) cc_final: 0.7990 (p0) REVERT: C 853 TYR cc_start: 0.4766 (OUTLIER) cc_final: 0.3697 (m-10) outliers start: 40 outliers final: 20 residues processed: 200 average time/residue: 0.1803 time to fit residues: 59.0794 Evaluate side-chains 136 residues out of total 3064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 114 time to evaluate : 1.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 606 ASN Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 853 TYR Chi-restraints excluded: chain C residue 982 SER Chi-restraints excluded: chain C residue 1126 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 347 random chunks: chunk 196 optimal weight: 0.9990 chunk 31 optimal weight: 10.0000 chunk 235 optimal weight: 20.0000 chunk 152 optimal weight: 1.9990 chunk 56 optimal weight: 7.9990 chunk 204 optimal weight: 3.9990 chunk 84 optimal weight: 4.9990 chunk 308 optimal weight: 0.6980 chunk 157 optimal weight: 3.9990 chunk 282 optimal weight: 1.9990 chunk 39 optimal weight: 8.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 69 HIS A 121 ASN A 207 HIS A 901 GLN A 935 GLN ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN B 913 GLN C 121 ASN C 207 HIS C 218 GLN C 655 HIS C 901 GLN ** D 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.107442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.077120 restraints weight = 169656.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.079634 restraints weight = 80946.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.081774 restraints weight = 48037.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.082131 restraints weight = 32309.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.082000 restraints weight = 26790.920| |-----------------------------------------------------------------------------| r_work (final): 0.3565 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3564 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3564 r_free = 0.3564 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3564 r_free = 0.3564 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3564 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.2691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 28859 Z= 0.235 Angle : 0.713 15.148 39393 Z= 0.364 Chirality : 0.049 0.583 4611 Planarity : 0.005 0.055 4975 Dihedral : 6.322 47.682 3756 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.69 % Favored : 96.23 % Rotamer: Outliers : 1.54 % Allowed : 5.71 % Favored : 92.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.55 (0.13), residues: 3448 helix: -0.01 (0.19), residues: 665 sheet: -1.29 (0.17), residues: 850 loop : -1.23 (0.13), residues: 1933 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 854 TYR 0.023 0.002 TYR E 50 PHE 0.024 0.002 PHE B 559 TRP 0.033 0.002 TRP C 64 HIS 0.009 0.001 HIS A 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00530 / 0.24 (28759) covalent geometry : angle 0.68204 / 0.36 (39142) SS BOND : bond 0.00323 / 0.22 ( 37) SS BOND : angle 1.09153 / 0.75 ( 74) hydrogen bonds : bond 0.04612 / 3.03 ( 960) hydrogen bonds : angle 6.93152 / 4.78 ( 2712) Misc. bond : bond 0.00461 / 0.31 ( 4) link_BETA1-4 : bond 0.00321 / 0.19 ( 15) link_BETA1-4 : angle 1.26997 / 0.95 ( 45) link_NAG-ASN : bond 0.00649 / 0.39 ( 44) link_NAG-ASN : angle 3.54255 / 2.47 ( 132) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6896 Ramachandran restraints generated. 3448 Oldfield, 0 Emsley, 3448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6896 Ramachandran restraints generated. 3448 Oldfield, 0 Emsley, 3448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 3064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 131 time to evaluate : 0.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 207 HIS cc_start: 0.7427 (OUTLIER) cc_final: 0.6941 (m-70) REVERT: B 105 ILE cc_start: 0.8252 (mt) cc_final: 0.8026 (tt) REVERT: B 902 MET cc_start: 0.9274 (mmp) cc_final: 0.8857 (mmp) REVERT: C 853 TYR cc_start: 0.4817 (OUTLIER) cc_final: 0.4026 (m-80) REVERT: C 902 MET cc_start: 0.8775 (mmt) cc_final: 0.8510 (mmt) REVERT: D 69 ASP cc_start: 0.8208 (OUTLIER) cc_final: 0.7131 (t0) outliers start: 47 outliers final: 23 residues processed: 167 average time/residue: 0.1782 time to fit residues: 49.0314 Evaluate side-chains 131 residues out of total 3064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 105 time to evaluate : 1.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 853 TYR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 245 HIS Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 606 ASN Chi-restraints excluded: chain C residue 773 GLU Chi-restraints excluded: chain C residue 853 TYR Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain D residue 69 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 347 random chunks: chunk 344 optimal weight: 40.0000 chunk 108 optimal weight: 6.9990 chunk 169 optimal weight: 0.7980 chunk 43 optimal weight: 9.9990 chunk 305 optimal weight: 0.9990 chunk 42 optimal weight: 20.0000 chunk 187 optimal weight: 0.7980 chunk 168 optimal weight: 0.7980 chunk 1 optimal weight: 2.9990 chunk 191 optimal weight: 0.9990 chunk 222 optimal weight: 8.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 99 ASN A 207 HIS ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 556 ASN C 207 HIS ** D 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 137 ASN ** D 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.108709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.079034 restraints weight = 164703.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.081898 restraints weight = 91241.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.082262 restraints weight = 50041.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.082704 restraints weight = 41775.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.082829 restraints weight = 38707.992| |-----------------------------------------------------------------------------| r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3583 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3583 r_free = 0.3583 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3583 r_free = 0.3583 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3583 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.3116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 28859 Z= 0.140 Angle : 0.620 14.695 39393 Z= 0.317 Chirality : 0.047 0.551 4611 Planarity : 0.004 0.058 4975 Dihedral : 5.825 48.335 3756 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.37 % Favored : 96.55 % Rotamer: Outliers : 1.44 % Allowed : 6.23 % Favored : 92.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.25 (0.14), residues: 3448 helix: 0.57 (0.20), residues: 667 sheet: -1.16 (0.17), residues: 864 loop : -1.14 (0.13), residues: 1917 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 158 TYR 0.022 0.001 TYR E 50 PHE 0.029 0.002 PHE C 855 TRP 0.024 0.002 TRP C 64 HIS 0.020 0.001 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 (28759) covalent geometry : angle 0.59091 / 0.31 (39142) SS BOND : bond 0.00317 / 0.22 ( 37) SS BOND : angle 1.42910 / 1.10 ( 74) hydrogen bonds : bond 0.03903 / 2.59 ( 960) hydrogen bonds : angle 6.39702 / 4.40 ( 2712) Misc. bond : bond 0.00113 / 0.07 ( 4) link_BETA1-4 : bond 0.00258 / 0.17 ( 15) link_BETA1-4 : angle 1.13145 / 0.81 ( 45) link_NAG-ASN : bond 0.00451 / 0.23 ( 44) link_NAG-ASN : angle 3.08677 / 2.17 ( 132) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6896 Ramachandran restraints generated. 3448 Oldfield, 0 Emsley, 3448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6896 Ramachandran restraints generated. 3448 Oldfield, 0 Emsley, 3448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 3064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 126 time to evaluate : 1.053 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 190 ARG cc_start: 0.3871 (mtt180) cc_final: 0.3372 (ttt180) REVERT: A 207 HIS cc_start: 0.7678 (OUTLIER) cc_final: 0.6763 (m90) REVERT: A 237 ARG cc_start: 0.7688 (ptp90) cc_final: 0.6872 (ptp90) REVERT: B 556 ASN cc_start: 0.6994 (t0) cc_final: 0.6708 (t0) REVERT: B 902 MET cc_start: 0.9409 (mmp) cc_final: 0.9035 (mmp) REVERT: B 979 ASP cc_start: 0.7725 (m-30) cc_final: 0.7427 (t0) REVERT: C 855 PHE cc_start: 0.7061 (m-80) cc_final: 0.6841 (m-80) REVERT: C 983 ARG cc_start: 0.8004 (mtp180) cc_final: 0.7303 (mtp180) REVERT: D 69 ASP cc_start: 0.8168 (OUTLIER) cc_final: 0.7126 (t0) outliers start: 44 outliers final: 20 residues processed: 161 average time/residue: 0.1892 time to fit residues: 50.2399 Evaluate side-chains 126 residues out of total 3064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 104 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 853 TYR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 1089 PHE Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain D residue 69 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 347 random chunks: chunk 237 optimal weight: 0.6980 chunk 210 optimal weight: 6.9990 chunk 124 optimal weight: 0.9990 chunk 153 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 chunk 145 optimal weight: 0.0020 chunk 114 optimal weight: 4.9990 chunk 284 optimal weight: 1.9990 chunk 341 optimal weight: 10.0000 chunk 215 optimal weight: 0.0570 chunk 293 optimal weight: 3.9990 overall best weight: 0.7510 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 207 HIS B 196 ASN B 218 GLN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS C 239 GLN C 955 ASN ** D 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.109136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.080763 restraints weight = 131172.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.082690 restraints weight = 78880.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.082976 restraints weight = 48242.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.083403 restraints weight = 38879.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.083544 restraints weight = 35392.629| |-----------------------------------------------------------------------------| r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3593 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3593 r_free = 0.3593 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3593 r_free = 0.3593 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3593 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.3431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 28859 Z= 0.129 Angle : 0.592 13.830 39393 Z= 0.303 Chirality : 0.046 0.516 4611 Planarity : 0.004 0.068 4975 Dihedral : 5.408 48.606 3748 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.43 % Favored : 96.49 % Rotamer: Outliers : 1.64 % Allowed : 6.53 % Favored : 91.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.04 (0.14), residues: 3448 helix: 0.92 (0.20), residues: 667 sheet: -1.07 (0.17), residues: 859 loop : -1.06 (0.13), residues: 1922 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 158 TYR 0.023 0.001 TYR E 50 PHE 0.021 0.001 PHE B 86 TRP 0.017 0.001 TRP A 64 HIS 0.030 0.001 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 (28759) covalent geometry : angle 0.56497 / 0.30 (39142) SS BOND : bond 0.00318 / 0.20 ( 37) SS BOND : angle 1.57093 / 1.05 ( 74) hydrogen bonds : bond 0.03680 / 2.44 ( 960) hydrogen bonds : angle 6.06284 / 4.16 ( 2712) Misc. bond : bond 0.00150 / 0.10 ( 4) link_BETA1-4 : bond 0.00328 / 0.22 ( 15) link_BETA1-4 : angle 1.14668 / 0.82 ( 45) link_NAG-ASN : bond 0.00438 / 0.22 ( 44) link_NAG-ASN : angle 2.87258 / 2.01 ( 132) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6896 Ramachandran restraints generated. 3448 Oldfield, 0 Emsley, 3448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6896 Ramachandran restraints generated. 3448 Oldfield, 0 Emsley, 3448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 3064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 115 time to evaluate : 0.971 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 190 ARG cc_start: 0.3721 (mtt180) cc_final: 0.2763 (ttt180) REVERT: A 207 HIS cc_start: 0.7585 (OUTLIER) cc_final: 0.6211 (m90) REVERT: B 556 ASN cc_start: 0.6912 (t0) cc_final: 0.6624 (t0) REVERT: B 869 MET cc_start: 0.8590 (OUTLIER) cc_final: 0.8321 (mpp) REVERT: B 902 MET cc_start: 0.9290 (mmp) cc_final: 0.8959 (mmp) REVERT: B 979 ASP cc_start: 0.7679 (m-30) cc_final: 0.7436 (t0) REVERT: C 95 THR cc_start: 0.8407 (OUTLIER) cc_final: 0.8181 (p) REVERT: C 190 ARG cc_start: 0.4428 (mtt180) cc_final: 0.3514 (ttm170) REVERT: C 983 ARG cc_start: 0.7971 (mtp180) cc_final: 0.7454 (mtp180) REVERT: D 69 ASP cc_start: 0.8047 (p0) cc_final: 0.7025 (t0) outliers start: 50 outliers final: 33 residues processed: 155 average time/residue: 0.1702 time to fit residues: 43.7847 Evaluate side-chains 135 residues out of total 3064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 99 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 853 TYR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 1089 PHE Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain E residue 116 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 347 random chunks: chunk 121 optimal weight: 6.9990 chunk 89 optimal weight: 0.9990 chunk 55 optimal weight: 5.9990 chunk 111 optimal weight: 2.9990 chunk 320 optimal weight: 1.9990 chunk 270 optimal weight: 2.9990 chunk 224 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 309 optimal weight: 9.9990 chunk 147 optimal weight: 10.0000 chunk 84 optimal weight: 0.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 207 HIS B 207 HIS ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS C 955 ASN ** E 39 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 = 0.4180 r_free = 0.4180 target = 0.121265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.090618 restraints weight = 147757.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.093549 restraints weight = 87876.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.093656 restraints weight = 46614.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.094048 restraints weight = 45226.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.094407 restraints weight = 39769.207| |-----------------------------------------------------------------------------| r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3543 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3543 r_free = 0.3543 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3543 r_free = 0.3543 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3543 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.3543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 28859 Z= 0.206 Angle : 0.627 14.044 39393 Z= 0.320 Chirality : 0.047 0.524 4611 Planarity : 0.004 0.068 4975 Dihedral : 5.464 47.832 3748 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.01 % Favored : 95.91 % Rotamer: Outliers : 1.71 % Allowed : 6.99 % Favored : 91.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.04 (0.14), residues: 3448 helix: 0.92 (0.20), residues: 678 sheet: -1.05 (0.17), residues: 844 loop : -1.09 (0.14), residues: 1926 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 815 TYR 0.018 0.002 TYR E 50 PHE 0.027 0.002 PHE C 306 TRP 0.014 0.001 TRP E 47 HIS 0.021 0.001 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00462 / 0.21 (28759) covalent geometry : angle 0.60019 / 0.31 (39142) SS BOND : bond 0.00293 / 0.21 ( 37) SS BOND : angle 1.20121 / 0.78 ( 74) hydrogen bonds : bond 0.03764 / 2.49 ( 960) hydrogen bonds : angle 6.05907 / 4.16 ( 2712) Misc. bond : bond 0.00134 / 0.08 ( 4) link_BETA1-4 : bond 0.00293 / 0.17 ( 15) link_BETA1-4 : angle 1.27527 / 0.96 ( 45) link_NAG-ASN : bond 0.00569 / 0.33 ( 44) link_NAG-ASN : angle 2.99992 / 2.07 ( 132) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6896 Ramachandran restraints generated. 3448 Oldfield, 0 Emsley, 3448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6896 Ramachandran restraints generated. 3448 Oldfield, 0 Emsley, 3448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 3064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 99 time to evaluate : 1.064 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 ARG cc_start: 0.3700 (mtt180) cc_final: 0.2983 (ttt180) REVERT: A 207 HIS cc_start: 0.7655 (OUTLIER) cc_final: 0.6653 (m90) REVERT: B 869 MET cc_start: 0.8651 (OUTLIER) cc_final: 0.8423 (mpp) REVERT: B 979 ASP cc_start: 0.7718 (m-30) cc_final: 0.7434 (t0) REVERT: C 95 THR cc_start: 0.8510 (OUTLIER) cc_final: 0.8268 (p) REVERT: C 983 ARG cc_start: 0.7970 (mtp180) cc_final: 0.7449 (mtp180) REVERT: D 69 ASP cc_start: 0.7962 (p0) cc_final: 0.6836 (t0) REVERT: E 48 ILE cc_start: 0.2607 (OUTLIER) cc_final: 0.2305 (mp) outliers start: 52 outliers final: 35 residues processed: 140 average time/residue: 0.1829 time to fit residues: 43.0088 Evaluate side-chains 134 residues out of total 3064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 95 time to evaluate : 1.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 853 TYR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 577 ARG Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 1089 PHE Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 116 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 347 random chunks: chunk 293 optimal weight: 2.9990 chunk 7 optimal weight: 5.9990 chunk 305 optimal weight: 0.6980 chunk 166 optimal weight: 4.9990 chunk 136 optimal weight: 20.0000 chunk 208 optimal weight: 0.3980 chunk 109 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 151 optimal weight: 0.5980 chunk 317 optimal weight: 6.9990 chunk 37 optimal weight: 30.0000 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 207 HIS ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS C 239 GLN C 955 ASN C1010 GLN ** D 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.119883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.087117 restraints weight = 102238.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.088704 restraints weight = 71138.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.090579 restraints weight = 51117.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.090371 restraints weight = 42173.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.090393 restraints weight = 38007.765| |-----------------------------------------------------------------------------| r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3575 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3575 r_free = 0.3575 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3575 r_free = 0.3575 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3575 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.3738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 28859 Z= 0.148 Angle : 0.585 13.876 39393 Z= 0.298 Chirality : 0.046 0.511 4611 Planarity : 0.004 0.067 4975 Dihedral : 5.236 47.846 3746 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.72 % Favored : 96.20 % Rotamer: Outliers : 1.61 % Allowed : 7.58 % Favored : 90.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.93 (0.14), residues: 3448 helix: 1.11 (0.20), residues: 678 sheet: -1.02 (0.17), residues: 854 loop : -1.04 (0.14), residues: 1916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1107 TYR 0.019 0.001 TYR E 50 PHE 0.022 0.001 PHE B 86 TRP 0.013 0.001 TRP E 47 HIS 0.019 0.001 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.15 (28759) covalent geometry : angle 0.56089 / 0.29 (39142) SS BOND : bond 0.00267 / 0.20 ( 37) SS BOND : angle 0.91507 / 0.58 ( 74) hydrogen bonds : bond 0.03547 / 2.36 ( 960) hydrogen bonds : angle 5.89208 / 4.03 ( 2712) Misc. bond : bond 0.00135 / 0.09 ( 4) link_BETA1-4 : bond 0.00273 / 0.16 ( 15) link_BETA1-4 : angle 1.20770 / 0.87 ( 45) link_NAG-ASN : bond 0.00454 / 0.23 ( 44) link_NAG-ASN : angle 2.78872 / 1.92 ( 132) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6896 Ramachandran restraints generated. 3448 Oldfield, 0 Emsley, 3448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6896 Ramachandran restraints generated. 3448 Oldfield, 0 Emsley, 3448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 3064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 104 time to evaluate : 1.058 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 ARG cc_start: 0.3650 (mtt180) cc_final: 0.3107 (ttt180) REVERT: A 207 HIS cc_start: 0.7523 (OUTLIER) cc_final: 0.6827 (m90) REVERT: B 869 MET cc_start: 0.8696 (OUTLIER) cc_final: 0.8479 (mpp) REVERT: B 902 MET cc_start: 0.9257 (OUTLIER) cc_final: 0.8868 (mmt) REVERT: C 190 ARG cc_start: 0.4546 (mtt180) cc_final: 0.3566 (ttm170) REVERT: C 983 ARG cc_start: 0.7822 (mtp180) cc_final: 0.7353 (mtp180) REVERT: D 69 ASP cc_start: 0.7927 (p0) cc_final: 0.6800 (t0) outliers start: 49 outliers final: 34 residues processed: 145 average time/residue: 0.1791 time to fit residues: 44.0124 Evaluate side-chains 131 residues out of total 3064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 94 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 853 TYR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 577 ARG Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 1089 PHE Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain E residue 116 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 347 random chunks: chunk 68 optimal weight: 4.9990 chunk 306 optimal weight: 0.7980 chunk 27 optimal weight: 3.9990 chunk 51 optimal weight: 0.6980 chunk 145 optimal weight: 9.9990 chunk 117 optimal weight: 2.9990 chunk 226 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 119 optimal weight: 0.9980 chunk 318 optimal weight: 30.0000 chunk 285 optimal weight: 3.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 207 HIS ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS D 89 GLN ** D 198 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 = 0.4160 r_free = 0.4160 target = 0.108170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.078896 restraints weight = 149346.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.081007 restraints weight = 83837.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.082442 restraints weight = 48403.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.082036 restraints weight = 46574.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.082469 restraints weight = 42547.816| |-----------------------------------------------------------------------------| r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3568 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3568 r_free = 0.3568 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3568 r_free = 0.3568 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3568 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.3862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.125 28859 Z= 0.167 Angle : 0.613 15.520 39393 Z= 0.314 Chirality : 0.046 0.508 4611 Planarity : 0.004 0.063 4975 Dihedral : 5.229 47.578 3746 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.95 % Favored : 95.97 % Rotamer: Outliers : 1.77 % Allowed : 7.74 % Favored : 90.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.14), residues: 3448 helix: 1.12 (0.20), residues: 670 sheet: -0.98 (0.17), residues: 854 loop : -1.02 (0.14), residues: 1924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 815 TYR 0.017 0.001 TYR E 50 PHE 0.045 0.002 PHE C 133 TRP 0.016 0.001 TRP A 64 HIS 0.011 0.001 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.17 (28759) covalent geometry : angle 0.57855 / 0.30 (39142) SS BOND : bond 0.00400 / 0.30 ( 37) SS BOND : angle 2.94125 / 1.99 ( 74) hydrogen bonds : bond 0.03608 / 2.41 ( 960) hydrogen bonds : angle 5.90471 / 4.05 ( 2712) Misc. bond : bond 0.00131 / 0.08 ( 4) link_BETA1-4 : bond 0.00262 / 0.13 ( 15) link_BETA1-4 : angle 1.20542 / 0.89 ( 45) link_NAG-ASN : bond 0.00480 / 0.26 ( 44) link_NAG-ASN : angle 2.76443 / 1.90 ( 132) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6896 Ramachandran restraints generated. 3448 Oldfield, 0 Emsley, 3448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6896 Ramachandran restraints generated. 3448 Oldfield, 0 Emsley, 3448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 3064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 95 time to evaluate : 1.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 ARG cc_start: 0.3714 (mtt180) cc_final: 0.3454 (ttt180) REVERT: A 218 GLN cc_start: 0.7907 (mm-40) cc_final: 0.7622 (mm110) REVERT: B 902 MET cc_start: 0.9255 (OUTLIER) cc_final: 0.8870 (mmp) REVERT: C 190 ARG cc_start: 0.4566 (mtt180) cc_final: 0.3582 (ttm170) REVERT: C 237 ARG cc_start: 0.7774 (OUTLIER) cc_final: 0.6755 (ptp90) REVERT: C 983 ARG cc_start: 0.8034 (mtp180) cc_final: 0.7465 (mtp180) REVERT: D 69 ASP cc_start: 0.7845 (p0) cc_final: 0.6741 (t0) REVERT: E 48 ILE cc_start: 0.2809 (OUTLIER) cc_final: 0.2493 (mt) outliers start: 54 outliers final: 39 residues processed: 139 average time/residue: 0.1872 time to fit residues: 43.4513 Evaluate side-chains 135 residues out of total 3064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 93 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 853 TYR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 577 ARG Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 1089 PHE Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 237 ARG Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 148 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 347 random chunks: chunk 0 optimal weight: 3.9990 chunk 289 optimal weight: 3.9990 chunk 227 optimal weight: 0.7980 chunk 200 optimal weight: 0.9990 chunk 270 optimal weight: 0.7980 chunk 96 optimal weight: 0.9980 chunk 202 optimal weight: 4.9990 chunk 158 optimal weight: 3.9990 chunk 162 optimal weight: 3.9990 chunk 337 optimal weight: 40.0000 chunk 302 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 207 HIS A 501 ASN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 804 GLN B 935 GLN C 207 HIS D 198 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.108519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.080743 restraints weight = 137626.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.082178 restraints weight = 73401.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.081853 restraints weight = 50955.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.082452 restraints weight = 49405.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.082365 restraints weight = 40761.585| |-----------------------------------------------------------------------------| r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3558 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3558 r_free = 0.3558 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3558 r_free = 0.3558 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3558 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.4048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 28859 Z= 0.149 Angle : 0.588 13.404 39393 Z= 0.301 Chirality : 0.046 0.496 4611 Planarity : 0.004 0.060 4975 Dihedral : 5.084 47.610 3746 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.98 % Favored : 95.94 % Rotamer: Outliers : 1.57 % Allowed : 8.30 % Favored : 90.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.84 (0.14), residues: 3448 helix: 1.15 (0.20), residues: 676 sheet: -0.85 (0.18), residues: 830 loop : -1.03 (0.14), residues: 1942 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 854 TYR 0.017 0.001 TYR E 50 PHE 0.025 0.001 PHE B 86 TRP 0.014 0.001 TRP A 64 HIS 0.008 0.001 HIS E 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 (28759) covalent geometry : angle 0.55819 / 0.29 (39142) SS BOND : bond 0.00280 / 0.21 ( 37) SS BOND : angle 2.40630 / 1.68 ( 74) hydrogen bonds : bond 0.03463 / 2.31 ( 960) hydrogen bonds : angle 5.79778 / 3.97 ( 2712) Misc. bond : bond 0.00131 / 0.08 ( 4) link_BETA1-4 : bond 0.00290 / 0.19 ( 15) link_BETA1-4 : angle 1.17631 / 0.86 ( 45) link_NAG-ASN : bond 0.00439 / 0.23 ( 44) link_NAG-ASN : angle 2.63492 / 1.81 ( 132) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6896 Ramachandran restraints generated. 3448 Oldfield, 0 Emsley, 3448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6896 Ramachandran restraints generated. 3448 Oldfield, 0 Emsley, 3448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 3064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 103 time to evaluate : 1.106 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 ARG cc_start: 0.3728 (mtt180) cc_final: 0.3430 (ttt180) REVERT: A 207 HIS cc_start: 0.7498 (OUTLIER) cc_final: 0.6901 (m-70) REVERT: A 265 TYR cc_start: 0.7869 (p90) cc_final: 0.7636 (p90) REVERT: A 1029 MET cc_start: 0.8543 (tpp) cc_final: 0.8162 (ttm) REVERT: B 902 MET cc_start: 0.9192 (OUTLIER) cc_final: 0.8795 (mmp) REVERT: B 1029 MET cc_start: 0.8642 (tpp) cc_final: 0.8260 (tpp) REVERT: C 190 ARG cc_start: 0.4471 (mtt180) cc_final: 0.3477 (ttm170) REVERT: C 237 ARG cc_start: 0.7750 (OUTLIER) cc_final: 0.6659 (ptp90) REVERT: C 983 ARG cc_start: 0.8020 (mtp180) cc_final: 0.7403 (mtp180) REVERT: D 69 ASP cc_start: 0.7976 (p0) cc_final: 0.6935 (t0) REVERT: E 48 ILE cc_start: 0.2780 (OUTLIER) cc_final: 0.2481 (mt) outliers start: 48 outliers final: 37 residues processed: 140 average time/residue: 0.1870 time to fit residues: 44.0294 Evaluate side-chains 135 residues out of total 3064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 94 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 853 TYR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 1089 PHE Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 237 ARG Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 148 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 347 random chunks: chunk 20 optimal weight: 1.9990 chunk 313 optimal weight: 10.0000 chunk 323 optimal weight: 1.9990 chunk 181 optimal weight: 0.0870 chunk 243 optimal weight: 5.9990 chunk 191 optimal weight: 4.9990 chunk 130 optimal weight: 8.9990 chunk 309 optimal weight: 6.9990 chunk 69 optimal weight: 0.7980 chunk 346 optimal weight: 0.4980 chunk 318 optimal weight: 8.9990 overall best weight: 1.0762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 207 HIS ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 81 ASN C 207 HIS C 239 GLN C 955 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.108491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.078885 restraints weight = 155308.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.081947 restraints weight = 81433.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.082705 restraints weight = 44883.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.083000 restraints weight = 35477.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.083205 restraints weight = 34661.005| |-----------------------------------------------------------------------------| r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3576 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3576 r_free = 0.3576 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3576 r_free = 0.3576 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3576 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.4143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 28859 Z= 0.147 Angle : 0.588 13.219 39393 Z= 0.302 Chirality : 0.046 0.491 4611 Planarity : 0.004 0.058 4975 Dihedral : 5.044 47.541 3746 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.98 % Favored : 95.94 % Rotamer: Outliers : 1.61 % Allowed : 8.33 % Favored : 90.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.14), residues: 3448 helix: 1.15 (0.20), residues: 676 sheet: -0.76 (0.18), residues: 814 loop : -1.03 (0.14), residues: 1958 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 158 TYR 0.016 0.001 TYR E 50 PHE 0.033 0.001 PHE A 855 TRP 0.015 0.001 TRP A 64 HIS 0.010 0.001 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.15 (28759) covalent geometry : angle 0.55974 / 0.29 (39142) SS BOND : bond 0.00320 / 0.23 ( 37) SS BOND : angle 2.26146 / 1.60 ( 74) hydrogen bonds : bond 0.03470 / 2.33 ( 960) hydrogen bonds : angle 5.76058 / 3.94 ( 2712) Misc. bond : bond 0.00130 / 0.08 ( 4) link_BETA1-4 : bond 0.00271 / 0.18 ( 15) link_BETA1-4 : angle 1.18475 / 0.87 ( 45) link_NAG-ASN : bond 0.00445 / 0.23 ( 44) link_NAG-ASN : angle 2.61162 / 1.79 ( 132) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6896 Ramachandran restraints generated. 3448 Oldfield, 0 Emsley, 3448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6896 Ramachandran restraints generated. 3448 Oldfield, 0 Emsley, 3448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 3064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 98 time to evaluate : 1.139 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 ARG cc_start: 0.4094 (mtt180) cc_final: 0.3737 (mtt180) REVERT: A 207 HIS cc_start: 0.7235 (OUTLIER) cc_final: 0.6753 (m-70) REVERT: A 218 GLN cc_start: 0.7785 (mm-40) cc_final: 0.7460 (mm110) REVERT: A 237 ARG cc_start: 0.7692 (ptp90) cc_final: 0.7345 (ptp90) REVERT: A 265 TYR cc_start: 0.7865 (p90) cc_final: 0.7624 (p90) REVERT: A 1029 MET cc_start: 0.8482 (tpp) cc_final: 0.8191 (ttm) REVERT: B 902 MET cc_start: 0.9211 (OUTLIER) cc_final: 0.8821 (mmp) REVERT: C 237 ARG cc_start: 0.7796 (OUTLIER) cc_final: 0.6834 (ptp90) REVERT: C 983 ARG cc_start: 0.7933 (mtp180) cc_final: 0.7534 (mtm180) REVERT: D 69 ASP cc_start: 0.8002 (p0) cc_final: 0.6988 (t0) REVERT: E 48 ILE cc_start: 0.2743 (OUTLIER) cc_final: 0.2436 (mp) outliers start: 49 outliers final: 37 residues processed: 136 average time/residue: 0.1814 time to fit residues: 41.9013 Evaluate side-chains 134 residues out of total 3064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 93 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 853 TYR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 1089 PHE Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 237 ARG Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 148 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 347 random chunks: chunk 158 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 225 optimal weight: 0.9990 chunk 132 optimal weight: 10.0000 chunk 12 optimal weight: 0.7980 chunk 57 optimal weight: 0.9990 chunk 102 optimal weight: 4.9990 chunk 50 optimal weight: 4.9990 chunk 316 optimal weight: 8.9990 chunk 229 optimal weight: 7.9990 chunk 152 optimal weight: 0.0370 overall best weight: 0.9664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 81 ASN C 207 HIS C 239 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.108476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.080158 restraints weight = 131958.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.082415 restraints weight = 73335.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.082170 restraints weight = 42138.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.082613 restraints weight = 41008.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.082596 restraints weight = 35791.653| |-----------------------------------------------------------------------------| r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3569 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3569 r_free = 0.3569 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3569 r_free = 0.3569 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3569 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.4149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.207 28859 Z= 0.189 Angle : 0.714 59.196 39393 Z= 0.406 Chirality : 0.048 1.092 4611 Planarity : 0.005 0.202 4975 Dihedral : 5.047 47.541 3746 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.03 % Favored : 95.88 % Rotamer: Outliers : 1.51 % Allowed : 8.53 % Favored : 89.96 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 1.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.14), residues: 3448 helix: 1.16 (0.20), residues: 676 sheet: -0.76 (0.18), residues: 814 loop : -1.02 (0.14), residues: 1958 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 158 TYR 0.016 0.001 TYR E 50 PHE 0.026 0.001 PHE A 855 TRP 0.018 0.001 TRP D 34 HIS 0.305 0.004 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.19 (28759) covalent geometry : angle 0.69470 / 0.40 (39142) SS BOND : bond 0.00364 / 0.24 ( 37) SS BOND : angle 1.68950 / 1.24 ( 74) hydrogen bonds : bond 0.03450 / 2.31 ( 960) hydrogen bonds : angle 5.75942 / 3.94 ( 2712) Misc. bond : bond 0.00130 / 0.08 ( 4) link_BETA1-4 : bond 0.00329 / 0.22 ( 15) link_BETA1-4 : angle 1.17776 / 0.85 ( 45) link_NAG-ASN : bond 0.00444 / 0.23 ( 44) link_NAG-ASN : angle 2.61159 / 1.79 ( 132) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5321.47 seconds wall clock time: 92 minutes 59.09 seconds (5579.09 seconds total)