Starting phenix.real_space_refine on Thu Jan 15 17:16:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7my2_24077/01_2026/7my2_24077.cif Found real_map, /net/cci-nas-00/data/ceres_data/7my2_24077/01_2026/7my2_24077.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7my2_24077/01_2026/7my2_24077.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7my2_24077/01_2026/7my2_24077.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7my2_24077/01_2026/7my2_24077.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7my2_24077/01_2026/7my2_24077.map" } resolution = 2.65 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= 0.031 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 127 5.16 5 C 17735 2.51 5 N 4562 2.21 5 O 5460 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 157 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 27884 Number of models: 1 Model: "" Number of chains: 25 Chain: "B" Number of atoms: 8062 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1036, 8062 Classifications: {'peptide': 1036} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 56, 'TRANS': 979} Chain breaks: 6 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 2, 'GLN:plan1': 2, 'PHE:plan': 1, 'ASP:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "C" Number of atoms: 8083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1038, 8083 Classifications: {'peptide': 1038} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 56, 'TRANS': 981} Chain breaks: 6 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 2, 'GLN:plan1': 2, 'PHE:plan': 1, 'ARG:plan': 1, 'ASP:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 35 Chain: "E" Number of atoms: 8114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1042, 8114 Classifications: {'peptide': 1042} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 56, 'TRANS': 985} Chain breaks: 6 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 2, 'GLN:plan1': 2, 'PHE:plan': 1, 'ARG:plan': 1, 'ASP:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 35 Chain: "H" Number of atoms: 910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 910 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 2, 'TRANS': 117} Chain: "A" Number of atoms: 910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 910 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 2, 'TRANS': 117} Chain: "D" Number of atoms: 910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 910 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 2, 'TRANS': 117} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "V" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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 dihedrals: 30 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 dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "E" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 6.52, per 1000 atoms: 0.23 Number of scatterers: 27884 At special positions: 0 Unit cell: (146.205, 152.19, 200.925, 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 127 16.00 O 5460 8.00 N 4562 7.00 C 17735 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.04 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.02 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 166 " distance=2.03 Simple disulfide: pdb=" SG CYS E 291 " - pdb=" SG CYS E 301 " distance=2.03 Simple disulfide: pdb=" SG CYS E 336 " - pdb=" SG CYS E 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 432 " distance=2.03 Simple disulfide: pdb=" SG CYS E 391 " - pdb=" SG CYS E 525 " distance=2.03 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " distance=2.03 Simple disulfide: pdb=" SG CYS E 538 " - pdb=" SG CYS E 590 " distance=2.03 Simple disulfide: pdb=" SG CYS E 617 " - pdb=" SG CYS E 649 " distance=2.03 Simple disulfide: pdb=" SG CYS E 662 " - pdb=" SG CYS E 671 " distance=2.03 Simple disulfide: pdb=" SG CYS E 738 " - pdb=" SG CYS E 760 " distance=2.02 Simple disulfide: pdb=" SG CYS E 743 " - pdb=" SG CYS E 749 " distance=2.03 Simple disulfide: pdb=" SG CYS E1032 " - pdb=" SG CYS E1043 " distance=2.03 Simple disulfide: pdb=" SG CYS E1082 " - pdb=" SG CYS E1126 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 92 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 92 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " 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 " - " BMA R 2 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " NAG-ASN " NAG B1301 " - " ASN B 282 " " NAG B1302 " - " ASN B 657 " " NAG B1303 " - " ASN B 616 " " NAG B1304 " - " ASN B 709 " " NAG B1305 " - " ASN B 61 " " NAG B1306 " - " ASN B 234 " " NAG B1307 " - " ASN B 603 " " NAG B1308 " - " ASN B 165 " " NAG B1309 " - " ASN B 343 " " NAG B1310 " - " ASN B1074 " " NAG C1301 " - " ASN C 282 " " NAG C1302 " - " ASN C 657 " " NAG C1303 " - " ASN C 616 " " NAG C1304 " - " ASN C 709 " " NAG C1305 " - " ASN C1074 " " NAG C1306 " - " ASN C 61 " " NAG C1307 " - " ASN C 234 " " NAG C1308 " - " ASN C 165 " " NAG C1309 " - " ASN C 343 " " NAG C1310 " - " ASN C 603 " " NAG E1301 " - " ASN E 657 " " NAG E1302 " - " ASN E 616 " " NAG E1303 " - " ASN E 709 " " NAG E1304 " - " ASN E1074 " " NAG E1305 " - " ASN E 61 " " NAG E1306 " - " ASN E 234 " " NAG E1307 " - " ASN E 603 " " NAG E1308 " - " ASN E 165 " " NAG E1309 " - " ASN E 343 " " NAG F 1 " - " ASN B1098 " " NAG G 1 " - " ASN B 717 " " NAG I 1 " - " ASN B 801 " " NAG J 1 " - " ASN B 331 " " NAG K 1 " - " ASN B1134 " " NAG L 1 " - " ASN C1098 " " NAG M 1 " - " ASN C 717 " " NAG N 1 " - " ASN C 801 " " NAG O 1 " - " ASN C1134 " " NAG P 1 " - " ASN C 331 " " NAG Q 1 " - " ASN E1134 " " NAG R 1 " - " ASN E1098 " " NAG S 1 " - " ASN E 717 " " NAG T 1 " - " ASN E 282 " " NAG U 1 " - " ASN E 801 " " NAG V 1 " - " ASN E 331 " Time building additional restraints: 2.72 Conformation dependent library (CDL) restraints added in 1.4 seconds 6856 Ramachandran restraints generated. 3428 Oldfield, 0 Emsley, 3428 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6480 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 46 sheets defined 22.6% alpha, 25.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.39 Creating SS restraints... Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 339 through 344 Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 383 through 387 Processing helix chain 'B' and resid 405 through 410 removed outlier: 5.893A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'B' and resid 619 through 624 Processing helix chain 'B' and resid 633 through 637 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.832A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLY B 769 " --> pdb=" O ARG B 765 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ILE B 770 " --> pdb=" O ALA B 766 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ALA B 771 " --> pdb=" O LEU B 767 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.535A pdb=" N LEU B 821 " --> pdb=" O PRO B 817 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 removed outlier: 3.565A pdb=" N GLY B 885 " --> pdb=" O THR B 881 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 890 removed outlier: 3.700A pdb=" N GLY B 889 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.521A pdb=" N ALA B 903 " --> pdb=" O PRO B 899 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.526A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 940 removed outlier: 3.774A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.023A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 983 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 3.724A pdb=" N GLU B 990 " --> pdb=" O PRO B 986 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1147 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 365 through 370 removed outlier: 3.741A pdb=" N TYR C 369 " --> pdb=" O TYR C 365 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASN C 370 " --> pdb=" O SER C 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 365 through 370' Processing helix chain 'C' and resid 384 through 388 removed outlier: 3.819A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 407 removed outlier: 3.931A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 422 Processing helix chain 'C' and resid 630 through 634 removed outlier: 3.589A pdb=" N ARG C 634 " --> pdb=" O PRO C 631 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 755 removed outlier: 4.250A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.594A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU C 773 " --> pdb=" O GLY C 769 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N GLN C 774 " --> pdb=" O ILE C 770 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.583A pdb=" N LEU C 821 " --> pdb=" O PRO C 817 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 890 removed outlier: 3.636A pdb=" N GLY C 889 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 removed outlier: 3.502A pdb=" N TYR C 904 " --> pdb=" O MET C 900 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 918 Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.871A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.032A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.814A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU C 984 " --> pdb=" O ILE C 980 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1034 removed outlier: 3.825A pdb=" N GLU C 990 " --> pdb=" O PRO C 986 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLY C 999 " --> pdb=" O ARG C 995 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL C1033 " --> pdb=" O MET C1029 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU C1034 " --> pdb=" O SER C1030 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1148 Processing helix chain 'E' and resid 294 through 304 Processing helix chain 'E' and resid 338 through 343 Processing helix chain 'E' and resid 365 through 369 Processing helix chain 'E' and resid 385 through 390 removed outlier: 3.688A pdb=" N ASN E 388 " --> pdb=" O THR E 385 " (cutoff:3.500A) Processing helix chain 'E' and resid 406 through 410 removed outlier: 3.898A pdb=" N ILE E 410 " --> pdb=" O VAL E 407 " (cutoff:3.500A) Processing helix chain 'E' and resid 417 through 422 removed outlier: 3.564A pdb=" N TYR E 421 " --> pdb=" O LYS E 417 " (cutoff:3.500A) Processing helix chain 'E' and resid 502 through 506 removed outlier: 3.947A pdb=" N GLN E 506 " --> pdb=" O VAL E 503 " (cutoff:3.500A) Processing helix chain 'E' and resid 619 through 624 Processing helix chain 'E' and resid 630 through 635 removed outlier: 3.862A pdb=" N VAL E 635 " --> pdb=" O PRO E 631 " (cutoff:3.500A) Processing helix chain 'E' and resid 737 through 743 Processing helix chain 'E' and resid 746 through 754 Processing helix chain 'E' and resid 755 through 757 No H-bonds generated for 'chain 'E' and resid 755 through 757' Processing helix chain 'E' and resid 758 through 783 removed outlier: 3.767A pdb=" N GLN E 762 " --> pdb=" O SER E 758 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLU E 773 " --> pdb=" O GLY E 769 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N GLN E 774 " --> pdb=" O ILE E 770 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ASP E 775 " --> pdb=" O ALA E 771 " (cutoff:3.500A) Processing helix chain 'E' and resid 816 through 826 removed outlier: 3.582A pdb=" N LEU E 821 " --> pdb=" O PRO E 817 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL E 826 " --> pdb=" O LEU E 822 " (cutoff:3.500A) Processing helix chain 'E' and resid 866 through 885 Processing helix chain 'E' and resid 897 through 908 Processing helix chain 'E' and resid 913 through 918 Processing helix chain 'E' and resid 919 through 940 removed outlier: 3.660A pdb=" N ILE E 934 " --> pdb=" O ALA E 930 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N GLN E 935 " --> pdb=" O ILE E 931 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N ASP E 936 " --> pdb=" O GLY E 932 " (cutoff:3.500A) Processing helix chain 'E' and resid 945 through 965 removed outlier: 3.970A pdb=" N VAL E 951 " --> pdb=" O LYS E 947 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N VAL E 952 " --> pdb=" O LEU E 948 " (cutoff:3.500A) Processing helix chain 'E' and resid 966 through 968 No H-bonds generated for 'chain 'E' and resid 966 through 968' Processing helix chain 'E' and resid 976 through 983 removed outlier: 3.673A pdb=" N ILE E 980 " --> pdb=" O VAL E 976 " (cutoff:3.500A) Processing helix chain 'E' and resid 985 through 1033 removed outlier: 5.480A pdb=" N VAL E 991 " --> pdb=" O PRO E 987 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N GLN E 992 " --> pdb=" O GLU E 988 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLY E 999 " --> pdb=" O ARG E 995 " (cutoff:3.500A) Processing helix chain 'E' and resid 1140 through 1148 removed outlier: 4.299A pdb=" N GLU E1144 " --> pdb=" O PRO E1140 " (cutoff:3.500A) Processing helix chain 'H' and resid 62 through 65 removed outlier: 3.838A pdb=" N GLY H 65 " --> pdb=" O SER H 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 62 through 65' Processing helix chain 'A' and resid 83 through 87 Processing helix chain 'D' and resid 63 through 65 No H-bonds generated for 'chain 'D' and resid 63 through 65' Processing helix chain 'D' and resid 83 through 87 removed outlier: 3.783A pdb=" N THR D 87 " --> pdb=" O PRO D 84 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 28 through 30 removed outlier: 7.868A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.540A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.241A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 42 through 43 removed outlier: 6.290A pdb=" N PHE B 43 " --> pdb=" O ARG E 567 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N GLY E 566 " --> pdb=" O ASP E 574 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N ASP E 574 " --> pdb=" O ILE E 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.999A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.790A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL B 126 " --> pdb=" O SER B 172 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N SER B 172 " --> pdb=" O VAL B 126 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 311 through 319 removed outlier: 7.145A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 326 through 327 removed outlier: 5.858A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 378 through 380 Processing sheet with id=AA8, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.411A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 702 through 704 Processing sheet with id=AB2, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.613A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.613A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.516A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AB6, first strand: chain 'C' and resid 29 through 30 removed outlier: 3.633A pdb=" N THR C 29 " --> pdb=" O VAL C 62 " (cutoff:3.500A) removed outlier: 8.936A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA C 93 " --> pdb=" O TYR C 266 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLY C 268 " --> pdb=" O TYR C 91 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N TYR C 91 " --> pdb=" O GLY C 268 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.456A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.465A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.539A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 84 through 85 removed outlier: 7.182A pdb=" N ARG C 237 " --> pdb=" O PHE C 106 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N PHE C 106 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N GLN C 239 " --> pdb=" O TRP C 104 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N TRP C 104 " --> pdb=" O GLN C 239 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N LEU C 241 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.595A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 326 through 327 removed outlier: 3.678A pdb=" N THR C 553 " --> pdb=" O ASP C 586 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 376 through 379 Processing sheet with id=AC3, first strand: chain 'C' and resid 452 through 453 removed outlier: 3.687A pdb=" N TYR C 453 " --> pdb=" O GLN C 493 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLN C 493 " --> pdb=" O TYR C 453 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.446A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 702 through 704 removed outlier: 3.503A pdb=" N ASN C 703 " --> pdb=" O ILE E 788 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 711 through 714 removed outlier: 3.624A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 717 through 728 removed outlier: 3.647A pdb=" N GLY C1059 " --> pdb=" O ALA C1056 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.619A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AD1, first strand: chain 'E' and resid 29 through 31 removed outlier: 8.189A pdb=" N ASN E 61 " --> pdb=" O TYR E 269 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N TYR E 269 " --> pdb=" O ASN E 61 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N TYR E 91 " --> pdb=" O GLY E 268 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N PHE E 201 " --> pdb=" O ASP E 228 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ASP E 228 " --> pdb=" O PHE E 201 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ILE E 203 " --> pdb=" O LEU E 226 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLU E 224 " --> pdb=" O SER E 205 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N HIS E 207 " --> pdb=" O ALA E 222 " (cutoff:3.500A) removed outlier: 9.114A pdb=" N ALA E 222 " --> pdb=" O HIS E 207 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N VAL E 36 " --> pdb=" O LEU E 223 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 47 through 55 removed outlier: 4.036A pdb=" N ASP E 287 " --> pdb=" O LYS E 278 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 169 through 172 removed outlier: 6.306A pdb=" N ARG E 102 " --> pdb=" O ASN E 121 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLY E 103 " --> pdb=" O LEU E 241 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 309 through 319 removed outlier: 6.175A pdb=" N LYS E 310 " --> pdb=" O GLY E 601 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N GLY E 601 " --> pdb=" O LYS E 310 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N ILE E 312 " --> pdb=" O THR E 599 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N THR E 599 " --> pdb=" O ILE E 312 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N GLN E 314 " --> pdb=" O VAL E 597 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N VAL E 597 " --> pdb=" O GLN E 314 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N SER E 316 " --> pdb=" O VAL E 595 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N GLY E 594 " --> pdb=" O GLN E 613 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 356 through 358 removed outlier: 3.708A pdb=" N VAL E 395 " --> pdb=" O ILE E 358 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ASN E 394 " --> pdb=" O GLU E 516 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N PHE E 400 " --> pdb=" O VAL E 510 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N VAL E 510 " --> pdb=" O PHE E 400 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ILE E 402 " --> pdb=" O TYR E 508 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TRP E 436 " --> pdb=" O ARG E 509 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL E 511 " --> pdb=" O ILE E 434 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N CYS E 432 " --> pdb=" O LEU E 513 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 452 through 454 Processing sheet with id=AD7, first strand: chain 'E' and resid 654 through 655 removed outlier: 6.106A pdb=" N GLU E 654 " --> pdb=" O ALA E 694 " (cutoff:3.500A) removed outlier: 8.463A pdb=" N THR E 696 " --> pdb=" O GLU E 654 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ALA E 672 " --> pdb=" O PRO E 665 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 711 through 714 removed outlier: 3.615A pdb=" N THR E1076 " --> pdb=" O SER E1097 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ALA E1078 " --> pdb=" O PHE E1095 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N PHE E1095 " --> pdb=" O ALA E1078 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 717 through 728 removed outlier: 3.664A pdb=" N MET E1050 " --> pdb=" O VAL E1065 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N TYR E1067 " --> pdb=" O HIS E1048 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N HIS E1048 " --> pdb=" O TYR E1067 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 733 through 736 removed outlier: 4.592A pdb=" N LYS E 733 " --> pdb=" O LEU E 861 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 1120 through 1122 Processing sheet with id=AE3, first strand: chain 'H' and resid 5 through 7 removed outlier: 3.637A pdb=" N THR H 77 " --> pdb=" O ASP H 72 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.769A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N THR H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N MET H 34 " --> pdb=" O THR H 50 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'A' and resid 4 through 5 removed outlier: 3.644A pdb=" N VAL A 5 " --> pdb=" O ALA A 23 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA A 23 " --> pdb=" O VAL A 5 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'A' and resid 45 through 51 removed outlier: 6.588A pdb=" N TRP A 36 " --> pdb=" O VAL A 48 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N THR A 50 " --> pdb=" O MET A 34 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N MET A 34 " --> pdb=" O THR A 50 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N TYR A 102 " --> pdb=" O ALA A 94 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'A' and resid 45 through 51 removed outlier: 6.588A pdb=" N TRP A 36 " --> pdb=" O VAL A 48 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N THR A 50 " --> pdb=" O MET A 34 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N MET A 34 " --> pdb=" O THR A 50 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 4 through 5 removed outlier: 3.816A pdb=" N THR D 77 " --> pdb=" O ASP D 72 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 57 through 59 removed outlier: 3.694A pdb=" N PHE D 58 " --> pdb=" O THR D 50 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N THR D 50 " --> pdb=" O PHE D 58 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N PHE D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N ARG D 38 " --> pdb=" O PHE D 47 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N MET D 34 " --> pdb=" O ILE D 51 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 57 through 59 removed outlier: 3.694A pdb=" N PHE D 58 " --> pdb=" O THR D 50 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N THR D 50 " --> pdb=" O PHE D 58 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N PHE D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N ARG D 38 " --> pdb=" O PHE D 47 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N MET D 34 " --> pdb=" O ILE D 51 " (cutoff:3.500A) 1044 hydrogen bonds defined for protein. 2823 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: 6.75 Time building geometry restraints manager: 3.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.28: 4492 1.28 - 1.42: 7452 1.42 - 1.56: 16402 1.56 - 1.69: 1 1.69 - 1.83: 167 Bond restraints: 28514 Sorted by residual: bond pdb=" C PRO B 899 " pdb=" O PRO B 899 " ideal model delta sigma weight residual 1.237 1.143 0.095 1.26e-02 6.30e+03 5.66e+01 bond pdb=" C PRO E 897 " pdb=" O PRO E 897 " ideal model delta sigma weight residual 1.233 1.147 0.086 1.16e-02 7.43e+03 5.46e+01 bond pdb=" C PRO C 897 " pdb=" O PRO C 897 " ideal model delta sigma weight residual 1.233 1.147 0.085 1.16e-02 7.43e+03 5.42e+01 bond pdb=" C PRO C 899 " pdb=" O PRO C 899 " ideal model delta sigma weight residual 1.237 1.145 0.092 1.26e-02 6.30e+03 5.34e+01 bond pdb=" C PRO E 899 " pdb=" O PRO E 899 " ideal model delta sigma weight residual 1.237 1.147 0.090 1.26e-02 6.30e+03 5.13e+01 ... (remaining 28509 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.72: 37946 2.72 - 5.44: 766 5.44 - 8.16: 74 8.16 - 10.88: 5 10.88 - 13.60: 2 Bond angle restraints: 38793 Sorted by residual: angle pdb=" C THR B 941 " pdb=" CA THR B 941 " pdb=" CB THR B 941 " ideal model delta sigma weight residual 109.42 121.78 -12.36 1.35e+00 5.49e-01 8.39e+01 angle pdb=" N PRO C 897 " pdb=" CA PRO C 897 " pdb=" CB PRO C 897 " ideal model delta sigma weight residual 103.31 96.41 6.90 8.90e-01 1.26e+00 6.01e+01 angle pdb=" C TYR C 904 " pdb=" CA TYR C 904 " pdb=" CB TYR C 904 " ideal model delta sigma weight residual 110.38 96.78 13.60 2.04e+00 2.40e-01 4.45e+01 angle pdb=" N PRO E 897 " pdb=" CA PRO E 897 " pdb=" CB PRO E 897 " ideal model delta sigma weight residual 103.31 97.93 5.38 8.90e-01 1.26e+00 3.65e+01 angle pdb=" CA PHE C 888 " pdb=" CB PHE C 888 " pdb=" CG PHE C 888 " ideal model delta sigma weight residual 113.80 119.61 -5.81 1.00e+00 1.00e+00 3.37e+01 ... (remaining 38788 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.80: 16596 22.80 - 45.59: 963 45.59 - 68.39: 150 68.39 - 91.19: 66 91.19 - 113.98: 20 Dihedral angle restraints: 17795 sinusoidal: 7707 harmonic: 10088 Sorted by residual: dihedral pdb=" CB CYS C 391 " pdb=" SG CYS C 391 " pdb=" SG CYS C 525 " pdb=" CB CYS C 525 " ideal model delta sinusoidal sigma weight residual -86.00 -171.92 85.92 1 1.00e+01 1.00e-02 8.92e+01 dihedral pdb=" CB CYS C 336 " pdb=" SG CYS C 336 " pdb=" SG CYS C 361 " pdb=" CB CYS C 361 " ideal model delta sinusoidal sigma weight residual -86.00 -9.69 -76.31 1 1.00e+01 1.00e-02 7.33e+01 dihedral pdb=" CB CYS C 538 " pdb=" SG CYS C 538 " pdb=" SG CYS C 590 " pdb=" CB CYS C 590 " ideal model delta sinusoidal sigma weight residual -86.00 -15.79 -70.21 1 1.00e+01 1.00e-02 6.35e+01 ... (remaining 17792 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.180: 4490 0.180 - 0.361: 62 0.361 - 0.541: 10 0.541 - 0.722: 1 0.722 - 0.902: 2 Chirality restraints: 4565 Sorted by residual: chirality pdb=" C1 NAG B1307 " pdb=" ND2 ASN B 603 " pdb=" C2 NAG B1307 " pdb=" O5 NAG B1307 " both_signs ideal model delta sigma weight residual False -2.40 -1.50 -0.90 2.00e-01 2.50e+01 2.04e+01 chirality pdb=" C1 NAG E1307 " pdb=" ND2 ASN E 603 " pdb=" C2 NAG E1307 " pdb=" O5 NAG E1307 " both_signs ideal model delta sigma weight residual False -2.40 -1.66 -0.74 2.00e-01 2.50e+01 1.36e+01 chirality pdb=" C1 NAG C1306 " pdb=" ND2 ASN C 61 " pdb=" C2 NAG C1306 " pdb=" O5 NAG C1306 " both_signs ideal model delta sigma weight residual False -2.40 -1.74 -0.66 2.00e-01 2.50e+01 1.09e+01 ... (remaining 4562 not shown) Planarity restraints: 4978 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1308 " -0.339 2.00e-02 2.50e+03 2.89e-01 1.04e+03 pdb=" C7 NAG B1308 " 0.085 2.00e-02 2.50e+03 pdb=" C8 NAG B1308 " -0.171 2.00e-02 2.50e+03 pdb=" N2 NAG B1308 " 0.509 2.00e-02 2.50e+03 pdb=" O7 NAG B1308 " -0.083 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG E1308 " -0.200 2.00e-02 2.50e+03 1.66e-01 3.43e+02 pdb=" C7 NAG E1308 " 0.054 2.00e-02 2.50e+03 pdb=" C8 NAG E1308 " -0.145 2.00e-02 2.50e+03 pdb=" N2 NAG E1308 " 0.270 2.00e-02 2.50e+03 pdb=" O7 NAG E1308 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1306 " -0.158 2.00e-02 2.50e+03 1.31e-01 2.14e+02 pdb=" C7 NAG B1306 " 0.045 2.00e-02 2.50e+03 pdb=" C8 NAG B1306 " -0.118 2.00e-02 2.50e+03 pdb=" N2 NAG B1306 " 0.210 2.00e-02 2.50e+03 pdb=" O7 NAG B1306 " 0.020 2.00e-02 2.50e+03 ... (remaining 4975 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.62: 400 2.62 - 3.19: 25152 3.19 - 3.76: 40185 3.76 - 4.33: 57756 4.33 - 4.90: 94926 Nonbonded interactions: 218419 Sorted by model distance: nonbonded pdb=" OH TYR B 369 " pdb=" O PRO B 384 " model vdw 2.056 3.040 nonbonded pdb=" OH TYR E 369 " pdb=" O PRO E 384 " model vdw 2.094 3.040 nonbonded pdb=" OG1 THR B 323 " pdb=" OE1 GLU B 324 " model vdw 2.118 3.040 nonbonded pdb=" OH TYR C 91 " pdb=" OE1 GLU C 191 " model vdw 2.125 3.040 nonbonded pdb=" O SER E 375 " pdb=" NZ LYS E 378 " model vdw 2.160 3.120 ... (remaining 218414 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'H' } ncs_group { reference = (chain 'B' and (resid 26 through 189 or (resid 190 and (name N or name CA or nam \ e C or name O or name CB )) or resid 191 through 243 or resid 262 through 675 or \ resid 691 through 1309)) selection = (chain 'C' and (resid 26 through 243 or resid 262 through 675 or resid 691 throu \ gh 1309)) selection = (chain 'E' and (resid 26 through 175 or resid 187 through 243 or resid 262 throu \ gh 675 or resid 691 through 1309)) } ncs_group { reference = (chain 'F' and resid 1) selection = (chain 'I' and resid 1) selection = (chain 'J' and resid 1) selection = (chain 'K' and resid 1) selection = (chain 'L' and resid 1) selection = (chain 'M' and resid 1) selection = (chain 'N' and resid 1) selection = (chain 'O' and resid 1) selection = (chain 'P' and resid 1) selection = (chain 'Q' and resid 1) selection = (chain 'R' and resid 1) selection = (chain 'T' and resid 1) } ncs_group { reference = chain 'G' selection = chain 'S' selection = chain 'U' selection = chain 'V' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 18.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.560 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 28.240 Find NCS groups from input model: 0.820 Set up NCS constraints: 0.050 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: 0.000 Load rotamer database and sin/cos tables:7.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 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 : 0.007 0.095 28621 Z= 0.443 Angle : 0.915 14.293 39072 Z= 0.530 Chirality : 0.065 0.902 4565 Planarity : 0.008 0.289 4933 Dihedral : 15.175 113.982 11189 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 1.04 % Allowed : 1.04 % Favored : 97.92 % Cbeta Deviations : 0.22 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -2.12 (0.14), residues: 3428 helix: 0.38 (0.21), residues: 659 sheet: -0.74 (0.18), residues: 734 loop : -2.41 (0.12), residues: 2035 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 457 TYR 0.030 0.002 TYR B 453 PHE 0.031 0.002 PHE C 906 TRP 0.048 0.003 TRP B 64 HIS 0.007 0.001 HIS E1064 Details of bonding type rmsd covalent geometry : bond 0.00748 (28514) covalent geometry : angle 0.88349 (38793) SS BOND : bond 0.00365 ( 42) SS BOND : angle 1.66685 ( 84) hydrogen bonds : bond 0.14656 ( 1010) hydrogen bonds : angle 7.28709 ( 2823) link_BETA1-4 : bond 0.00538 ( 20) link_BETA1-4 : angle 1.76267 ( 60) link_NAG-ASN : bond 0.00798 ( 45) link_NAG-ASN : angle 3.83601 ( 135) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6856 Ramachandran restraints generated. 3428 Oldfield, 0 Emsley, 3428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6856 Ramachandran restraints generated. 3428 Oldfield, 0 Emsley, 3428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 139 time to evaluate : 1.199 Fit side-chains revert: symmetry clash REVERT: B 776 LYS cc_start: 0.8814 (tttm) cc_final: 0.8546 (tttm) REVERT: C 895 GLN cc_start: 0.9220 (OUTLIER) cc_final: 0.9013 (pt0) REVERT: E 200 TYR cc_start: 0.8527 (m-80) cc_final: 0.8264 (m-80) REVERT: E 239 GLN cc_start: 0.7533 (tm-30) cc_final: 0.6943 (tm-30) REVERT: E 392 PHE cc_start: 0.7570 (t80) cc_final: 0.7259 (t80) REVERT: E 421 TYR cc_start: 0.8045 (m-80) cc_final: 0.7770 (m-80) REVERT: E 820 ASP cc_start: 0.8395 (OUTLIER) cc_final: 0.8171 (m-30) REVERT: H 59 TYR cc_start: 0.6038 (m-80) cc_final: 0.5654 (m-10) REVERT: H 77 THR cc_start: 0.4784 (t) cc_final: 0.4576 (p) REVERT: H 79 TYR cc_start: 0.7204 (m-80) cc_final: 0.6171 (m-80) REVERT: H 95 ASP cc_start: 0.6054 (t0) cc_final: 0.4626 (p0) REVERT: D 100 MET cc_start: -0.0783 (mmt) cc_final: -0.1368 (mpt) outliers start: 31 outliers final: 8 residues processed: 169 average time/residue: 0.6292 time to fit residues: 126.6710 Evaluate side-chains 115 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 105 time to evaluate : 1.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 936 ASP Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 939 SER Chi-restraints excluded: chain C residue 940 SER Chi-restraints excluded: chain C residue 943 SER Chi-restraints excluded: chain C residue 1073 LYS Chi-restraints excluded: chain E residue 820 ASP Chi-restraints excluded: chain E residue 936 ASP Chi-restraints excluded: chain E residue 1073 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 197 optimal weight: 0.6980 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 0.5980 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 0.5980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 501 ASN B 901 GLN C 501 ASN C 853 GLN C 901 GLN ** E 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 501 ASN E 506 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.146400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.077360 restraints weight = 54666.687| |-----------------------------------------------------------------------------| r_work (start): 0.2957 rms_B_bonded: 3.35 r_work: 0.2815 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work: 0.2702 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.0914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 28621 Z= 0.144 Angle : 0.659 11.974 39072 Z= 0.331 Chirality : 0.048 0.483 4565 Planarity : 0.005 0.052 4933 Dihedral : 9.330 73.613 5107 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 0.71 % Allowed : 7.93 % Favored : 91.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.63 (0.14), residues: 3428 helix: 1.21 (0.21), residues: 664 sheet: -0.47 (0.19), residues: 746 loop : -2.25 (0.12), residues: 2018 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 319 TYR 0.016 0.001 TYR C 170 PHE 0.023 0.001 PHE H 37 TRP 0.022 0.002 TRP C 633 HIS 0.003 0.001 HIS C 245 Details of bonding type rmsd covalent geometry : bond 0.00337 (28514) covalent geometry : angle 0.63720 (38793) SS BOND : bond 0.00365 ( 42) SS BOND : angle 1.34400 ( 84) hydrogen bonds : bond 0.05611 ( 1010) hydrogen bonds : angle 5.88477 ( 2823) link_BETA1-4 : bond 0.00535 ( 20) link_BETA1-4 : angle 1.89993 ( 60) link_NAG-ASN : bond 0.00301 ( 45) link_NAG-ASN : angle 2.54394 ( 135) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6856 Ramachandran restraints generated. 3428 Oldfield, 0 Emsley, 3428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6856 Ramachandran restraints generated. 3428 Oldfield, 0 Emsley, 3428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 129 time to evaluate : 1.038 Fit side-chains revert: symmetry clash REVERT: C 820 ASP cc_start: 0.8827 (OUTLIER) cc_final: 0.8533 (m-30) REVERT: C 1144 GLU cc_start: 0.8158 (mt-10) cc_final: 0.7702 (tm-30) REVERT: E 200 TYR cc_start: 0.8345 (m-80) cc_final: 0.8045 (m-80) REVERT: E 239 GLN cc_start: 0.7678 (tm-30) cc_final: 0.7157 (tm-30) REVERT: E 392 PHE cc_start: 0.7649 (t80) cc_final: 0.7283 (t80) REVERT: E 740 MET cc_start: 0.9273 (OUTLIER) cc_final: 0.9072 (ttt) REVERT: H 59 TYR cc_start: 0.5879 (m-80) cc_final: 0.5442 (m-10) REVERT: H 77 THR cc_start: 0.5206 (t) cc_final: 0.4957 (p) REVERT: H 79 TYR cc_start: 0.7176 (m-80) cc_final: 0.6229 (m-80) REVERT: H 95 ASP cc_start: 0.6343 (t0) cc_final: 0.4905 (p0) REVERT: H 100 MET cc_start: 0.5818 (mpt) cc_final: 0.5587 (mpt) REVERT: A 100 MET cc_start: 0.3054 (mtp) cc_final: 0.2759 (ptp) outliers start: 21 outliers final: 7 residues processed: 139 average time/residue: 0.6193 time to fit residues: 103.2313 Evaluate side-chains 123 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 114 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain C residue 820 ASP Chi-restraints excluded: chain C residue 939 SER Chi-restraints excluded: chain C residue 940 SER Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 436 TRP Chi-restraints excluded: chain E residue 740 MET Chi-restraints excluded: chain E residue 810 SER Chi-restraints excluded: chain E residue 985 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 328 optimal weight: 20.0000 chunk 169 optimal weight: 2.9990 chunk 304 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 231 optimal weight: 3.9990 chunk 329 optimal weight: 7.9990 chunk 134 optimal weight: 2.9990 chunk 341 optimal weight: 3.9990 chunk 107 optimal weight: 5.9990 chunk 149 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 804 GLN C 853 GLN C1002 GLN ** E 448 ASN ** 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 = 0.4074 r_free = 0.4074 target = 0.145143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.076829 restraints weight = 55210.133| |-----------------------------------------------------------------------------| r_work (start): 0.2874 rms_B_bonded: 4.00 r_work: 0.2704 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.1116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.104 28621 Z= 0.356 Angle : 0.757 15.459 39072 Z= 0.382 Chirality : 0.053 0.454 4565 Planarity : 0.005 0.053 4933 Dihedral : 8.154 57.589 5088 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer: Outliers : 1.61 % Allowed : 11.72 % Favored : 86.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.70 (0.14), residues: 3428 helix: 1.14 (0.21), residues: 669 sheet: -0.59 (0.18), residues: 765 loop : -2.28 (0.12), residues: 1994 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E1039 TYR 0.020 0.002 TYR C1067 PHE 0.023 0.002 PHE E 168 TRP 0.031 0.002 TRP B 64 HIS 0.006 0.001 HIS E1058 Details of bonding type rmsd covalent geometry : bond 0.00888 (28514) covalent geometry : angle 0.73557 (38793) SS BOND : bond 0.00505 ( 42) SS BOND : angle 1.62418 ( 84) hydrogen bonds : bond 0.07431 ( 1010) hydrogen bonds : angle 5.99388 ( 2823) link_BETA1-4 : bond 0.00425 ( 20) link_BETA1-4 : angle 1.98931 ( 60) link_NAG-ASN : bond 0.00469 ( 45) link_NAG-ASN : angle 2.64302 ( 135) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6856 Ramachandran restraints generated. 3428 Oldfield, 0 Emsley, 3428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6856 Ramachandran restraints generated. 3428 Oldfield, 0 Emsley, 3428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 112 time to evaluate : 1.143 Fit side-chains revert: symmetry clash REVERT: B 994 ASP cc_start: 0.8833 (OUTLIER) cc_final: 0.8565 (m-30) REVERT: C 265 TYR cc_start: 0.6448 (OUTLIER) cc_final: 0.6220 (t80) REVERT: C 820 ASP cc_start: 0.8763 (OUTLIER) cc_final: 0.8546 (m-30) REVERT: C 1144 GLU cc_start: 0.8139 (mt-10) cc_final: 0.7703 (tm-30) REVERT: E 200 TYR cc_start: 0.8415 (m-80) cc_final: 0.8163 (m-80) REVERT: E 392 PHE cc_start: 0.7598 (t80) cc_final: 0.7300 (t80) REVERT: H 46 LYS cc_start: 0.8253 (tppt) cc_final: 0.7935 (mppt) REVERT: H 77 THR cc_start: 0.5255 (t) cc_final: 0.4993 (p) REVERT: H 79 TYR cc_start: 0.7273 (m-80) cc_final: 0.6414 (m-10) REVERT: H 95 ASP cc_start: 0.6295 (t0) cc_final: 0.4719 (p0) REVERT: H 100 MET cc_start: 0.5708 (mpt) cc_final: 0.5497 (mpt) REVERT: D 100 MET cc_start: -0.0386 (mpt) cc_final: -0.0677 (mpt) outliers start: 48 outliers final: 22 residues processed: 148 average time/residue: 0.5841 time to fit residues: 104.5093 Evaluate side-chains 135 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 110 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain C residue 265 TYR Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 820 ASP Chi-restraints excluded: chain C residue 939 SER Chi-restraints excluded: chain C residue 940 SER Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain E residue 195 LYS Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 436 TRP Chi-restraints excluded: chain E residue 810 SER Chi-restraints excluded: chain E residue 916 LEU Chi-restraints excluded: chain E residue 985 ASP Chi-restraints excluded: chain E residue 1040 VAL Chi-restraints excluded: chain E residue 1043 CYS Chi-restraints excluded: chain H residue 63 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 40 optimal weight: 7.9990 chunk 216 optimal weight: 5.9990 chunk 285 optimal weight: 0.5980 chunk 275 optimal weight: 0.5980 chunk 36 optimal weight: 3.9990 chunk 140 optimal weight: 9.9990 chunk 242 optimal weight: 2.9990 chunk 333 optimal weight: 0.9980 chunk 329 optimal weight: 7.9990 chunk 337 optimal weight: 20.0000 chunk 161 optimal weight: 2.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 853 GLN C 954 GLN ** E 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.146362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.076705 restraints weight = 54699.072| |-----------------------------------------------------------------------------| r_work (start): 0.2909 rms_B_bonded: 3.45 r_work: 0.2764 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work: 0.2651 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.1233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 28621 Z= 0.217 Angle : 0.660 15.293 39072 Z= 0.332 Chirality : 0.049 0.452 4565 Planarity : 0.005 0.056 4933 Dihedral : 7.146 57.199 5088 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 2.18 % Allowed : 13.13 % Favored : 84.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.46 (0.14), residues: 3428 helix: 1.44 (0.21), residues: 666 sheet: -0.40 (0.18), residues: 751 loop : -2.17 (0.12), residues: 2011 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E1039 TYR 0.021 0.001 TYR B 170 PHE 0.021 0.002 PHE H 37 TRP 0.022 0.002 TRP B 64 HIS 0.004 0.001 HIS E1064 Details of bonding type rmsd covalent geometry : bond 0.00541 (28514) covalent geometry : angle 0.63855 (38793) SS BOND : bond 0.00408 ( 42) SS BOND : angle 1.76252 ( 84) hydrogen bonds : bond 0.06152 ( 1010) hydrogen bonds : angle 5.70750 ( 2823) link_BETA1-4 : bond 0.00428 ( 20) link_BETA1-4 : angle 1.70633 ( 60) link_NAG-ASN : bond 0.00267 ( 45) link_NAG-ASN : angle 2.39901 ( 135) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6856 Ramachandran restraints generated. 3428 Oldfield, 0 Emsley, 3428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6856 Ramachandran restraints generated. 3428 Oldfield, 0 Emsley, 3428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 117 time to evaluate : 1.312 Fit side-chains revert: symmetry clash REVERT: C 820 ASP cc_start: 0.8861 (OUTLIER) cc_final: 0.8612 (m-30) REVERT: C 1144 GLU cc_start: 0.8102 (mt-10) cc_final: 0.7669 (tm-30) REVERT: E 200 TYR cc_start: 0.8441 (m-80) cc_final: 0.8188 (m-80) REVERT: E 392 PHE cc_start: 0.7770 (t80) cc_final: 0.7163 (t80) REVERT: H 46 LYS cc_start: 0.8247 (tppt) cc_final: 0.7890 (mppt) REVERT: H 59 TYR cc_start: 0.6370 (m-80) cc_final: 0.6019 (m-10) REVERT: H 77 THR cc_start: 0.5307 (t) cc_final: 0.5041 (p) REVERT: H 79 TYR cc_start: 0.7214 (m-80) cc_final: 0.6357 (m-80) REVERT: H 95 ASP cc_start: 0.6331 (t0) cc_final: 0.4828 (p0) REVERT: H 98 MET cc_start: 0.3484 (mpp) cc_final: 0.2775 (mpp) REVERT: A 107 THR cc_start: 0.4930 (OUTLIER) cc_final: 0.4712 (p) REVERT: D 100 MET cc_start: -0.0949 (mpt) cc_final: -0.1330 (mpt) outliers start: 65 outliers final: 32 residues processed: 171 average time/residue: 0.5436 time to fit residues: 113.6694 Evaluate side-chains 145 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 111 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 170 TYR Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 820 ASP Chi-restraints excluded: chain C residue 940 SER Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain E residue 195 LYS Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 436 TRP Chi-restraints excluded: chain E residue 786 LYS Chi-restraints excluded: chain E residue 810 SER Chi-restraints excluded: chain E residue 916 LEU Chi-restraints excluded: chain E residue 985 ASP Chi-restraints excluded: chain E residue 1039 ARG Chi-restraints excluded: chain E residue 1043 CYS Chi-restraints excluded: chain E residue 1094 VAL Chi-restraints excluded: chain E residue 1130 ILE Chi-restraints excluded: chain E residue 1136 THR Chi-restraints excluded: chain A residue 107 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 120 optimal weight: 1.9990 chunk 261 optimal weight: 0.0060 chunk 213 optimal weight: 0.8980 chunk 276 optimal weight: 0.0270 chunk 12 optimal weight: 5.9990 chunk 316 optimal weight: 0.5980 chunk 207 optimal weight: 0.8980 chunk 188 optimal weight: 2.9990 chunk 229 optimal weight: 0.9990 chunk 79 optimal weight: 0.5980 chunk 125 optimal weight: 0.8980 overall best weight: 0.4254 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 992 GLN ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 853 GLN C 957 GLN ** E 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 935 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.141413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.075307 restraints weight = 55859.183| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 3.65 r_work: 0.2812 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.1637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 28621 Z= 0.109 Angle : 0.582 13.132 39072 Z= 0.291 Chirality : 0.045 0.437 4565 Planarity : 0.004 0.054 4933 Dihedral : 6.045 56.701 5087 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 2.18 % Allowed : 13.97 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.14 (0.14), residues: 3428 helix: 1.75 (0.22), residues: 671 sheet: -0.16 (0.19), residues: 745 loop : -2.00 (0.13), residues: 2012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 328 TYR 0.022 0.001 TYR B 170 PHE 0.027 0.001 PHE E 168 TRP 0.023 0.001 TRP H 52A HIS 0.002 0.000 HIS E 519 Details of bonding type rmsd covalent geometry : bond 0.00245 (28514) covalent geometry : angle 0.56494 (38793) SS BOND : bond 0.00327 ( 42) SS BOND : angle 1.29517 ( 84) hydrogen bonds : bond 0.04528 ( 1010) hydrogen bonds : angle 5.28069 ( 2823) link_BETA1-4 : bond 0.00468 ( 20) link_BETA1-4 : angle 1.31948 ( 60) link_NAG-ASN : bond 0.00351 ( 45) link_NAG-ASN : angle 2.13158 ( 135) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6856 Ramachandran restraints generated. 3428 Oldfield, 0 Emsley, 3428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6856 Ramachandran restraints generated. 3428 Oldfield, 0 Emsley, 3428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 124 time to evaluate : 1.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 387 LEU cc_start: -0.1415 (OUTLIER) cc_final: -0.1627 (tt) REVERT: C 820 ASP cc_start: 0.8589 (OUTLIER) cc_final: 0.8260 (m-30) REVERT: C 1041 ASP cc_start: 0.9028 (t0) cc_final: 0.8641 (t0) REVERT: C 1144 GLU cc_start: 0.8115 (mt-10) cc_final: 0.7693 (tm-30) REVERT: E 140 PHE cc_start: 0.8145 (p90) cc_final: 0.7877 (p90) REVERT: E 200 TYR cc_start: 0.8226 (m-80) cc_final: 0.7951 (m-80) REVERT: E 392 PHE cc_start: 0.7845 (t80) cc_final: 0.7253 (t80) REVERT: E 935 GLN cc_start: 0.9016 (OUTLIER) cc_final: 0.8628 (tp-100) REVERT: H 46 LYS cc_start: 0.8258 (tppt) cc_final: 0.7969 (mppt) REVERT: H 59 TYR cc_start: 0.6461 (m-80) cc_final: 0.6193 (m-10) REVERT: H 77 THR cc_start: 0.5576 (t) cc_final: 0.5233 (p) REVERT: H 79 TYR cc_start: 0.7175 (m-80) cc_final: 0.6284 (m-80) REVERT: H 95 ASP cc_start: 0.6268 (t0) cc_final: 0.4831 (p0) REVERT: H 98 MET cc_start: 0.3693 (mpp) cc_final: 0.3308 (mpp) REVERT: A 100 MET cc_start: 0.3035 (mtp) cc_final: 0.2729 (ptm) REVERT: D 100 MET cc_start: -0.0899 (mpt) cc_final: -0.1123 (mpt) outliers start: 65 outliers final: 21 residues processed: 176 average time/residue: 0.5457 time to fit residues: 117.4885 Evaluate side-chains 138 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 114 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain C residue 170 TYR Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 820 ASP Chi-restraints excluded: chain C residue 940 SER Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain E residue 175 PHE Chi-restraints excluded: chain E residue 436 TRP Chi-restraints excluded: chain E residue 810 SER Chi-restraints excluded: chain E residue 916 LEU Chi-restraints excluded: chain E residue 935 GLN Chi-restraints excluded: chain E residue 985 ASP Chi-restraints excluded: chain E residue 1092 GLU Chi-restraints excluded: chain E residue 1094 VAL Chi-restraints excluded: chain E residue 1130 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 85 optimal weight: 0.7980 chunk 37 optimal weight: 40.0000 chunk 196 optimal weight: 0.0570 chunk 276 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 chunk 268 optimal weight: 2.9990 chunk 43 optimal weight: 20.0000 chunk 77 optimal weight: 0.9990 chunk 238 optimal weight: 2.9990 chunk 267 optimal weight: 4.9990 chunk 175 optimal weight: 0.7980 overall best weight: 1.1302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 437 ASN ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 853 GLN C 957 GLN C1002 GLN E 751 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.139471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.071953 restraints weight = 55444.746| |-----------------------------------------------------------------------------| r_work (start): 0.2951 rms_B_bonded: 3.10 r_work: 0.2806 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.2692 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.1665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 28621 Z= 0.163 Angle : 0.606 14.069 39072 Z= 0.304 Chirality : 0.047 0.433 4565 Planarity : 0.004 0.052 4933 Dihedral : 5.968 56.150 5087 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 1.81 % Allowed : 14.88 % Favored : 83.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.09 (0.14), residues: 3428 helix: 1.81 (0.22), residues: 674 sheet: -0.12 (0.19), residues: 755 loop : -1.99 (0.13), residues: 1999 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E1039 TYR 0.027 0.001 TYR D 102 PHE 0.032 0.001 PHE E 175 TRP 0.024 0.002 TRP H 52A HIS 0.003 0.001 HIS E1064 Details of bonding type rmsd covalent geometry : bond 0.00402 (28514) covalent geometry : angle 0.58880 (38793) SS BOND : bond 0.00315 ( 42) SS BOND : angle 1.39429 ( 84) hydrogen bonds : bond 0.05319 ( 1010) hydrogen bonds : angle 5.30282 ( 2823) link_BETA1-4 : bond 0.00391 ( 20) link_BETA1-4 : angle 1.39822 ( 60) link_NAG-ASN : bond 0.00265 ( 45) link_NAG-ASN : angle 2.15302 ( 135) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6856 Ramachandran restraints generated. 3428 Oldfield, 0 Emsley, 3428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6856 Ramachandran restraints generated. 3428 Oldfield, 0 Emsley, 3428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 117 time to evaluate : 1.141 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 387 LEU cc_start: -0.1225 (OUTLIER) cc_final: -0.1455 (tt) REVERT: C 820 ASP cc_start: 0.8814 (OUTLIER) cc_final: 0.8562 (m-30) REVERT: C 1041 ASP cc_start: 0.9194 (t0) cc_final: 0.8709 (t0) REVERT: C 1144 GLU cc_start: 0.8113 (mt-10) cc_final: 0.7718 (tm-30) REVERT: E 140 PHE cc_start: 0.8183 (p90) cc_final: 0.7895 (p90) REVERT: E 200 TYR cc_start: 0.8404 (m-80) cc_final: 0.8128 (m-80) REVERT: E 392 PHE cc_start: 0.7950 (t80) cc_final: 0.7369 (t80) REVERT: H 46 LYS cc_start: 0.8271 (tppt) cc_final: 0.7938 (mppt) REVERT: H 59 TYR cc_start: 0.6572 (m-80) cc_final: 0.6295 (m-10) REVERT: H 77 THR cc_start: 0.5499 (t) cc_final: 0.5136 (p) REVERT: H 79 TYR cc_start: 0.7194 (m-80) cc_final: 0.6330 (m-80) REVERT: H 95 ASP cc_start: 0.6364 (t0) cc_final: 0.4866 (p0) REVERT: H 98 MET cc_start: 0.3961 (mpp) cc_final: 0.3579 (mpp) REVERT: A 100 MET cc_start: 0.3126 (mtp) cc_final: 0.2898 (ptp) outliers start: 54 outliers final: 34 residues processed: 165 average time/residue: 0.5574 time to fit residues: 111.6342 Evaluate side-chains 148 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 112 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1066 THR Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain C residue 170 TYR Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 820 ASP Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain E residue 436 TRP Chi-restraints excluded: chain E residue 622 VAL Chi-restraints excluded: chain E residue 729 VAL Chi-restraints excluded: chain E residue 780 GLU Chi-restraints excluded: chain E residue 810 SER Chi-restraints excluded: chain E residue 916 LEU Chi-restraints excluded: chain E residue 985 ASP Chi-restraints excluded: chain E residue 1039 ARG Chi-restraints excluded: chain E residue 1040 VAL Chi-restraints excluded: chain E residue 1043 CYS Chi-restraints excluded: chain E residue 1094 VAL Chi-restraints excluded: chain E residue 1130 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 162 optimal weight: 2.9990 chunk 219 optimal weight: 1.9990 chunk 296 optimal weight: 0.7980 chunk 311 optimal weight: 4.9990 chunk 301 optimal weight: 0.9990 chunk 128 optimal weight: 1.9990 chunk 291 optimal weight: 1.9990 chunk 329 optimal weight: 7.9990 chunk 67 optimal weight: 0.9990 chunk 223 optimal weight: 1.9990 chunk 292 optimal weight: 3.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 957 GLN C1002 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.138984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.071256 restraints weight = 55186.918| |-----------------------------------------------------------------------------| r_work (start): 0.2939 rms_B_bonded: 3.09 r_work: 0.2793 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work: 0.2680 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.1699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 28621 Z= 0.186 Angle : 0.615 13.426 39072 Z= 0.309 Chirality : 0.047 0.433 4565 Planarity : 0.004 0.051 4933 Dihedral : 5.930 56.112 5086 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 2.05 % Allowed : 15.32 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.08 (0.14), residues: 3428 helix: 1.77 (0.21), residues: 674 sheet: -0.10 (0.19), residues: 755 loop : -1.97 (0.13), residues: 1999 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E1039 TYR 0.021 0.001 TYR B 170 PHE 0.026 0.001 PHE E 168 TRP 0.026 0.002 TRP H 52A HIS 0.003 0.001 HIS E1064 Details of bonding type rmsd covalent geometry : bond 0.00460 (28514) covalent geometry : angle 0.59701 (38793) SS BOND : bond 0.00319 ( 42) SS BOND : angle 1.40760 ( 84) hydrogen bonds : bond 0.05594 ( 1010) hydrogen bonds : angle 5.31345 ( 2823) link_BETA1-4 : bond 0.00389 ( 20) link_BETA1-4 : angle 1.40335 ( 60) link_NAG-ASN : bond 0.00266 ( 45) link_NAG-ASN : angle 2.18277 ( 135) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6856 Ramachandran restraints generated. 3428 Oldfield, 0 Emsley, 3428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6856 Ramachandran restraints generated. 3428 Oldfield, 0 Emsley, 3428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 116 time to evaluate : 1.081 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 820 ASP cc_start: 0.8834 (OUTLIER) cc_final: 0.8615 (m-30) REVERT: C 1041 ASP cc_start: 0.9183 (t0) cc_final: 0.8691 (t0) REVERT: C 1144 GLU cc_start: 0.8079 (mt-10) cc_final: 0.7683 (tm-30) REVERT: E 140 PHE cc_start: 0.8114 (p90) cc_final: 0.7813 (p90) REVERT: E 200 TYR cc_start: 0.8390 (m-80) cc_final: 0.8118 (m-80) REVERT: E 392 PHE cc_start: 0.7923 (t80) cc_final: 0.7339 (t80) REVERT: H 46 LYS cc_start: 0.8221 (tppt) cc_final: 0.7899 (mppt) REVERT: H 59 TYR cc_start: 0.6706 (m-80) cc_final: 0.6442 (m-10) REVERT: H 77 THR cc_start: 0.5488 (t) cc_final: 0.5136 (p) REVERT: H 79 TYR cc_start: 0.7219 (m-80) cc_final: 0.6322 (m-80) REVERT: H 95 ASP cc_start: 0.6375 (t0) cc_final: 0.4870 (p0) REVERT: H 98 MET cc_start: 0.4014 (mpp) cc_final: 0.3618 (mpp) REVERT: A 100 MET cc_start: 0.3360 (mtp) cc_final: 0.3112 (ptp) outliers start: 61 outliers final: 38 residues processed: 170 average time/residue: 0.5567 time to fit residues: 115.3228 Evaluate side-chains 150 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 111 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain B residue 1066 THR Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 820 ASP Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain E residue 195 LYS Chi-restraints excluded: chain E residue 436 TRP Chi-restraints excluded: chain E residue 622 VAL Chi-restraints excluded: chain E residue 729 VAL Chi-restraints excluded: chain E residue 780 GLU Chi-restraints excluded: chain E residue 810 SER Chi-restraints excluded: chain E residue 916 LEU Chi-restraints excluded: chain E residue 985 ASP Chi-restraints excluded: chain E residue 1039 ARG Chi-restraints excluded: chain E residue 1040 VAL Chi-restraints excluded: chain E residue 1043 CYS Chi-restraints excluded: chain E residue 1094 VAL Chi-restraints excluded: chain E residue 1130 ILE Chi-restraints excluded: chain E residue 1136 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 315 optimal weight: 6.9990 chunk 122 optimal weight: 0.3980 chunk 132 optimal weight: 9.9990 chunk 163 optimal weight: 0.8980 chunk 58 optimal weight: 0.8980 chunk 277 optimal weight: 0.5980 chunk 201 optimal weight: 0.9990 chunk 210 optimal weight: 2.9990 chunk 232 optimal weight: 4.9990 chunk 246 optimal weight: 9.9990 chunk 235 optimal weight: 0.0970 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 450 ASN ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 853 GLN C 957 GLN A 105 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.142100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.072874 restraints weight = 54582.307| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 3.37 r_work: 0.2822 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work: 0.2707 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.1918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 28621 Z= 0.115 Angle : 0.582 12.909 39072 Z= 0.288 Chirality : 0.045 0.430 4565 Planarity : 0.004 0.051 4933 Dihedral : 5.644 56.476 5086 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 1.58 % Allowed : 16.02 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.93 (0.14), residues: 3428 helix: 1.98 (0.21), residues: 666 sheet: -0.04 (0.19), residues: 757 loop : -1.88 (0.13), residues: 2005 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 328 TYR 0.021 0.001 TYR B 170 PHE 0.019 0.001 PHE H 37 TRP 0.031 0.002 TRP H 52A HIS 0.002 0.000 HIS E1064 Details of bonding type rmsd covalent geometry : bond 0.00266 (28514) covalent geometry : angle 0.56634 (38793) SS BOND : bond 0.00263 ( 42) SS BOND : angle 1.18000 ( 84) hydrogen bonds : bond 0.04655 ( 1010) hydrogen bonds : angle 5.12497 ( 2823) link_BETA1-4 : bond 0.00442 ( 20) link_BETA1-4 : angle 1.25279 ( 60) link_NAG-ASN : bond 0.00294 ( 45) link_NAG-ASN : angle 2.07479 ( 135) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6856 Ramachandran restraints generated. 3428 Oldfield, 0 Emsley, 3428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6856 Ramachandran restraints generated. 3428 Oldfield, 0 Emsley, 3428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 117 time to evaluate : 1.111 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 820 ASP cc_start: 0.8759 (OUTLIER) cc_final: 0.8476 (m-30) REVERT: C 1039 ARG cc_start: 0.9078 (OUTLIER) cc_final: 0.8723 (ptm160) REVERT: C 1041 ASP cc_start: 0.9158 (t0) cc_final: 0.8660 (t0) REVERT: C 1144 GLU cc_start: 0.8070 (mt-10) cc_final: 0.7663 (tm-30) REVERT: E 140 PHE cc_start: 0.8088 (p90) cc_final: 0.7827 (p90) REVERT: E 200 TYR cc_start: 0.8376 (m-80) cc_final: 0.8107 (m-80) REVERT: E 392 PHE cc_start: 0.8003 (t80) cc_final: 0.7426 (t80) REVERT: H 46 LYS cc_start: 0.8273 (tppt) cc_final: 0.7936 (mppt) REVERT: H 59 TYR cc_start: 0.6746 (m-80) cc_final: 0.6499 (m-10) REVERT: H 77 THR cc_start: 0.5518 (t) cc_final: 0.5160 (p) REVERT: H 79 TYR cc_start: 0.7151 (m-80) cc_final: 0.6302 (m-80) REVERT: H 95 ASP cc_start: 0.6432 (t0) cc_final: 0.4925 (p0) REVERT: H 98 MET cc_start: 0.4144 (mpp) cc_final: 0.3880 (mpp) REVERT: A 98 MET cc_start: 0.1778 (OUTLIER) cc_final: 0.1180 (pmm) REVERT: A 100 MET cc_start: 0.3373 (mtp) cc_final: 0.3151 (ptp) REVERT: D 100 MET cc_start: -0.1812 (mpt) cc_final: -0.2500 (pmm) outliers start: 47 outliers final: 28 residues processed: 161 average time/residue: 0.5523 time to fit residues: 108.0040 Evaluate side-chains 144 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 113 time to evaluate : 1.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 820 ASP Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1039 ARG Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain E residue 436 TRP Chi-restraints excluded: chain E residue 780 GLU Chi-restraints excluded: chain E residue 810 SER Chi-restraints excluded: chain E residue 916 LEU Chi-restraints excluded: chain E residue 985 ASP Chi-restraints excluded: chain E residue 1094 VAL Chi-restraints excluded: chain E residue 1130 ILE Chi-restraints excluded: chain A residue 98 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 117 optimal weight: 0.9980 chunk 15 optimal weight: 0.0570 chunk 188 optimal weight: 0.6980 chunk 177 optimal weight: 0.0060 chunk 239 optimal weight: 4.9990 chunk 213 optimal weight: 9.9990 chunk 110 optimal weight: 6.9990 chunk 16 optimal weight: 0.4980 chunk 314 optimal weight: 5.9990 chunk 45 optimal weight: 2.9990 chunk 199 optimal weight: 0.5980 overall best weight: 0.3714 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 853 GLN C 957 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.143134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.076405 restraints weight = 54461.417| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 3.83 r_work: 0.2825 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.2208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 28621 Z= 0.103 Angle : 0.557 10.806 39072 Z= 0.277 Chirality : 0.045 0.415 4565 Planarity : 0.004 0.050 4933 Dihedral : 5.364 56.482 5086 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 1.41 % Allowed : 16.39 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.79 (0.14), residues: 3428 helix: 1.99 (0.21), residues: 685 sheet: -0.05 (0.19), residues: 772 loop : -1.74 (0.13), residues: 1971 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 71 TYR 0.036 0.001 TYR C 170 PHE 0.025 0.001 PHE E 168 TRP 0.038 0.002 TRP H 52A HIS 0.002 0.000 HIS E1064 Details of bonding type rmsd covalent geometry : bond 0.00234 (28514) covalent geometry : angle 0.54187 (38793) SS BOND : bond 0.00270 ( 42) SS BOND : angle 1.13717 ( 84) hydrogen bonds : bond 0.04143 ( 1010) hydrogen bonds : angle 4.94803 ( 2823) link_BETA1-4 : bond 0.00437 ( 20) link_BETA1-4 : angle 1.21642 ( 60) link_NAG-ASN : bond 0.00296 ( 45) link_NAG-ASN : angle 1.97948 ( 135) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6856 Ramachandran restraints generated. 3428 Oldfield, 0 Emsley, 3428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6856 Ramachandran restraints generated. 3428 Oldfield, 0 Emsley, 3428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 124 time to evaluate : 1.088 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 528 LYS cc_start: 0.8550 (OUTLIER) cc_final: 0.8350 (mtmp) REVERT: C 820 ASP cc_start: 0.8553 (OUTLIER) cc_final: 0.8260 (m-30) REVERT: C 1005 GLN cc_start: 0.8992 (mm-40) cc_final: 0.8568 (mt0) REVERT: C 1041 ASP cc_start: 0.8981 (t0) cc_final: 0.8603 (t0) REVERT: C 1144 GLU cc_start: 0.8095 (mt-10) cc_final: 0.7746 (tm-30) REVERT: E 140 PHE cc_start: 0.8058 (p90) cc_final: 0.7775 (p90) REVERT: E 200 TYR cc_start: 0.8258 (m-80) cc_final: 0.8007 (m-80) REVERT: E 392 PHE cc_start: 0.8134 (t80) cc_final: 0.7581 (t80) REVERT: H 46 LYS cc_start: 0.8246 (tppt) cc_final: 0.7935 (mppt) REVERT: H 59 TYR cc_start: 0.6717 (m-80) cc_final: 0.6475 (m-10) REVERT: H 77 THR cc_start: 0.5891 (t) cc_final: 0.5528 (p) REVERT: H 79 TYR cc_start: 0.7125 (m-80) cc_final: 0.6252 (m-80) REVERT: H 95 ASP cc_start: 0.6588 (t0) cc_final: 0.5171 (p0) REVERT: A 98 MET cc_start: 0.2325 (OUTLIER) cc_final: 0.1951 (pmm) REVERT: D 100 MET cc_start: -0.1606 (OUTLIER) cc_final: -0.2304 (pmm) outliers start: 42 outliers final: 28 residues processed: 161 average time/residue: 0.6031 time to fit residues: 116.4246 Evaluate side-chains 145 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 113 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 820 ASP Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain E residue 436 TRP Chi-restraints excluded: chain E residue 810 SER Chi-restraints excluded: chain E residue 916 LEU Chi-restraints excluded: chain E residue 977 LEU Chi-restraints excluded: chain E residue 985 ASP Chi-restraints excluded: chain E residue 1040 VAL Chi-restraints excluded: chain E residue 1094 VAL Chi-restraints excluded: chain E residue 1130 ILE Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain D residue 100 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 179 optimal weight: 1.9990 chunk 285 optimal weight: 0.9980 chunk 254 optimal weight: 0.4980 chunk 214 optimal weight: 7.9990 chunk 158 optimal weight: 0.2980 chunk 138 optimal weight: 2.9990 chunk 150 optimal weight: 5.9990 chunk 10 optimal weight: 0.0770 chunk 78 optimal weight: 0.6980 chunk 206 optimal weight: 6.9990 chunk 94 optimal weight: 0.7980 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 853 GLN C 957 GLN C1002 GLN ** E 207 HIS ** 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 = 0.4129 r_free = 0.4129 target = 0.142988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.076523 restraints weight = 54150.533| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 3.73 r_work: 0.2827 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.2266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 28621 Z= 0.105 Angle : 0.562 10.935 39072 Z= 0.278 Chirality : 0.045 0.412 4565 Planarity : 0.004 0.050 4933 Dihedral : 5.307 56.385 5086 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 1.28 % Allowed : 16.86 % Favored : 81.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.71 (0.14), residues: 3428 helix: 2.05 (0.21), residues: 685 sheet: 0.02 (0.19), residues: 772 loop : -1.69 (0.13), residues: 1971 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 328 TYR 0.029 0.001 TYR C 170 PHE 0.031 0.001 PHE B 168 TRP 0.042 0.001 TRP H 52A HIS 0.005 0.000 HIS E 207 Details of bonding type rmsd covalent geometry : bond 0.00243 (28514) covalent geometry : angle 0.54719 (38793) SS BOND : bond 0.00239 ( 42) SS BOND : angle 1.08359 ( 84) hydrogen bonds : bond 0.04228 ( 1010) hydrogen bonds : angle 4.92914 ( 2823) link_BETA1-4 : bond 0.00428 ( 20) link_BETA1-4 : angle 1.21357 ( 60) link_NAG-ASN : bond 0.00280 ( 45) link_NAG-ASN : angle 1.96379 ( 135) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6856 Ramachandran restraints generated. 3428 Oldfield, 0 Emsley, 3428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6856 Ramachandran restraints generated. 3428 Oldfield, 0 Emsley, 3428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 120 time to evaluate : 1.042 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 820 ASP cc_start: 0.8579 (OUTLIER) cc_final: 0.8297 (m-30) REVERT: C 1005 GLN cc_start: 0.8993 (mm-40) cc_final: 0.8547 (mt0) REVERT: C 1041 ASP cc_start: 0.8987 (t0) cc_final: 0.8605 (t0) REVERT: C 1144 GLU cc_start: 0.8126 (mt-10) cc_final: 0.7742 (tm-30) REVERT: E 140 PHE cc_start: 0.8041 (p90) cc_final: 0.7775 (p90) REVERT: E 200 TYR cc_start: 0.8274 (m-80) cc_final: 0.8029 (m-80) REVERT: E 392 PHE cc_start: 0.8125 (t80) cc_final: 0.7575 (t80) REVERT: H 22 CYS cc_start: 0.1602 (t) cc_final: 0.1375 (t) REVERT: H 46 LYS cc_start: 0.8228 (tppt) cc_final: 0.7927 (mppt) REVERT: H 59 TYR cc_start: 0.6655 (m-80) cc_final: 0.6434 (m-10) REVERT: H 77 THR cc_start: 0.5943 (t) cc_final: 0.5604 (p) REVERT: H 79 TYR cc_start: 0.7129 (m-80) cc_final: 0.6312 (m-80) REVERT: H 95 ASP cc_start: 0.6568 (t0) cc_final: 0.5122 (p0) REVERT: A 98 MET cc_start: 0.2314 (OUTLIER) cc_final: 0.2108 (pmm) REVERT: D 100 MET cc_start: -0.1371 (OUTLIER) cc_final: -0.2053 (pmm) outliers start: 38 outliers final: 29 residues processed: 154 average time/residue: 0.5743 time to fit residues: 106.8958 Evaluate side-chains 149 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 117 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain C residue 170 TYR Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 820 ASP Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 436 TRP Chi-restraints excluded: chain E residue 810 SER Chi-restraints excluded: chain E residue 916 LEU Chi-restraints excluded: chain E residue 985 ASP Chi-restraints excluded: chain E residue 1040 VAL Chi-restraints excluded: chain E residue 1094 VAL Chi-restraints excluded: chain E residue 1130 ILE Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain D residue 100 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 317 optimal weight: 0.0270 chunk 12 optimal weight: 7.9990 chunk 331 optimal weight: 10.0000 chunk 134 optimal weight: 9.9990 chunk 5 optimal weight: 4.9990 chunk 104 optimal weight: 1.9990 chunk 300 optimal weight: 0.9990 chunk 184 optimal weight: 0.9980 chunk 264 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 101 optimal weight: 1.9990 overall best weight: 1.0042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 853 GLN C 957 GLN D 82AASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.141868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.074951 restraints weight = 54276.413| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 3.87 r_work: 0.2782 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.2224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 28621 Z= 0.147 Angle : 0.583 11.246 39072 Z= 0.289 Chirality : 0.046 0.412 4565 Planarity : 0.004 0.049 4933 Dihedral : 5.382 56.146 5086 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 1.31 % Allowed : 17.13 % Favored : 81.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.75 (0.14), residues: 3428 helix: 1.99 (0.21), residues: 688 sheet: -0.02 (0.19), residues: 778 loop : -1.70 (0.13), residues: 1962 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E1039 TYR 0.022 0.001 TYR C 170 PHE 0.028 0.001 PHE B 168 TRP 0.043 0.002 TRP H 52A HIS 0.007 0.001 HIS E 207 Details of bonding type rmsd covalent geometry : bond 0.00360 (28514) covalent geometry : angle 0.56744 (38793) SS BOND : bond 0.00316 ( 42) SS BOND : angle 1.22901 ( 84) hydrogen bonds : bond 0.04790 ( 1010) hydrogen bonds : angle 4.99164 ( 2823) link_BETA1-4 : bond 0.00392 ( 20) link_BETA1-4 : angle 1.26897 ( 60) link_NAG-ASN : bond 0.00255 ( 45) link_NAG-ASN : angle 2.00772 ( 135) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15254.30 seconds wall clock time: 258 minutes 57.53 seconds (15537.53 seconds total)