Starting phenix.real_space_refine on Tue Aug 26 10:22:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zby_39916/08_2025/8zby_39916.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zby_39916/08_2025/8zby_39916.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.67 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8zby_39916/08_2025/8zby_39916.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zby_39916/08_2025/8zby_39916.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8zby_39916/08_2025/8zby_39916.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zby_39916/08_2025/8zby_39916.map" } resolution = 3.67 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2232 atoms to isotropic. 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 159 5.16 5 C 21777 2.51 5 N 5619 2.21 5 O 6660 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 64 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 34215 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 7929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1010, 7929 Classifications: {'peptide': 1010} Link IDs: {'PTRANS': 52, 'TRANS': 957} Chain breaks: 8 Chain: "H" Number of atoms: 1661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1661 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 208} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 1591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1591 Classifications: {'peptide': 213} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 195} Chain breaks: 1 Chain: "B" Number of atoms: 7929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1010, 7929 Classifications: {'peptide': 1010} Link IDs: {'PTRANS': 52, 'TRANS': 957} Chain breaks: 8 Chain: "G" Number of atoms: 1661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1661 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 208} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 1591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1591 Classifications: {'peptide': 213} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 195} Chain breaks: 1 Chain: "C" Number of atoms: 7929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1010, 7929 Classifications: {'peptide': 1010} Link IDs: {'PTRANS': 52, 'TRANS': 957} Chain breaks: 8 Chain: "I" Number of atoms: 1661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1661 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 208} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 1591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1591 Classifications: {'peptide': 213} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 195} Chain breaks: 1 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 8.60, per 1000 atoms: 0.25 Number of scatterers: 34215 At special positions: 0 Unit cell: (149.16, 157.08, 238.92, 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 159 16.00 O 6660 8.00 N 5619 7.00 C 21777 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=51, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 103 " - pdb=" SG CYS H 108 " distance=2.03 Simple disulfide: pdb=" SG CYS H 154 " - pdb=" SG CYS H 210 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 89 " distance=2.03 Simple disulfide: pdb=" SG CYS D 145 " - pdb=" SG CYS D 204 " distance=2.03 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=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 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 G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 103 " - pdb=" SG CYS G 108 " distance=2.03 Simple disulfide: pdb=" SG CYS G 154 " - pdb=" SG CYS G 210 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 89 " distance=2.03 Simple disulfide: pdb=" SG CYS E 145 " - pdb=" SG CYS E 204 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 103 " - pdb=" SG CYS I 108 " distance=2.03 Simple disulfide: pdb=" SG CYS I 154 " - pdb=" SG CYS I 210 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 89 " distance=2.03 Simple disulfide: pdb=" SG CYS F 145 " - pdb=" SG CYS F 204 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 234 " " NAG A1303 " - " ASN A 282 " " NAG A1304 " - " ASN A 331 " " NAG A1305 " - " ASN A 616 " " NAG A1306 " - " ASN A 709 " " NAG A1307 " - " ASN A1074 " " NAG A1308 " - " ASN A 343 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 234 " " NAG B1303 " - " ASN B 282 " " NAG B1304 " - " ASN B 331 " " NAG B1305 " - " ASN B 616 " " NAG B1306 " - " ASN B 709 " " NAG B1307 " - " ASN B1074 " " NAG B1308 " - " ASN B 343 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 234 " " NAG C1303 " - " ASN C 282 " " NAG C1304 " - " ASN C 331 " " NAG C1305 " - " ASN C 616 " " NAG C1306 " - " ASN C 709 " " NAG C1307 " - " ASN C1074 " " NAG C1308 " - " ASN C 343 " " NAG J 1 " - " ASN A 717 " " NAG K 1 " - " ASN A 801 " " NAG L 1 " - " ASN A1098 " " NAG M 1 " - " ASN A1134 " " NAG N 1 " - " ASN B 717 " " NAG O 1 " - " ASN B 801 " " NAG P 1 " - " ASN B1098 " " NAG Q 1 " - " ASN B1134 " " NAG R 1 " - " ASN C 717 " " NAG S 1 " - " ASN C 801 " " NAG T 1 " - " ASN C1098 " " NAG U 1 " - " ASN C1134 " Time building additional restraints: 3.27 Conformation dependent library (CDL) restraints added in 1.4 seconds Enol-peptide restraints added in 1.2 microseconds 8508 Ramachandran restraints generated. 4254 Oldfield, 0 Emsley, 4254 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8118 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 78 sheets defined 18.4% alpha, 32.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.88 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 367 through 371 removed outlier: 3.551A pdb=" N ASN A 370 " --> pdb=" O VAL A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 387 Processing helix chain 'A' and resid 403 through 407 Processing helix chain 'A' and resid 738 through 743 Processing helix chain 'A' and resid 746 through 757 removed outlier: 3.595A pdb=" N GLY A 757 " --> pdb=" O LEU A 753 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 782 removed outlier: 3.724A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 823 Processing helix chain 'A' and resid 850 through 856 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 891 removed outlier: 4.149A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 910 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.445A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 946 through 967 Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.737A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.600A pdb=" N VAL A 991 " --> pdb=" O CYS A 987 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N GLY A 999 " --> pdb=" O ARG A 995 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N GLN A1002 " --> pdb=" O THR A 998 " (cutoff:3.500A) Processing helix chain 'H' and resid 108 through 112 removed outlier: 3.680A pdb=" N TRP H 111 " --> pdb=" O CYS H 108 " (cutoff:3.500A) Processing helix chain 'H' and resid 170 through 172 No H-bonds generated for 'chain 'H' and resid 170 through 172' Processing helix chain 'D' and resid 80 through 84 removed outlier: 3.762A pdb=" N GLU D 84 " --> pdb=" O SER D 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 138 Processing helix chain 'D' and resid 192 through 199 removed outlier: 3.534A pdb=" N HIS D 199 " --> pdb=" O GLN D 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 383 through 387 Processing helix chain 'B' and resid 403 through 410 removed outlier: 3.712A pdb=" N VAL B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 738 through 743 Processing helix chain 'B' and resid 746 through 757 Processing helix chain 'B' and resid 758 through 782 removed outlier: 3.707A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 824 removed outlier: 3.669A pdb=" N ASN B 824 " --> pdb=" O ASP B 820 " (cutoff:3.500A) Processing helix chain 'B' and resid 850 through 856 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.908A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 910 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.345A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 946 through 967 Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.687A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 989 through 1033 removed outlier: 4.591A pdb=" N GLY B 999 " --> pdb=" O ARG B 995 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N GLN B1002 " --> pdb=" O THR B 998 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 32 removed outlier: 4.022A pdb=" N ASP G 31 " --> pdb=" O ILE G 28 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N TYR G 32 " --> pdb=" O PHE G 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 28 through 32' Processing helix chain 'G' and resid 106 through 112 removed outlier: 3.800A pdb=" N GLN G 109 " --> pdb=" O ASN G 106 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ARG G 110 " --> pdb=" O SER G 107 " (cutoff:3.500A) Processing helix chain 'G' and resid 170 through 172 No H-bonds generated for 'chain 'G' and resid 170 through 172' Processing helix chain 'E' and resid 80 through 84 removed outlier: 3.729A pdb=" N GLU E 84 " --> pdb=" O SER E 81 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 138 Processing helix chain 'E' and resid 192 through 199 removed outlier: 3.671A pdb=" N LYS E 197 " --> pdb=" O PRO E 193 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N SER E 198 " --> pdb=" O GLU E 194 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N HIS E 199 " --> pdb=" O GLN E 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 367 through 371 removed outlier: 3.632A pdb=" N ASN C 370 " --> pdb=" O VAL C 367 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU C 371 " --> pdb=" O LEU C 368 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 367 through 371' Processing helix chain 'C' and resid 383 through 387 removed outlier: 3.919A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 738 through 743 removed outlier: 3.558A pdb=" N ILE C 742 " --> pdb=" O CYS C 738 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 756 Processing helix chain 'C' and resid 758 through 782 removed outlier: 3.568A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 823 Processing helix chain 'C' and resid 850 through 856 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 891 removed outlier: 4.053A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.520A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 912 through 916 removed outlier: 3.872A pdb=" N VAL C 915 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 946 through 967 removed outlier: 3.535A pdb=" N SER C 967 " --> pdb=" O VAL C 963 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.657A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.654A pdb=" N VAL C 991 " --> pdb=" O CYS C 987 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N GLY C 999 " --> pdb=" O ARG C 995 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N GLN C1002 " --> pdb=" O THR C 998 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 32 removed outlier: 3.868A pdb=" N ASP I 31 " --> pdb=" O ILE I 28 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N TYR I 32 " --> pdb=" O PHE I 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 28 through 32' Processing helix chain 'I' and resid 108 through 112 removed outlier: 3.700A pdb=" N TRP I 111 " --> pdb=" O CYS I 108 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N MET I 112 " --> pdb=" O GLN I 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 108 through 112' Processing helix chain 'I' and resid 170 through 172 No H-bonds generated for 'chain 'I' and resid 170 through 172' Processing helix chain 'F' and resid 80 through 84 removed outlier: 3.716A pdb=" N GLU F 84 " --> pdb=" O SER F 81 " (cutoff:3.500A) Processing helix chain 'F' and resid 132 through 138 removed outlier: 3.593A pdb=" N ALA F 138 " --> pdb=" O GLU F 134 " (cutoff:3.500A) Processing helix chain 'F' and resid 192 through 197 removed outlier: 3.709A pdb=" N LYS F 197 " --> pdb=" O PRO F 193 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.576A pdb=" N VAL A 62 " --> pdb=" O THR A 29 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ALA A 264 " --> pdb=" O ILE A 95 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N GLY A 89 " --> pdb=" O LEU A 270 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLU A 96 " --> pdb=" O ASN A 188 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ASN A 188 " --> pdb=" O GLU A 96 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LYS A 195 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LYS A 202 " --> pdb=" O LYS A 195 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ILE A 197 " --> pdb=" O TYR A 200 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 50 through 53 Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.704A pdb=" N CYS A 131 " --> pdb=" O SER A 116 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 311 through 318 removed outlier: 3.573A pdb=" N GLY A 311 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N THR A 599 " --> pdb=" O GLY A 311 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N TYR A 313 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR A 315 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 325 through 327 removed outlier: 6.632A pdb=" N ILE A 326 " --> pdb=" O ASN A 542 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLY A 550 " --> pdb=" O VAL A 539 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N THR A 588 " --> pdb=" O VAL A 551 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N THR A 553 " --> pdb=" O ASP A 586 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.855A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N TRP A 436 " --> pdb=" O ARG A 509 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N ALA A 435 " --> pdb=" O PHE A 375 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 452 through 454 removed outlier: 3.564A pdb=" N TYR A 453 " --> pdb=" O ARG A 493 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.606A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.166A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.365A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.005A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N LYS B 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.624A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL A1068 " --> pdb=" O THR A 719 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N SER A 721 " --> pdb=" O THR A1066 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.624A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL A1068 " --> pdb=" O THR A 719 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N SER A 721 " --> pdb=" O THR A1066 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 733 through 736 removed outlier: 3.934A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AB6, first strand: chain 'A' and resid 1120 through 1122 removed outlier: 4.213A pdb=" N ILE A1081 " --> pdb=" O HIS A1088 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N CYS A1082 " --> pdb=" O VAL A1133 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 3 through 6 removed outlier: 3.631A pdb=" N GLN H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER H 25 " --> pdb=" O GLN H 3 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL H 5 " --> pdb=" O LYS H 23 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N THR H 71 " --> pdb=" O TYR H 80 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N GLU H 82 " --> pdb=" O THR H 69 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR H 69 " --> pdb=" O GLU H 82 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 10 through 12 removed outlier: 7.302A pdb=" N ILE H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N TRP H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N TRP H 50 " --> pdb=" O ASN H 59 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ASN H 59 " --> pdb=" O TRP H 50 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.769A pdb=" N THR H 116 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 134 through 138 removed outlier: 3.701A pdb=" N GLY H 153 " --> pdb=" O LEU H 138 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N TYR H 190 " --> pdb=" O ASP H 158 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 134 through 138 removed outlier: 3.701A pdb=" N GLY H 153 " --> pdb=" O LEU H 138 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N TYR H 190 " --> pdb=" O ASP H 158 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 165 through 168 removed outlier: 4.498A pdb=" N TYR H 208 " --> pdb=" O VAL H 225 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 9 through 12 removed outlier: 3.553A pdb=" N GLY D 12 " --> pdb=" O THR D 108 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 18 through 23 removed outlier: 3.544A pdb=" N VAL D 18 " --> pdb=" O ILE D 76 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE D 76 " --> pdb=" O VAL D 18 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 45 through 49 removed outlier: 7.079A pdb=" N TRP D 36 " --> pdb=" O LEU D 48 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ASP D 86 " --> pdb=" O GLN D 39 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLY D 98 " --> pdb=" O ASP D 93 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 125 through 129 removed outlier: 3.708A pdb=" N VAL D 144 " --> pdb=" O PHE D 129 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA D 141 " --> pdb=" O LEU D 191 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N TYR D 183 " --> pdb=" O ASP D 149 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 125 through 129 removed outlier: 3.708A pdb=" N VAL D 144 " --> pdb=" O PHE D 129 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA D 141 " --> pdb=" O LEU D 191 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N TYR D 183 " --> pdb=" O ASP D 149 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 164 through 166 removed outlier: 4.175A pdb=" N TRP D 159 " --> pdb=" O VAL D 166 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.510A pdb=" N VAL B 62 " --> pdb=" O THR B 29 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA B 264 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N GLY B 89 " --> pdb=" O LEU B 270 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLU B 96 " --> pdb=" O ASN B 188 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ASN B 188 " --> pdb=" O GLU B 96 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU B 189 " --> pdb=" O THR B 208 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LYS B 195 " --> pdb=" O LYS B 202 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LYS B 202 " --> pdb=" O LYS B 195 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ILE B 197 " --> pdb=" O TYR B 200 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 50 through 53 Processing sheet with id=AD3, first strand: chain 'B' and resid 83 through 85 removed outlier: 3.564A pdb=" N ILE B 119 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N GLU B 132 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N CYS B 166 " --> pdb=" O GLU B 132 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 311 through 318 removed outlier: 3.638A pdb=" N GLY B 311 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N THR B 599 " --> pdb=" O GLY B 311 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N TYR B 313 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N THR B 315 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA B 609 " --> pdb=" O ILE B 598 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 325 through 327 removed outlier: 6.640A pdb=" N ILE B 326 " --> pdb=" O ASN B 542 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N GLY B 550 " --> pdb=" O VAL B 539 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N THR B 588 " --> pdb=" O VAL B 551 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU B 585 " --> pdb=" O VAL B 576 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.648A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD8, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.646A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.156A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.386A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 701 through 702 removed outlier: 6.489A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.670A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER B 721 " --> pdb=" O THR B1066 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.670A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER B 721 " --> pdb=" O THR B1066 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N VAL B1094 " --> pdb=" O THR B1105 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N THR B1105 " --> pdb=" O VAL B1094 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.038A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B' and resid 1120 through 1122 removed outlier: 4.370A pdb=" N ILE B1081 " --> pdb=" O HIS B1088 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N CYS B1082 " --> pdb=" O VAL B1133 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 3 through 6 removed outlier: 3.524A pdb=" N GLN G 3 " --> pdb=" O SER G 25 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL G 5 " --> pdb=" O LYS G 23 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLU G 82 " --> pdb=" O THR G 69 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'G' and resid 10 through 11 removed outlier: 3.566A pdb=" N THR G 124 " --> pdb=" O GLU G 10 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL G 37 " --> pdb=" O PHE G 95 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ILE G 34 " --> pdb=" O ILE G 51 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N ARG G 38 " --> pdb=" O TRP G 47 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N TRP G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N TRP G 50 " --> pdb=" O ASN G 59 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ASN G 59 " --> pdb=" O TRP G 50 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'G' and resid 134 through 138 removed outlier: 3.723A pdb=" N PHE G 136 " --> pdb=" O LEU G 155 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU G 155 " --> pdb=" O PHE G 136 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLY G 153 " --> pdb=" O LEU G 138 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU G 152 " --> pdb=" O VAL G 196 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N TYR G 190 " --> pdb=" O ASP G 158 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'G' and resid 134 through 138 removed outlier: 3.723A pdb=" N PHE G 136 " --> pdb=" O LEU G 155 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU G 155 " --> pdb=" O PHE G 136 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLY G 153 " --> pdb=" O LEU G 138 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU G 152 " --> pdb=" O VAL G 196 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N TYR G 190 " --> pdb=" O ASP G 158 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'G' and resid 165 through 168 removed outlier: 4.496A pdb=" N TYR G 208 " --> pdb=" O VAL G 225 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'E' and resid 9 through 12 removed outlier: 7.341A pdb=" N ALA E 10 " --> pdb=" O THR E 108 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF2 Processing sheet with id=AF3, first strand: chain 'E' and resid 20 through 23 removed outlier: 3.514A pdb=" N LEU E 74 " --> pdb=" O ILE E 20 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'E' and resid 45 through 49 removed outlier: 7.139A pdb=" N TRP E 36 " --> pdb=" O LEU E 48 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ASP E 86 " --> pdb=" O GLN E 39 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA E 91 " --> pdb=" O VAL E 100 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ASP E 93 " --> pdb=" O GLY E 98 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLY E 98 " --> pdb=" O ASP E 93 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'E' and resid 125 through 129 removed outlier: 6.320A pdb=" N TYR E 183 " --> pdb=" O ASP E 149 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'E' and resid 125 through 129 removed outlier: 6.320A pdb=" N TYR E 183 " --> pdb=" O ASP E 149 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'E' and resid 164 through 166 removed outlier: 4.659A pdb=" N TRP E 159 " --> pdb=" O VAL E 166 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 28 through 31 removed outlier: 3.511A pdb=" N VAL C 62 " --> pdb=" O THR C 29 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA C 264 " --> pdb=" O ILE C 95 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N GLY C 89 " --> pdb=" O LEU C 270 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLU C 96 " --> pdb=" O ASN C 188 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ASN C 188 " --> pdb=" O GLU C 96 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THR C 208 " --> pdb=" O LEU C 189 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LYS C 195 " --> pdb=" O LYS C 202 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LYS C 202 " --> pdb=" O LYS C 195 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ILE C 197 " --> pdb=" O TYR C 200 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 50 through 53 Processing sheet with id=AG1, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.548A pdb=" N SER C 116 " --> pdb=" O CYS C 131 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N CYS C 131 " --> pdb=" O SER C 116 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N GLU C 132 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N CYS C 166 " --> pdb=" O GLU C 132 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'C' and resid 311 through 318 removed outlier: 3.689A pdb=" N GLY C 311 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N THR C 599 " --> pdb=" O GLY C 311 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N TYR C 313 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N THR C 315 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'C' and resid 325 through 327 removed outlier: 6.625A pdb=" N ILE C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLY C 550 " --> pdb=" O VAL C 539 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU C 546 " --> pdb=" O PHE C 543 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N THR C 588 " --> pdb=" O VAL C 551 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N THR C 553 " --> pdb=" O ASP C 586 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.842A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TRP C 436 " --> pdb=" O ARG C 509 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AG6, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.726A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.218A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.441A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.572A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N SER C 721 " --> pdb=" O THR C1066 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.572A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N SER C 721 " --> pdb=" O THR C1066 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N THR C1105 " --> pdb=" O VAL C1094 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.075A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'C' and resid 1081 through 1082 removed outlier: 3.943A pdb=" N CYS C1082 " --> pdb=" O VAL C1133 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH2 Processing sheet with id=AH3, first strand: chain 'C' and resid 1088 through 1090 Processing sheet with id=AH4, first strand: chain 'I' and resid 3 through 6 removed outlier: 3.765A pdb=" N GLN I 3 " --> pdb=" O SER I 25 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER I 25 " --> pdb=" O GLN I 3 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL I 5 " --> pdb=" O LYS I 23 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL I 18 " --> pdb=" O LEU I 83 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR I 71 " --> pdb=" O TYR I 80 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N GLU I 82 " --> pdb=" O THR I 69 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N THR I 69 " --> pdb=" O GLU I 82 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'I' and resid 10 through 12 removed outlier: 3.565A pdb=" N THR I 124 " --> pdb=" O GLU I 10 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'I' and resid 58 through 60 removed outlier: 3.943A pdb=" N ASN I 59 " --> pdb=" O TRP I 50 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N TRP I 50 " --> pdb=" O ASN I 59 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N TRP I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N ARG I 38 " --> pdb=" O TRP I 47 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLY I 49 " --> pdb=" O TRP I 36 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ILE I 34 " --> pdb=" O ILE I 51 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ASN I 33 " --> pdb=" O SER I 99 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL I 37 " --> pdb=" O PHE I 95 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N PHE I 95 " --> pdb=" O VAL I 37 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N THR I 116 " --> pdb=" O ARG I 98 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'I' and resid 134 through 138 removed outlier: 3.680A pdb=" N GLY I 153 " --> pdb=" O LEU I 138 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N TYR I 190 " --> pdb=" O ASP I 158 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'I' and resid 134 through 138 removed outlier: 3.680A pdb=" N GLY I 153 " --> pdb=" O LEU I 138 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N TYR I 190 " --> pdb=" O ASP I 158 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N SER I 191 " --> pdb=" O VAL I 183 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'I' and resid 165 through 168 removed outlier: 4.473A pdb=" N TYR I 208 " --> pdb=" O VAL I 225 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'F' and resid 9 through 12 removed outlier: 7.349A pdb=" N ALA F 10 " --> pdb=" O THR F 108 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI1 Processing sheet with id=AI2, first strand: chain 'F' and resid 18 through 23 removed outlier: 3.847A pdb=" N VAL F 18 " --> pdb=" O ILE F 76 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ILE F 76 " --> pdb=" O VAL F 18 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'F' and resid 45 through 49 removed outlier: 3.524A pdb=" N LEU F 48 " --> pdb=" O TRP F 36 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N TRP F 36 " --> pdb=" O LEU F 48 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ASP F 86 " --> pdb=" O GLN F 39 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLY F 98 " --> pdb=" O ASP F 93 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'F' and resid 125 through 129 removed outlier: 3.542A pdb=" N VAL F 144 " --> pdb=" O PHE F 129 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU F 143 " --> pdb=" O LEU F 189 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N TYR F 183 " --> pdb=" O ASP F 149 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'F' and resid 125 through 129 removed outlier: 3.542A pdb=" N VAL F 144 " --> pdb=" O PHE F 129 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU F 143 " --> pdb=" O LEU F 189 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N TYR F 183 " --> pdb=" O ASP F 149 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'F' and resid 164 through 166 removed outlier: 4.383A pdb=" N TRP F 159 " --> pdb=" O VAL F 166 " (cutoff:3.500A) 1292 hydrogen bonds defined for protein. 3501 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: 9.90 Time building geometry restraints manager: 4.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10790 1.34 - 1.46: 8420 1.46 - 1.58: 15611 1.58 - 1.70: 0 1.70 - 1.82: 198 Bond restraints: 35019 Sorted by residual: bond pdb=" C1 NAG O 1 " pdb=" O5 NAG O 1 " ideal model delta sigma weight residual 1.406 1.460 -0.054 2.00e-02 2.50e+03 7.40e+00 bond pdb=" C1 NAG K 2 " pdb=" O5 NAG K 2 " ideal model delta sigma weight residual 1.406 1.452 -0.046 2.00e-02 2.50e+03 5.24e+00 bond pdb=" C ASN C 81 " pdb=" N PRO C 82 " ideal model delta sigma weight residual 1.330 1.355 -0.025 1.25e-02 6.40e+03 4.02e+00 bond pdb=" C1 NAG A1303 " pdb=" O5 NAG A1303 " ideal model delta sigma weight residual 1.406 1.446 -0.040 2.00e-02 2.50e+03 3.92e+00 bond pdb=" C1 NAG B1303 " pdb=" O5 NAG B1303 " ideal model delta sigma weight residual 1.406 1.445 -0.039 2.00e-02 2.50e+03 3.74e+00 ... (remaining 35014 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.72: 46404 1.72 - 3.45: 1095 3.45 - 5.17: 133 5.17 - 6.89: 37 6.89 - 8.62: 10 Bond angle restraints: 47679 Sorted by residual: angle pdb=" N LYS I 12 " pdb=" CA LYS I 12 " pdb=" C LYS I 12 " ideal model delta sigma weight residual 108.86 114.55 -5.69 1.41e+00 5.03e-01 1.63e+01 angle pdb=" CB LYS B 814 " pdb=" CG LYS B 814 " pdb=" CD LYS B 814 " ideal model delta sigma weight residual 111.30 119.92 -8.62 2.30e+00 1.89e-01 1.40e+01 angle pdb=" CA GLU B 406 " pdb=" CB GLU B 406 " pdb=" CG GLU B 406 " ideal model delta sigma weight residual 114.10 121.05 -6.95 2.00e+00 2.50e-01 1.21e+01 angle pdb=" C TYR C 756 " pdb=" N GLY C 757 " pdb=" CA GLY C 757 " ideal model delta sigma weight residual 122.42 117.81 4.61 1.36e+00 5.41e-01 1.15e+01 angle pdb=" CB GLU H 82 " pdb=" CG GLU H 82 " pdb=" CD GLU H 82 " ideal model delta sigma weight residual 112.60 118.27 -5.67 1.70e+00 3.46e-01 1.11e+01 ... (remaining 47674 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.03: 19699 18.03 - 36.06: 1499 36.06 - 54.10: 257 54.10 - 72.13: 35 72.13 - 90.16: 23 Dihedral angle restraints: 21513 sinusoidal: 8910 harmonic: 12603 Sorted by residual: dihedral pdb=" CB CYS B 291 " pdb=" SG CYS B 291 " pdb=" SG CYS B 301 " pdb=" CB CYS B 301 " ideal model delta sinusoidal sigma weight residual 93.00 -176.84 -90.16 1 1.00e+01 1.00e-02 9.63e+01 dihedral pdb=" CB CYS C 291 " pdb=" SG CYS C 291 " pdb=" SG CYS C 301 " pdb=" CB CYS C 301 " ideal model delta sinusoidal sigma weight residual 93.00 -177.35 -89.65 1 1.00e+01 1.00e-02 9.54e+01 dihedral pdb=" CB CYS A 291 " pdb=" SG CYS A 291 " pdb=" SG CYS A 301 " pdb=" CB CYS A 301 " ideal model delta sinusoidal sigma weight residual 93.00 -177.74 -89.26 1 1.00e+01 1.00e-02 9.48e+01 ... (remaining 21510 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 4463 0.056 - 0.112: 955 0.112 - 0.168: 119 0.168 - 0.224: 6 0.224 - 0.280: 1 Chirality restraints: 5544 Sorted by residual: chirality pdb=" C1 NAG O 1 " pdb=" ND2 ASN B 801 " pdb=" C2 NAG O 1 " pdb=" O5 NAG O 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.68 0.28 2.00e-01 2.50e+01 1.96e+00 chirality pdb=" C1 NAG C1301 " pdb=" ND2 ASN C 61 " pdb=" C2 NAG C1301 " pdb=" O5 NAG C1301 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" C1 NAG B1301 " pdb=" ND2 ASN B 61 " pdb=" C2 NAG B1301 " pdb=" O5 NAG B1301 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-01 2.50e+01 1.20e+00 ... (remaining 5541 not shown) Planarity restraints: 6102 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1301 " 0.172 2.00e-02 2.50e+03 1.42e-01 2.50e+02 pdb=" C7 NAG A1301 " -0.049 2.00e-02 2.50e+03 pdb=" C8 NAG A1301 " 0.127 2.00e-02 2.50e+03 pdb=" N2 NAG A1301 " -0.227 2.00e-02 2.50e+03 pdb=" O7 NAG A1301 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1301 " 0.172 2.00e-02 2.50e+03 1.42e-01 2.50e+02 pdb=" C7 NAG B1301 " -0.048 2.00e-02 2.50e+03 pdb=" C8 NAG B1301 " 0.127 2.00e-02 2.50e+03 pdb=" N2 NAG B1301 " -0.227 2.00e-02 2.50e+03 pdb=" O7 NAG B1301 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1301 " 0.162 2.00e-02 2.50e+03 1.34e-01 2.23e+02 pdb=" C7 NAG C1301 " -0.046 2.00e-02 2.50e+03 pdb=" C8 NAG C1301 " 0.120 2.00e-02 2.50e+03 pdb=" N2 NAG C1301 " -0.214 2.00e-02 2.50e+03 pdb=" O7 NAG C1301 " -0.023 2.00e-02 2.50e+03 ... (remaining 6099 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 7315 2.79 - 3.32: 28314 3.32 - 3.84: 55564 3.84 - 4.37: 60157 4.37 - 4.90: 109234 Nonbonded interactions: 260584 Sorted by model distance: nonbonded pdb=" OE1 GLN I 185 " pdb=" OG SER I 191 " model vdw 2.260 3.040 nonbonded pdb=" OD1 ASP A 215 " pdb=" OH TYR A 266 " model vdw 2.267 3.040 nonbonded pdb=" OE2 GLU C 298 " pdb=" OG SER C 316 " model vdw 2.283 3.040 nonbonded pdb=" OD1 ASP B 215 " pdb=" OH TYR B 266 " model vdw 2.300 3.040 nonbonded pdb=" OE1 GLN G 185 " pdb=" OG SER G 191 " model vdw 2.304 3.040 ... (remaining 260579 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.020 Extract box with map and model: 0.470 Check model and map are aligned: 0.120 Set scattering table: 0.090 Process input model: 36.350 Find NCS groups from input model: 0.780 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7028 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 35118 Z= 0.163 Angle : 0.616 13.431 47925 Z= 0.311 Chirality : 0.046 0.280 5544 Planarity : 0.006 0.142 6066 Dihedral : 12.564 89.166 13242 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 0.03 % Allowed : 0.56 % Favored : 99.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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 aren not related in a simple way. whole: -0.56 (0.12), residues: 4254 helix: 0.65 (0.18), residues: 679 sheet: 0.73 (0.15), residues: 1142 loop : -1.27 (0.11), residues: 2433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 466 TYR 0.030 0.001 TYR D 50 PHE 0.022 0.001 PHE C 497 TRP 0.013 0.001 TRP H 111 HIS 0.002 0.000 HIS G 214 Details of bonding type rmsd covalent geometry : bond 0.00317 (35019) covalent geometry : angle 0.60737 (47679) SS BOND : bond 0.00236 ( 51) SS BOND : angle 0.77939 ( 102) hydrogen bonds : bond 0.24750 ( 1173) hydrogen bonds : angle 8.89453 ( 3501) link_BETA1-4 : bond 0.00607 ( 12) link_BETA1-4 : angle 1.13357 ( 36) link_NAG-ASN : bond 0.00408 ( 36) link_NAG-ASN : angle 2.16255 ( 108) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8508 Ramachandran restraints generated. 4254 Oldfield, 0 Emsley, 4254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8508 Ramachandran restraints generated. 4254 Oldfield, 0 Emsley, 4254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 3774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 388 time to evaluate : 1.271 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 265 TYR cc_start: 0.7515 (p90) cc_final: 0.6531 (p90) REVERT: B 699 LEU cc_start: 0.7732 (mm) cc_final: 0.7480 (mm) REVERT: B 998 THR cc_start: 0.7040 (m) cc_final: 0.6556 (p) REVERT: C 33 THR cc_start: 0.7375 (p) cc_final: 0.6988 (p) REVERT: C 314 GLN cc_start: 0.7917 (mt0) cc_final: 0.7487 (tt0) REVERT: C 495 TYR cc_start: 0.6811 (p90) cc_final: 0.6402 (p90) REVERT: C 767 LEU cc_start: 0.7371 (mt) cc_final: 0.6926 (mt) REVERT: I 119 GLN cc_start: 0.7581 (pp30) cc_final: 0.7316 (pp30) outliers start: 1 outliers final: 0 residues processed: 389 average time/residue: 0.2174 time to fit residues: 140.6796 Evaluate side-chains 284 residues out of total 3774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 284 time to evaluate : 1.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 197 optimal weight: 0.9990 chunk 388 optimal weight: 0.5980 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 4.9990 chunk 401 optimal weight: 7.9990 chunk 424 optimal weight: 40.0000 chunk 155 optimal weight: 6.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1036 GLN H 185 GLN B 317 ASN B 563 GLN ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 185 GLN ** E 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 32 ASN C 563 GLN C 777 ASN C1135 ASN ** I 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 199 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.199685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.163951 restraints weight = 43306.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.159232 restraints weight = 46931.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.160091 restraints weight = 47163.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.161065 restraints weight = 36146.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.161530 restraints weight = 28829.675| |-----------------------------------------------------------------------------| r_work (final): 0.3828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.1975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 35118 Z= 0.202 Angle : 0.593 9.296 47925 Z= 0.306 Chirality : 0.046 0.206 5544 Planarity : 0.004 0.044 6066 Dihedral : 5.150 57.962 5628 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 0.99 % Allowed : 7.00 % Favored : 92.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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 aren not related in a simple way. whole: -0.21 (0.12), residues: 4254 helix: 1.14 (0.19), residues: 681 sheet: 0.71 (0.14), residues: 1207 loop : -1.01 (0.12), residues: 2366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 457 TYR 0.029 0.002 TYR B 266 PHE 0.025 0.002 PHE C 86 TRP 0.016 0.002 TRP G 50 HIS 0.005 0.001 HIS C1058 Details of bonding type rmsd covalent geometry : bond 0.00472 (35019) covalent geometry : angle 0.58412 (47679) SS BOND : bond 0.00471 ( 51) SS BOND : angle 1.47909 ( 102) hydrogen bonds : bond 0.04797 ( 1173) hydrogen bonds : angle 5.94385 ( 3501) link_BETA1-4 : bond 0.00711 ( 12) link_BETA1-4 : angle 1.00010 ( 36) link_NAG-ASN : bond 0.00448 ( 36) link_NAG-ASN : angle 1.79206 ( 108) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8508 Ramachandran restraints generated. 4254 Oldfield, 0 Emsley, 4254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8508 Ramachandran restraints generated. 4254 Oldfield, 0 Emsley, 4254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 3774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 318 time to evaluate : 1.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 378 LYS cc_start: 0.7824 (tmmt) cc_final: 0.7221 (ptpt) REVERT: A 440 LYS cc_start: 0.7994 (mptt) cc_final: 0.7789 (mmtt) REVERT: A 775 ASP cc_start: 0.6913 (t0) cc_final: 0.6448 (m-30) REVERT: A 1122 VAL cc_start: 0.8632 (t) cc_final: 0.8290 (p) REVERT: D 50 TYR cc_start: 0.7634 (p90) cc_final: 0.7166 (p90) REVERT: B 153 MET cc_start: 0.4336 (mmm) cc_final: 0.3619 (mpp) REVERT: B 205 SER cc_start: 0.8765 (m) cc_final: 0.8414 (p) REVERT: B 1077 THR cc_start: 0.9120 (t) cc_final: 0.8837 (t) REVERT: C 814 LYS cc_start: 0.7750 (mmmt) cc_final: 0.7547 (mmtm) REVERT: C 902 MET cc_start: 0.8573 (mmm) cc_final: 0.8292 (tpt) REVERT: C 1029 MET cc_start: 0.8978 (tpp) cc_final: 0.8191 (ttm) REVERT: I 119 GLN cc_start: 0.7605 (pp30) cc_final: 0.7342 (pp30) REVERT: F 29 ILE cc_start: 0.5957 (mm) cc_final: 0.5734 (mm) outliers start: 37 outliers final: 25 residues processed: 347 average time/residue: 0.2298 time to fit residues: 129.9098 Evaluate side-chains 297 residues out of total 3774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 272 time to evaluate : 1.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 660 TYR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 660 TYR Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1051 SER Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 186 optimal weight: 0.0770 chunk 382 optimal weight: 6.9990 chunk 101 optimal weight: 0.9980 chunk 414 optimal weight: 9.9990 chunk 386 optimal weight: 0.9980 chunk 50 optimal weight: 5.9990 chunk 207 optimal weight: 3.9990 chunk 247 optimal weight: 10.0000 chunk 371 optimal weight: 2.9990 chunk 110 optimal weight: 5.9990 chunk 304 optimal weight: 4.9990 overall best weight: 1.8142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 563 GLN ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1011 GLN B 360 ASN B 563 GLN E 32 ASN C 563 GLN ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.193056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.154571 restraints weight = 42710.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.149528 restraints weight = 46795.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.149990 restraints weight = 48568.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.150880 restraints weight = 35801.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.152643 restraints weight = 29503.873| |-----------------------------------------------------------------------------| r_work (final): 0.3685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.2919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 35118 Z= 0.181 Angle : 0.552 7.712 47925 Z= 0.283 Chirality : 0.045 0.181 5544 Planarity : 0.004 0.042 6066 Dihedral : 4.611 51.255 5628 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.86 % Allowed : 9.29 % Favored : 88.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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 aren not related in a simple way. whole: -0.17 (0.12), residues: 4254 helix: 1.43 (0.20), residues: 681 sheet: 0.60 (0.14), residues: 1224 loop : -0.99 (0.12), residues: 2349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 995 TYR 0.028 0.001 TYR A 495 PHE 0.024 0.002 PHE A 800 TRP 0.018 0.002 TRP H 50 HIS 0.005 0.001 HIS C1058 Details of bonding type rmsd covalent geometry : bond 0.00434 (35019) covalent geometry : angle 0.54118 (47679) SS BOND : bond 0.00514 ( 51) SS BOND : angle 1.73909 ( 102) hydrogen bonds : bond 0.04788 ( 1173) hydrogen bonds : angle 5.35601 ( 3501) link_BETA1-4 : bond 0.00442 ( 12) link_BETA1-4 : angle 1.01338 ( 36) link_NAG-ASN : bond 0.00303 ( 36) link_NAG-ASN : angle 1.63188 ( 108) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8508 Ramachandran restraints generated. 4254 Oldfield, 0 Emsley, 4254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8508 Ramachandran restraints generated. 4254 Oldfield, 0 Emsley, 4254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 3774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 279 time to evaluate : 1.326 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 405 ASP cc_start: 0.7674 (m-30) cc_final: 0.7225 (m-30) REVERT: A 569 ILE cc_start: 0.7741 (mp) cc_final: 0.7215 (tt) REVERT: A 699 LEU cc_start: 0.8395 (OUTLIER) cc_final: 0.7957 (mm) REVERT: A 775 ASP cc_start: 0.6942 (t0) cc_final: 0.6509 (m-30) REVERT: D 50 TYR cc_start: 0.7895 (p90) cc_final: 0.7367 (p90) REVERT: B 153 MET cc_start: 0.3994 (mmm) cc_final: 0.3352 (mpp) REVERT: B 205 SER cc_start: 0.8801 (m) cc_final: 0.8541 (p) REVERT: B 360 ASN cc_start: 0.7904 (m-40) cc_final: 0.7562 (t0) REVERT: B 405 ASP cc_start: 0.7637 (m-30) cc_final: 0.7373 (m-30) REVERT: B 441 LEU cc_start: 0.8609 (OUTLIER) cc_final: 0.8303 (mt) REVERT: B 453 TYR cc_start: 0.8063 (p90) cc_final: 0.7828 (p90) REVERT: B 775 ASP cc_start: 0.6872 (t0) cc_final: 0.6635 (m-30) REVERT: B 1077 THR cc_start: 0.9328 (t) cc_final: 0.9028 (t) REVERT: E 50 TYR cc_start: 0.7873 (p90) cc_final: 0.7563 (p90) REVERT: E 86 ASP cc_start: 0.8271 (OUTLIER) cc_final: 0.7899 (p0) REVERT: C 205 SER cc_start: 0.8987 (m) cc_final: 0.8697 (p) REVERT: C 378 LYS cc_start: 0.8009 (OUTLIER) cc_final: 0.7609 (pttm) REVERT: C 405 ASP cc_start: 0.7346 (m-30) cc_final: 0.7099 (m-30) REVERT: C 814 LYS cc_start: 0.7832 (mmmt) cc_final: 0.7615 (mmtm) REVERT: C 902 MET cc_start: 0.8620 (mmm) cc_final: 0.8203 (tpt) REVERT: C 1029 MET cc_start: 0.8959 (tpp) cc_final: 0.8201 (ttm) REVERT: F 29 ILE cc_start: 0.6680 (mm) cc_final: 0.6449 (mm) outliers start: 70 outliers final: 45 residues processed: 330 average time/residue: 0.2320 time to fit residues: 124.2856 Evaluate side-chains 292 residues out of total 3774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 243 time to evaluate : 1.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 563 GLN Chi-restraints excluded: chain A residue 660 TYR Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 64 TRP Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 563 GLN Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 660 TYR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1051 SER Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain E residue 86 ASP Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 563 GLN Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1068 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 77 optimal weight: 0.5980 chunk 105 optimal weight: 7.9990 chunk 218 optimal weight: 0.7980 chunk 170 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 76 optimal weight: 0.6980 chunk 334 optimal weight: 0.6980 chunk 159 optimal weight: 6.9990 chunk 293 optimal weight: 5.9990 chunk 308 optimal weight: 0.0570 chunk 355 optimal weight: 0.0370 overall best weight: 0.4176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN A 563 GLN D 99 HIS B 563 GLN B 777 ASN ** E 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 563 GLN C 914 ASN I 106 ASN ** F 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.195992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.155796 restraints weight = 42444.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.150663 restraints weight = 51402.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.153441 restraints weight = 64513.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.154504 restraints weight = 37124.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.158544 restraints weight = 29949.488| |-----------------------------------------------------------------------------| r_work (final): 0.3731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.2975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 35118 Z= 0.093 Angle : 0.482 7.249 47925 Z= 0.245 Chirality : 0.042 0.176 5544 Planarity : 0.003 0.041 6066 Dihedral : 4.188 47.137 5628 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.30 % Allowed : 11.18 % Favored : 87.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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 aren not related in a simple way. whole: 0.10 (0.13), residues: 4254 helix: 1.91 (0.20), residues: 693 sheet: 0.67 (0.14), residues: 1220 loop : -0.86 (0.12), residues: 2341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 237 TYR 0.019 0.001 TYR C 265 PHE 0.012 0.001 PHE C 92 TRP 0.011 0.001 TRP B 64 HIS 0.002 0.000 HIS D 199 Details of bonding type rmsd covalent geometry : bond 0.00205 (35019) covalent geometry : angle 0.47439 (47679) SS BOND : bond 0.00413 ( 51) SS BOND : angle 1.27837 ( 102) hydrogen bonds : bond 0.03709 ( 1173) hydrogen bonds : angle 5.01722 ( 3501) link_BETA1-4 : bond 0.00449 ( 12) link_BETA1-4 : angle 0.93998 ( 36) link_NAG-ASN : bond 0.00296 ( 36) link_NAG-ASN : angle 1.40358 ( 108) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8508 Ramachandran restraints generated. 4254 Oldfield, 0 Emsley, 4254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8508 Ramachandran restraints generated. 4254 Oldfield, 0 Emsley, 4254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 3774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 268 time to evaluate : 1.304 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 133 PHE cc_start: 0.6671 (m-80) cc_final: 0.6355 (m-80) REVERT: A 405 ASP cc_start: 0.7519 (m-30) cc_final: 0.7232 (m-30) REVERT: A 569 ILE cc_start: 0.7686 (mp) cc_final: 0.7219 (tt) REVERT: A 699 LEU cc_start: 0.8394 (OUTLIER) cc_final: 0.7918 (mm) REVERT: A 775 ASP cc_start: 0.6943 (t0) cc_final: 0.6473 (m-30) REVERT: D 50 TYR cc_start: 0.7841 (p90) cc_final: 0.7092 (p90) REVERT: B 205 SER cc_start: 0.8828 (m) cc_final: 0.8584 (p) REVERT: B 360 ASN cc_start: 0.7799 (m-40) cc_final: 0.7534 (t0) REVERT: B 405 ASP cc_start: 0.7538 (m-30) cc_final: 0.7258 (m-30) REVERT: B 1077 THR cc_start: 0.9287 (t) cc_final: 0.8868 (t) REVERT: G 13 LYS cc_start: 0.5976 (tptp) cc_final: 0.5519 (tppt) REVERT: G 87 ARG cc_start: 0.7368 (mtp-110) cc_final: 0.7113 (mtp85) REVERT: C 205 SER cc_start: 0.8965 (m) cc_final: 0.8714 (p) REVERT: C 378 LYS cc_start: 0.7748 (OUTLIER) cc_final: 0.7390 (pttm) REVERT: C 902 MET cc_start: 0.8575 (mmm) cc_final: 0.8265 (tpt) REVERT: C 1029 MET cc_start: 0.9080 (tpp) cc_final: 0.8324 (ttm) REVERT: F 29 ILE cc_start: 0.6538 (mm) cc_final: 0.6273 (mm) outliers start: 49 outliers final: 33 residues processed: 302 average time/residue: 0.2310 time to fit residues: 113.6758 Evaluate side-chains 275 residues out of total 3774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 240 time to evaluate : 1.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 660 TYR Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 64 TRP Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 660 TYR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 563 GLN Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 137 optimal weight: 30.0000 chunk 274 optimal weight: 8.9990 chunk 249 optimal weight: 7.9990 chunk 247 optimal weight: 7.9990 chunk 49 optimal weight: 6.9990 chunk 16 optimal weight: 1.9990 chunk 298 optimal weight: 8.9990 chunk 285 optimal weight: 20.0000 chunk 76 optimal weight: 1.9990 chunk 120 optimal weight: 3.9990 chunk 371 optimal weight: 3.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN A 317 ASN A 563 GLN ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 907 ASN A 926 GLN A1048 HIS H 185 GLN B 87 ASN B 563 GLN B 777 ASN B 926 GLN G 106 ASN E 199 HIS C1106 GLN F 28 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.183490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.142956 restraints weight = 43159.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.138136 restraints weight = 46514.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.139401 restraints weight = 70952.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.140796 restraints weight = 39882.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.144349 restraints weight = 28959.769| |-----------------------------------------------------------------------------| r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.4132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.134 35118 Z= 0.345 Angle : 0.724 10.175 47925 Z= 0.373 Chirality : 0.050 0.210 5544 Planarity : 0.005 0.051 6066 Dihedral : 5.072 59.406 5628 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.65 % Favored : 95.28 % Rotamer: Outliers : 2.74 % Allowed : 11.71 % Favored : 85.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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 aren not related in a simple way. whole: -0.62 (0.12), residues: 4254 helix: 0.58 (0.19), residues: 720 sheet: 0.29 (0.14), residues: 1235 loop : -1.14 (0.12), residues: 2299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 357 TYR 0.046 0.002 TYR A 495 PHE 0.041 0.003 PHE C 86 TRP 0.029 0.002 TRP H 50 HIS 0.011 0.002 HIS B1058 Details of bonding type rmsd covalent geometry : bond 0.00839 (35019) covalent geometry : angle 0.71111 (47679) SS BOND : bond 0.00760 ( 51) SS BOND : angle 2.10232 ( 102) hydrogen bonds : bond 0.06070 ( 1173) hydrogen bonds : angle 5.44895 ( 3501) link_BETA1-4 : bond 0.00408 ( 12) link_BETA1-4 : angle 1.01054 ( 36) link_NAG-ASN : bond 0.00409 ( 36) link_NAG-ASN : angle 2.15669 ( 108) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8508 Ramachandran restraints generated. 4254 Oldfield, 0 Emsley, 4254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8508 Ramachandran restraints generated. 4254 Oldfield, 0 Emsley, 4254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 3774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 263 time to evaluate : 1.236 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 405 ASP cc_start: 0.7720 (m-30) cc_final: 0.7455 (m-30) REVERT: A 699 LEU cc_start: 0.8937 (OUTLIER) cc_final: 0.8524 (mm) REVERT: A 775 ASP cc_start: 0.7444 (t0) cc_final: 0.6964 (m-30) REVERT: D 38 GLN cc_start: 0.8247 (pp30) cc_final: 0.7291 (pp30) REVERT: D 50 TYR cc_start: 0.8040 (p90) cc_final: 0.7546 (p90) REVERT: B 153 MET cc_start: 0.3908 (mmm) cc_final: 0.3392 (mpp) REVERT: B 205 SER cc_start: 0.8946 (m) cc_final: 0.8695 (p) REVERT: B 360 ASN cc_start: 0.7935 (m-40) cc_final: 0.7614 (t0) REVERT: B 405 ASP cc_start: 0.7749 (m-30) cc_final: 0.7450 (m-30) REVERT: B 501 TYR cc_start: 0.8040 (m-10) cc_final: 0.7825 (m-10) REVERT: B 767 LEU cc_start: 0.8705 (OUTLIER) cc_final: 0.8434 (mt) REVERT: B 934 ILE cc_start: 0.8298 (tp) cc_final: 0.8018 (tp) REVERT: B 1077 THR cc_start: 0.9422 (t) cc_final: 0.9210 (m) REVERT: E 38 GLN cc_start: 0.7888 (pp30) cc_final: 0.7005 (pp30) REVERT: E 50 TYR cc_start: 0.7847 (p90) cc_final: 0.7637 (p90) REVERT: E 86 ASP cc_start: 0.8308 (p0) cc_final: 0.8030 (p0) REVERT: C 205 SER cc_start: 0.8998 (m) cc_final: 0.8781 (p) REVERT: C 378 LYS cc_start: 0.8015 (OUTLIER) cc_final: 0.7720 (pttm) REVERT: C 405 ASP cc_start: 0.7809 (m-30) cc_final: 0.7444 (m-30) REVERT: C 646 ARG cc_start: 0.7266 (mtp180) cc_final: 0.7011 (mtm-85) REVERT: C 775 ASP cc_start: 0.7329 (OUTLIER) cc_final: 0.6900 (m-30) REVERT: C 902 MET cc_start: 0.8669 (mmm) cc_final: 0.8395 (tpt) REVERT: C 965 GLN cc_start: 0.8210 (tt0) cc_final: 0.7947 (tt0) REVERT: C 988 GLU cc_start: 0.6132 (OUTLIER) cc_final: 0.4981 (mt-10) REVERT: C 1029 MET cc_start: 0.9109 (tpp) cc_final: 0.8293 (ttm) outliers start: 103 outliers final: 77 residues processed: 348 average time/residue: 0.2209 time to fit residues: 125.8865 Evaluate side-chains 308 residues out of total 3774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 226 time to evaluate : 1.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 660 TYR Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain B residue 64 TRP Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 660 TYR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain C residue 64 TRP Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 775 ASP Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 914 ASN Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain C residue 1068 VAL Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain I residue 51 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 42 optimal weight: 0.8980 chunk 280 optimal weight: 50.0000 chunk 339 optimal weight: 1.9990 chunk 394 optimal weight: 3.9990 chunk 329 optimal weight: 2.9990 chunk 111 optimal weight: 0.7980 chunk 229 optimal weight: 2.9990 chunk 77 optimal weight: 0.5980 chunk 202 optimal weight: 0.5980 chunk 306 optimal weight: 0.9990 chunk 430 optimal weight: 6.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 563 GLN A 907 ASN A 919 ASN H 106 ASN B 87 ASN B 563 GLN C 907 ASN ** F 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.189683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.151492 restraints weight = 42321.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.145276 restraints weight = 47713.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.146334 restraints weight = 55219.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.147105 restraints weight = 42885.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.149259 restraints weight = 30493.466| |-----------------------------------------------------------------------------| r_work (final): 0.3645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.4000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 35118 Z= 0.112 Angle : 0.519 7.735 47925 Z= 0.264 Chirality : 0.043 0.224 5544 Planarity : 0.003 0.045 6066 Dihedral : 4.523 58.052 5628 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.16 % Allowed : 13.31 % Favored : 84.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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 aren not related in a simple way. whole: -0.24 (0.13), residues: 4254 helix: 1.34 (0.20), residues: 729 sheet: 0.43 (0.14), residues: 1235 loop : -1.00 (0.12), residues: 2290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 357 TYR 0.021 0.001 TYR A 495 PHE 0.018 0.001 PHE A 86 TRP 0.013 0.001 TRP B 64 HIS 0.002 0.001 HIS G 35 Details of bonding type rmsd covalent geometry : bond 0.00256 (35019) covalent geometry : angle 0.50770 (47679) SS BOND : bond 0.00459 ( 51) SS BOND : angle 1.53861 ( 102) hydrogen bonds : bond 0.04137 ( 1173) hydrogen bonds : angle 4.95586 ( 3501) link_BETA1-4 : bond 0.00468 ( 12) link_BETA1-4 : angle 0.92286 ( 36) link_NAG-ASN : bond 0.00275 ( 36) link_NAG-ASN : angle 1.73101 ( 108) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8508 Ramachandran restraints generated. 4254 Oldfield, 0 Emsley, 4254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8508 Ramachandran restraints generated. 4254 Oldfield, 0 Emsley, 4254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 3774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 243 time to evaluate : 1.518 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 392 PHE cc_start: 0.8745 (OUTLIER) cc_final: 0.8463 (m-80) REVERT: A 405 ASP cc_start: 0.7739 (m-30) cc_final: 0.7518 (m-30) REVERT: A 699 LEU cc_start: 0.8894 (OUTLIER) cc_final: 0.8383 (mm) REVERT: A 775 ASP cc_start: 0.7116 (t0) cc_final: 0.6714 (m-30) REVERT: B 205 SER cc_start: 0.8919 (m) cc_final: 0.8688 (p) REVERT: B 360 ASN cc_start: 0.7900 (m-40) cc_final: 0.7599 (t0) REVERT: B 405 ASP cc_start: 0.7599 (m-30) cc_final: 0.7323 (m-30) REVERT: B 472 ILE cc_start: 0.7691 (pt) cc_final: 0.7398 (pt) REVERT: B 501 TYR cc_start: 0.7938 (m-10) cc_final: 0.7649 (m-10) REVERT: B 934 ILE cc_start: 0.7922 (tp) cc_final: 0.7688 (tp) REVERT: G 87 ARG cc_start: 0.7449 (mtp-110) cc_final: 0.7123 (mtp85) REVERT: E 86 ASP cc_start: 0.8302 (p0) cc_final: 0.7916 (p0) REVERT: C 378 LYS cc_start: 0.7737 (OUTLIER) cc_final: 0.7485 (pttm) REVERT: C 405 ASP cc_start: 0.7669 (m-30) cc_final: 0.7333 (m-30) REVERT: C 495 TYR cc_start: 0.7977 (OUTLIER) cc_final: 0.7305 (p90) REVERT: C 642 VAL cc_start: 0.8663 (t) cc_final: 0.8233 (p) REVERT: C 902 MET cc_start: 0.8363 (mmm) cc_final: 0.8084 (tpt) REVERT: C 965 GLN cc_start: 0.8072 (tt0) cc_final: 0.7855 (tt0) REVERT: C 1029 MET cc_start: 0.9073 (tpp) cc_final: 0.8477 (ttm) REVERT: C 1050 MET cc_start: 0.8277 (ptm) cc_final: 0.7714 (ptt) REVERT: F 29 ILE cc_start: 0.7165 (mm) cc_final: 0.6903 (mm) outliers start: 81 outliers final: 57 residues processed: 310 average time/residue: 0.2208 time to fit residues: 112.1908 Evaluate side-chains 281 residues out of total 3774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 220 time to evaluate : 1.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 563 GLN Chi-restraints excluded: chain A residue 660 TYR Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 907 ASN Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain H residue 64 PHE Chi-restraints excluded: chain B residue 64 TRP Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 563 GLN Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 660 TYR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 975 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1051 SER Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 64 PHE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 443 SER Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 756 TYR Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain F residue 49 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 237 optimal weight: 3.9990 chunk 201 optimal weight: 0.2980 chunk 53 optimal weight: 5.9990 chunk 369 optimal weight: 2.9990 chunk 273 optimal weight: 0.7980 chunk 159 optimal weight: 4.9990 chunk 282 optimal weight: 40.0000 chunk 188 optimal weight: 8.9990 chunk 260 optimal weight: 10.0000 chunk 368 optimal weight: 0.0070 chunk 186 optimal weight: 2.9990 overall best weight: 1.4202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 563 GLN ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 907 ASN B 87 ASN B 563 GLN C 907 ASN ** F 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.188138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.150089 restraints weight = 42583.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.143703 restraints weight = 50927.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.145051 restraints weight = 51523.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.145410 restraints weight = 45040.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.146202 restraints weight = 32461.988| |-----------------------------------------------------------------------------| r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.4112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 35118 Z= 0.149 Angle : 0.533 7.684 47925 Z= 0.270 Chirality : 0.044 0.186 5544 Planarity : 0.004 0.044 6066 Dihedral : 4.402 51.776 5628 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.40 % Allowed : 13.26 % Favored : 84.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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 aren not related in a simple way. whole: -0.21 (0.13), residues: 4254 helix: 1.28 (0.20), residues: 732 sheet: 0.48 (0.14), residues: 1227 loop : -0.98 (0.12), residues: 2295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 237 TYR 0.019 0.001 TYR A 453 PHE 0.015 0.001 PHE A 86 TRP 0.012 0.001 TRP B 64 HIS 0.004 0.001 HIS B1058 Details of bonding type rmsd covalent geometry : bond 0.00361 (35019) covalent geometry : angle 0.51986 (47679) SS BOND : bond 0.00436 ( 51) SS BOND : angle 1.94267 ( 102) hydrogen bonds : bond 0.04267 ( 1173) hydrogen bonds : angle 4.88218 ( 3501) link_BETA1-4 : bond 0.00402 ( 12) link_BETA1-4 : angle 0.89301 ( 36) link_NAG-ASN : bond 0.00216 ( 36) link_NAG-ASN : angle 1.72121 ( 108) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8508 Ramachandran restraints generated. 4254 Oldfield, 0 Emsley, 4254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8508 Ramachandran restraints generated. 4254 Oldfield, 0 Emsley, 4254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 3774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 230 time to evaluate : 1.089 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 378 LYS cc_start: 0.8173 (OUTLIER) cc_final: 0.7676 (ptpt) REVERT: A 405 ASP cc_start: 0.7800 (m-30) cc_final: 0.7569 (m-30) REVERT: A 699 LEU cc_start: 0.8926 (OUTLIER) cc_final: 0.8447 (mm) REVERT: A 775 ASP cc_start: 0.7140 (t0) cc_final: 0.6715 (m-30) REVERT: B 205 SER cc_start: 0.8914 (m) cc_final: 0.8693 (p) REVERT: B 360 ASN cc_start: 0.7884 (m-40) cc_final: 0.7610 (t0) REVERT: B 405 ASP cc_start: 0.7777 (m-30) cc_final: 0.7477 (m-30) REVERT: B 934 ILE cc_start: 0.7951 (tp) cc_final: 0.7714 (tp) REVERT: G 87 ARG cc_start: 0.7417 (mtp-110) cc_final: 0.7170 (mtp85) REVERT: E 38 GLN cc_start: 0.7916 (pp30) cc_final: 0.7096 (pp30) REVERT: E 50 TYR cc_start: 0.7950 (p90) cc_final: 0.7595 (p90) REVERT: E 86 ASP cc_start: 0.8265 (OUTLIER) cc_final: 0.7888 (p0) REVERT: C 378 LYS cc_start: 0.7679 (OUTLIER) cc_final: 0.7439 (pttm) REVERT: C 405 ASP cc_start: 0.7768 (m-30) cc_final: 0.7406 (m-30) REVERT: C 495 TYR cc_start: 0.8096 (OUTLIER) cc_final: 0.7394 (p90) REVERT: C 902 MET cc_start: 0.8480 (mmm) cc_final: 0.8220 (tpt) REVERT: C 965 GLN cc_start: 0.8109 (tt0) cc_final: 0.7883 (tt0) REVERT: C 1029 MET cc_start: 0.9120 (tpp) cc_final: 0.8288 (ttm) REVERT: C 1050 MET cc_start: 0.8497 (ptm) cc_final: 0.8129 (ptt) REVERT: F 29 ILE cc_start: 0.7200 (mm) cc_final: 0.6919 (mm) outliers start: 90 outliers final: 70 residues processed: 304 average time/residue: 0.2006 time to fit residues: 99.9100 Evaluate side-chains 294 residues out of total 3774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 219 time to evaluate : 1.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 563 GLN Chi-restraints excluded: chain A residue 660 TYR Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain B residue 64 TRP Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 660 TYR Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 975 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1051 SER Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 64 PHE Chi-restraints excluded: chain E residue 86 ASP Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 443 SER Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain F residue 49 ILE Chi-restraints excluded: chain F residue 89 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 35 optimal weight: 0.8980 chunk 329 optimal weight: 5.9990 chunk 45 optimal weight: 3.9990 chunk 157 optimal weight: 0.9980 chunk 397 optimal weight: 30.0000 chunk 90 optimal weight: 3.9990 chunk 42 optimal weight: 0.8980 chunk 313 optimal weight: 0.3980 chunk 203 optimal weight: 4.9990 chunk 113 optimal weight: 7.9990 chunk 175 optimal weight: 2.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 563 GLN ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 907 ASN A 914 ASN B 87 ASN B 563 GLN ** E 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.188515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.150592 restraints weight = 42547.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.143842 restraints weight = 47423.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.144598 restraints weight = 52769.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.146346 restraints weight = 35664.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.146680 restraints weight = 29258.612| |-----------------------------------------------------------------------------| r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.4168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 35118 Z= 0.135 Angle : 0.523 7.338 47925 Z= 0.264 Chirality : 0.043 0.253 5544 Planarity : 0.004 0.044 6066 Dihedral : 4.286 44.909 5628 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.26 % Allowed : 13.82 % Favored : 83.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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 aren not related in a simple way. whole: -0.15 (0.13), residues: 4254 helix: 1.35 (0.20), residues: 732 sheet: 0.55 (0.14), residues: 1218 loop : -0.96 (0.12), residues: 2304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 237 TYR 0.018 0.001 TYR A 453 PHE 0.013 0.001 PHE A 400 TRP 0.012 0.001 TRP B 64 HIS 0.003 0.001 HIS C1088 Details of bonding type rmsd covalent geometry : bond 0.00325 (35019) covalent geometry : angle 0.51006 (47679) SS BOND : bond 0.00449 ( 51) SS BOND : angle 1.82217 ( 102) hydrogen bonds : bond 0.04106 ( 1173) hydrogen bonds : angle 4.80728 ( 3501) link_BETA1-4 : bond 0.00409 ( 12) link_BETA1-4 : angle 0.88224 ( 36) link_NAG-ASN : bond 0.00208 ( 36) link_NAG-ASN : angle 1.71822 ( 108) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8508 Ramachandran restraints generated. 4254 Oldfield, 0 Emsley, 4254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8508 Ramachandran restraints generated. 4254 Oldfield, 0 Emsley, 4254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 3774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 234 time to evaluate : 0.935 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 378 LYS cc_start: 0.8092 (OUTLIER) cc_final: 0.7637 (ptpt) REVERT: A 405 ASP cc_start: 0.7786 (m-30) cc_final: 0.7511 (m-30) REVERT: A 699 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8454 (mm) REVERT: A 775 ASP cc_start: 0.7117 (t0) cc_final: 0.6716 (m-30) REVERT: D 20 ILE cc_start: 0.5969 (mt) cc_final: 0.5764 (mt) REVERT: D 38 GLN cc_start: 0.8276 (pp30) cc_final: 0.7918 (pt0) REVERT: B 205 SER cc_start: 0.8913 (m) cc_final: 0.8699 (p) REVERT: B 360 ASN cc_start: 0.7858 (m-40) cc_final: 0.7593 (t0) REVERT: B 405 ASP cc_start: 0.7761 (m-30) cc_final: 0.7484 (m-30) REVERT: B 900 MET cc_start: 0.8574 (OUTLIER) cc_final: 0.8229 (mtp) REVERT: B 934 ILE cc_start: 0.7931 (tp) cc_final: 0.7694 (tp) REVERT: G 87 ARG cc_start: 0.7429 (mtp-110) cc_final: 0.7185 (mtp85) REVERT: E 28 ASN cc_start: 0.8356 (t0) cc_final: 0.7987 (t0) REVERT: E 38 GLN cc_start: 0.7946 (pp30) cc_final: 0.7143 (pp30) REVERT: E 50 TYR cc_start: 0.7862 (p90) cc_final: 0.7511 (p90) REVERT: E 86 ASP cc_start: 0.8229 (OUTLIER) cc_final: 0.7864 (p0) REVERT: C 378 LYS cc_start: 0.7639 (OUTLIER) cc_final: 0.7385 (pttm) REVERT: C 405 ASP cc_start: 0.7804 (m-30) cc_final: 0.7423 (m-30) REVERT: C 495 TYR cc_start: 0.8070 (OUTLIER) cc_final: 0.7337 (p90) REVERT: C 902 MET cc_start: 0.8430 (mmm) cc_final: 0.8177 (tpt) REVERT: C 965 GLN cc_start: 0.8079 (tt0) cc_final: 0.7864 (tt0) REVERT: C 1029 MET cc_start: 0.9118 (tpp) cc_final: 0.8296 (ttm) REVERT: C 1050 MET cc_start: 0.8444 (ptm) cc_final: 0.8173 (ptt) REVERT: F 29 ILE cc_start: 0.7213 (mm) cc_final: 0.6931 (mm) outliers start: 85 outliers final: 70 residues processed: 302 average time/residue: 0.1943 time to fit residues: 94.6717 Evaluate side-chains 296 residues out of total 3774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 220 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 563 GLN Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 660 TYR Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain B residue 64 TRP Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 563 GLN Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 660 TYR Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 975 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1051 SER Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain E residue 86 ASP Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain F residue 49 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 121 optimal weight: 8.9990 chunk 377 optimal weight: 0.8980 chunk 365 optimal weight: 0.6980 chunk 81 optimal weight: 0.7980 chunk 200 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 187 optimal weight: 0.3980 chunk 116 optimal weight: 5.9990 chunk 178 optimal weight: 0.9980 chunk 426 optimal weight: 20.0000 chunk 323 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 563 GLN ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 907 ASN B 87 ASN B 563 GLN B 914 ASN ** E 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.189800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.152303 restraints weight = 42498.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.145509 restraints weight = 49320.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.146247 restraints weight = 52711.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.147841 restraints weight = 36040.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.149024 restraints weight = 28384.410| |-----------------------------------------------------------------------------| r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.4162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 35118 Z= 0.107 Angle : 0.509 9.576 47925 Z= 0.257 Chirality : 0.043 0.225 5544 Planarity : 0.003 0.048 6066 Dihedral : 4.151 38.293 5628 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.32 % Allowed : 13.90 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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 aren not related in a simple way. whole: -0.08 (0.13), residues: 4254 helix: 1.53 (0.20), residues: 729 sheet: 0.59 (0.14), residues: 1212 loop : -0.95 (0.12), residues: 2313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 237 TYR 0.021 0.001 TYR A 453 PHE 0.013 0.001 PHE A 400 TRP 0.011 0.001 TRP B 64 HIS 0.002 0.000 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00251 (35019) covalent geometry : angle 0.49672 (47679) SS BOND : bond 0.00403 ( 51) SS BOND : angle 1.79530 ( 102) hydrogen bonds : bond 0.03844 ( 1173) hydrogen bonds : angle 4.71634 ( 3501) link_BETA1-4 : bond 0.00475 ( 12) link_BETA1-4 : angle 0.90453 ( 36) link_NAG-ASN : bond 0.00219 ( 36) link_NAG-ASN : angle 1.69768 ( 108) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8508 Ramachandran restraints generated. 4254 Oldfield, 0 Emsley, 4254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8508 Ramachandran restraints generated. 4254 Oldfield, 0 Emsley, 4254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 3774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 234 time to evaluate : 0.814 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 378 LYS cc_start: 0.8071 (OUTLIER) cc_final: 0.7644 (ptpt) REVERT: A 392 PHE cc_start: 0.8772 (OUTLIER) cc_final: 0.8466 (m-80) REVERT: A 405 ASP cc_start: 0.7853 (m-30) cc_final: 0.7585 (m-30) REVERT: A 452 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.8539 (mt) REVERT: A 699 LEU cc_start: 0.8942 (OUTLIER) cc_final: 0.8480 (mm) REVERT: A 767 LEU cc_start: 0.8161 (OUTLIER) cc_final: 0.7897 (mm) REVERT: A 775 ASP cc_start: 0.7048 (t0) cc_final: 0.6649 (m-30) REVERT: D 20 ILE cc_start: 0.5939 (mt) cc_final: 0.5714 (mt) REVERT: D 38 GLN cc_start: 0.8237 (pp30) cc_final: 0.7897 (pt0) REVERT: B 205 SER cc_start: 0.8930 (m) cc_final: 0.8716 (p) REVERT: B 360 ASN cc_start: 0.7761 (m-40) cc_final: 0.7475 (t0) REVERT: B 405 ASP cc_start: 0.7755 (m-30) cc_final: 0.7484 (m-30) REVERT: B 900 MET cc_start: 0.8531 (OUTLIER) cc_final: 0.8142 (mtp) REVERT: B 934 ILE cc_start: 0.7856 (tp) cc_final: 0.7615 (tp) REVERT: G 87 ARG cc_start: 0.7426 (mtp-110) cc_final: 0.7182 (mtp85) REVERT: E 28 ASN cc_start: 0.8171 (t0) cc_final: 0.7942 (t0) REVERT: E 38 GLN cc_start: 0.7891 (pp30) cc_final: 0.7088 (pp30) REVERT: E 50 TYR cc_start: 0.7809 (p90) cc_final: 0.7423 (p90) REVERT: E 79 LEU cc_start: 0.7188 (tp) cc_final: 0.6976 (tp) REVERT: E 86 ASP cc_start: 0.8197 (OUTLIER) cc_final: 0.7829 (p0) REVERT: C 378 LYS cc_start: 0.7639 (OUTLIER) cc_final: 0.7392 (pttm) REVERT: C 405 ASP cc_start: 0.7835 (m-30) cc_final: 0.7467 (m-30) REVERT: C 495 TYR cc_start: 0.7999 (OUTLIER) cc_final: 0.7192 (p90) REVERT: C 902 MET cc_start: 0.8479 (mmm) cc_final: 0.8235 (tpt) REVERT: C 965 GLN cc_start: 0.8005 (tt0) cc_final: 0.7770 (tt0) REVERT: C 1029 MET cc_start: 0.9073 (tpp) cc_final: 0.8270 (ttm) REVERT: C 1050 MET cc_start: 0.8563 (ptm) cc_final: 0.8222 (ptt) REVERT: F 29 ILE cc_start: 0.7122 (mm) cc_final: 0.6866 (mm) outliers start: 87 outliers final: 65 residues processed: 302 average time/residue: 0.2024 time to fit residues: 99.3925 Evaluate side-chains 301 residues out of total 3774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 227 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 660 TYR Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain B residue 64 TRP Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 563 GLN Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 660 TYR Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 975 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 64 PHE Chi-restraints excluded: chain E residue 86 ASP Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 443 SER Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain F residue 49 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 125 optimal weight: 0.0370 chunk 430 optimal weight: 9.9990 chunk 46 optimal weight: 6.9990 chunk 226 optimal weight: 0.7980 chunk 384 optimal weight: 2.9990 chunk 166 optimal weight: 4.9990 chunk 335 optimal weight: 6.9990 chunk 389 optimal weight: 9.9990 chunk 127 optimal weight: 0.3980 chunk 407 optimal weight: 8.9990 chunk 331 optimal weight: 2.9990 overall best weight: 1.4462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 563 GLN ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 907 ASN B 87 ASN B 417 ASN B 563 GLN B 965 GLN ** E 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.188145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.149812 restraints weight = 42625.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.143242 restraints weight = 45365.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.144999 restraints weight = 54532.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.145822 restraints weight = 38915.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.146892 restraints weight = 29775.420| |-----------------------------------------------------------------------------| r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.4278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 35118 Z= 0.148 Angle : 0.535 11.227 47925 Z= 0.270 Chirality : 0.044 0.179 5544 Planarity : 0.004 0.043 6066 Dihedral : 4.151 34.583 5628 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.13 % Allowed : 14.16 % Favored : 83.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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 aren not related in a simple way. whole: -0.13 (0.13), residues: 4254 helix: 1.41 (0.20), residues: 735 sheet: 0.57 (0.14), residues: 1218 loop : -0.96 (0.13), residues: 2301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 237 TYR 0.022 0.001 TYR A 495 PHE 0.015 0.001 PHE A 86 TRP 0.011 0.001 TRP B 64 HIS 0.003 0.001 HIS C1088 Details of bonding type rmsd covalent geometry : bond 0.00360 (35019) covalent geometry : angle 0.52233 (47679) SS BOND : bond 0.00406 ( 51) SS BOND : angle 1.86930 ( 102) hydrogen bonds : bond 0.04124 ( 1173) hydrogen bonds : angle 4.72844 ( 3501) link_BETA1-4 : bond 0.00420 ( 12) link_BETA1-4 : angle 0.88398 ( 36) link_NAG-ASN : bond 0.00208 ( 36) link_NAG-ASN : angle 1.72839 ( 108) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8508 Ramachandran restraints generated. 4254 Oldfield, 0 Emsley, 4254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8508 Ramachandran restraints generated. 4254 Oldfield, 0 Emsley, 4254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 3774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 226 time to evaluate : 1.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 378 LYS cc_start: 0.8095 (OUTLIER) cc_final: 0.7667 (ptpt) REVERT: A 392 PHE cc_start: 0.8795 (OUTLIER) cc_final: 0.8499 (m-80) REVERT: A 405 ASP cc_start: 0.7784 (m-30) cc_final: 0.7517 (m-30) REVERT: A 699 LEU cc_start: 0.8967 (OUTLIER) cc_final: 0.8514 (mm) REVERT: A 767 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.7998 (mt) REVERT: A 775 ASP cc_start: 0.7130 (t0) cc_final: 0.6728 (m-30) REVERT: D 38 GLN cc_start: 0.8214 (pp30) cc_final: 0.7877 (pt0) REVERT: B 205 SER cc_start: 0.8915 (m) cc_final: 0.8703 (p) REVERT: B 360 ASN cc_start: 0.7805 (m-40) cc_final: 0.7525 (t0) REVERT: B 405 ASP cc_start: 0.7762 (m-30) cc_final: 0.7503 (m-30) REVERT: B 900 MET cc_start: 0.8579 (OUTLIER) cc_final: 0.8199 (mtp) REVERT: B 934 ILE cc_start: 0.7969 (tp) cc_final: 0.7722 (tp) REVERT: G 87 ARG cc_start: 0.7412 (mtp-110) cc_final: 0.7157 (mtp85) REVERT: E 28 ASN cc_start: 0.8197 (t0) cc_final: 0.7973 (t0) REVERT: E 38 GLN cc_start: 0.7927 (pp30) cc_final: 0.7091 (pp30) REVERT: E 50 TYR cc_start: 0.7884 (p90) cc_final: 0.7505 (p90) REVERT: E 86 ASP cc_start: 0.8192 (OUTLIER) cc_final: 0.7859 (p0) REVERT: C 378 LYS cc_start: 0.7663 (OUTLIER) cc_final: 0.7385 (pttm) REVERT: C 405 ASP cc_start: 0.7800 (m-30) cc_final: 0.7477 (m-30) REVERT: C 495 TYR cc_start: 0.8081 (OUTLIER) cc_final: 0.7314 (p90) REVERT: C 902 MET cc_start: 0.8396 (mmm) cc_final: 0.8179 (tpt) REVERT: C 965 GLN cc_start: 0.7999 (tt0) cc_final: 0.7771 (tt0) REVERT: C 1029 MET cc_start: 0.9144 (tpp) cc_final: 0.8311 (ttm) outliers start: 80 outliers final: 63 residues processed: 292 average time/residue: 0.2225 time to fit residues: 105.2689 Evaluate side-chains 292 residues out of total 3774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 221 time to evaluate : 1.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 660 TYR Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain B residue 64 TRP Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 660 TYR Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 965 GLN Chi-restraints excluded: chain B residue 975 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain E residue 86 ASP Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 443 SER Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain F residue 49 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 265 optimal weight: 30.0000 chunk 388 optimal weight: 8.9990 chunk 64 optimal weight: 3.9990 chunk 401 optimal weight: 20.0000 chunk 284 optimal weight: 40.0000 chunk 15 optimal weight: 0.1980 chunk 364 optimal weight: 0.9990 chunk 422 optimal weight: 7.9990 chunk 391 optimal weight: 6.9990 chunk 298 optimal weight: 6.9990 chunk 337 optimal weight: 5.9990 overall best weight: 3.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 563 GLN ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 907 ASN B 87 ASN B 563 GLN ** E 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.187691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.158764 restraints weight = 42562.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.158601 restraints weight = 101669.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.156991 restraints weight = 66351.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.156696 restraints weight = 42716.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.157378 restraints weight = 34267.519| |-----------------------------------------------------------------------------| r_work (final): 0.3822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.4286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.141 35118 Z= 0.220 Angle : 0.660 59.193 47925 Z= 0.357 Chirality : 0.046 0.738 5544 Planarity : 0.004 0.043 6066 Dihedral : 4.160 34.612 5628 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 1.97 % Allowed : 14.38 % Favored : 83.65 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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 aren not related in a simple way. whole: -0.15 (0.13), residues: 4254 helix: 1.35 (0.20), residues: 735 sheet: 0.58 (0.14), residues: 1212 loop : -0.97 (0.12), residues: 2307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 237 TYR 0.021 0.001 TYR A 495 PHE 0.016 0.001 PHE A 86 TRP 0.012 0.001 TRP B 64 HIS 0.004 0.001 HIS C1088 Details of bonding type rmsd covalent geometry : bond 0.00509 (35019) covalent geometry : angle 0.65028 (47679) SS BOND : bond 0.00425 ( 51) SS BOND : angle 1.82253 ( 102) hydrogen bonds : bond 0.04299 ( 1173) hydrogen bonds : angle 4.72758 ( 3501) link_BETA1-4 : bond 0.00432 ( 12) link_BETA1-4 : angle 0.87552 ( 36) link_NAG-ASN : bond 0.00224 ( 36) link_NAG-ASN : angle 1.73025 ( 108) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4886.80 seconds wall clock time: 86 minutes 5.00 seconds (5165.00 seconds total)