Starting phenix.real_space_refine on Mon Jul 6 08:37:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7tca_25807/07_2026/7tca_25807.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tca_25807/07_2026/7tca_25807.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7tca_25807/07_2026/7tca_25807.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tca_25807/07_2026/7tca_25807.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7tca_25807/07_2026/7tca_25807.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tca_25807/07_2026/7tca_25807.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7tca_25807/07_2026/7tca_25807.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7tca_25807/07_2026/7tca_25807.cif" } resolution = 3.85 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= 0.001 sd= 0.025 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 148 5.16 5 C 21430 2.51 5 N 5554 2.21 5 O 6573 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 33705 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 8715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1114, 8715 Classifications: {'peptide': 1114} Link IDs: {'PTRANS': 56, 'TRANS': 1057} Chain breaks: 2 Chain: "B" Number of atoms: 8755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1118, 8755 Classifications: {'peptide': 1118} Link IDs: {'PTRANS': 57, 'TRANS': 1060} Chain breaks: 1 Chain: "C" Number of atoms: 8755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1118, 8755 Classifications: {'peptide': 1118} Link IDs: {'PTRANS': 57, 'TRANS': 1060} Chain breaks: 1 Chain: "D" Number of atoms: 1749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1749 Classifications: {'peptide': 231} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 218} Chain: "E" Number of atoms: 1599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1599 Classifications: {'peptide': 216} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 200} Chain: "H" Number of atoms: 1749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1749 Classifications: {'peptide': 231} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 218} Chain: "L" Number of atoms: 1599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1599 Classifications: {'peptide': 216} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 200} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "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 chiralities: 2 Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Chain: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 8.75, per 1000 atoms: 0.26 Number of scatterers: 33705 At special positions: 0 Unit cell: (153.9, 216.315, 234.27, 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 148 16.00 O 6573 8.00 N 5554 7.00 C 21430 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=48, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 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 A 840 " - pdb=" SG CYS A 851 " distance=2.04 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 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 B 840 " - pdb=" SG CYS B 851 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.05 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.04 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 C 840 " - pdb=" SG CYS C 851 " 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 D 153 " - pdb=" SG CYS D 209 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 90 " distance=2.03 Simple disulfide: pdb=" SG CYS E 138 " - pdb=" SG CYS E 197 " distance=2.03 Simple disulfide: pdb=" SG CYS H 153 " - pdb=" SG CYS H 209 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 90 " distance=2.03 Simple disulfide: pdb=" SG CYS L 138 " - pdb=" SG CYS L 197 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 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 282 " " NAG A1302 " - " ASN A 709 " " NAG A1303 " - " ASN A1074 " " NAG A1305 " - " ASN A 331 " " NAG A1306 " - " ASN A 343 " " NAG A1307 " - " ASN A 616 " " NAG A1308 " - " ASN A 657 " " NAG A1309 " - " ASN A 603 " " NAG B1301 " - " ASN B 709 " " NAG B1302 " - " ASN B1074 " " NAG B1303 " - " ASN B 61 " " NAG B1304 " - " ASN B 657 " " NAG B1305 " - " ASN B 616 " " NAG B1306 " - " ASN B 603 " " NAG B1307 " - " ASN B 282 " " NAG B1308 " - " ASN B 234 " " NAG B1309 " - " ASN B 122 " " NAG C1301 " - " ASN C 709 " " NAG C1302 " - " ASN C1074 " " NAG C1303 " - " ASN C 61 " " NAG C1304 " - " ASN C 657 " " NAG C1305 " - " ASN C 616 " " NAG C1306 " - " ASN C 603 " " NAG C1307 " - " ASN C 282 " " NAG C1308 " - " ASN C 234 " " NAG C1309 " - " ASN C 122 " " NAG F 1 " - " ASN A 717 " " NAG G 1 " - " ASN A 801 " " NAG I 1 " - " ASN A1098 " " NAG J 1 " - " ASN A1134 " " NAG K 1 " - " ASN B 717 " " NAG M 1 " - " ASN B1098 " " NAG N 1 " - " ASN B1134 " " NAG O 1 " - " ASN B 331 " " NAG P 1 " - " ASN B 801 " " NAG Q 1 " - " ASN C 717 " " NAG R 1 " - " ASN C1098 " " NAG S 1 " - " ASN C1134 " " NAG T 1 " - " ASN C 331 " " NAG U 1 " - " ASN C 801 " Time building additional restraints: 3.22 Conformation dependent library (CDL) restraints added in 1.6 seconds 8444 Ramachandran restraints generated. 4222 Oldfield, 0 Emsley, 4222 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7898 Finding SS restraints... Secondary structure from input PDB file: 93 helices and 71 sheets defined 21.5% alpha, 26.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.64 Creating SS restraints... Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 383 through 387 removed outlier: 4.153A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 633 through 639 removed outlier: 3.519A pdb=" N TYR A 636 " --> pdb=" O TRP A 633 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR A 638 " --> pdb=" O VAL A 635 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLY A 639 " --> pdb=" O TYR A 636 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 removed outlier: 3.572A pdb=" N CYS A 743 " --> pdb=" O THR A 739 " (cutoff:3.500A) Processing helix chain 'A' and resid 747 through 754 Processing helix chain 'A' and resid 758 through 783 removed outlier: 4.299A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 837 through 845 removed outlier: 6.482A pdb=" N GLY A 842 " --> pdb=" O ASP A 839 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N ASP A 843 " --> pdb=" O CYS A 840 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ILE A 844 " --> pdb=" O LEU A 841 " (cutoff:3.500A) Processing helix chain 'A' and resid 848 through 856 Processing helix chain 'A' and resid 866 through 884 removed outlier: 3.533A pdb=" N ILE A 870 " --> pdb=" O THR A 866 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 891 removed outlier: 4.150A pdb=" N GLY A 891 " --> pdb=" O PHE A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.568A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 918 removed outlier: 4.193A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 940 removed outlier: 4.032A pdb=" N SER A 939 " --> pdb=" O GLN A 935 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N SER A 940 " --> pdb=" O ASP A 936 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 4.062A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 982 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.217A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ARG A1014 " --> pdb=" O GLN A1010 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ALA A1015 " --> pdb=" O GLN A1011 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N ALA A1016 " --> pdb=" O LEU A1012 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) Processing helix chain 'A' and resid 1116 through 1118 No H-bonds generated for 'chain 'A' and resid 1116 through 1118' Processing helix chain 'A' and resid 1140 through 1145 removed outlier: 3.967A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N LEU A1145 " --> pdb=" O LEU A1141 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1140 through 1145' Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 364 through 369 removed outlier: 3.570A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 408 removed outlier: 4.031A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 405 through 408' Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 502 through 505 removed outlier: 3.694A pdb=" N HIS B 505 " --> pdb=" O GLY B 502 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 502 through 505' Processing helix chain 'B' and resid 568 through 572 removed outlier: 3.881A pdb=" N THR B 572 " --> pdb=" O ILE B 569 " (cutoff:3.500A) Processing helix chain 'B' and resid 619 through 628 removed outlier: 4.087A pdb=" N ALA B 623 " --> pdb=" O GLU B 619 " (cutoff:3.500A) Processing helix chain 'B' and resid 630 through 638 removed outlier: 4.297A pdb=" N TYR B 636 " --> pdb=" O THR B 632 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N SER B 637 " --> pdb=" O TRP B 633 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 removed outlier: 3.539A pdb=" N TYR B 741 " --> pdb=" O ASP B 737 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.526A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU B 754 " --> pdb=" O SER B 750 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.658A pdb=" N THR B 768 " --> pdb=" O LYS B 764 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLY B 769 " --> pdb=" O ARG B 765 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ILE B 770 " --> pdb=" O ALA B 766 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ALA B 771 " --> pdb=" O LEU B 767 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 827 removed outlier: 3.743A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N THR B 827 " --> pdb=" O PHE B 823 " (cutoff:3.500A) Processing helix chain 'B' and resid 849 through 855 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.598A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLU B 918 " --> pdb=" O ASN B 914 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 913 through 918' Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 946 through 965 removed outlier: 3.549A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.552A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1034 removed outlier: 5.097A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA B1016 " --> pdb=" O LEU B1012 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU B1034 " --> pdb=" O SER B1030 " (cutoff:3.500A) Processing helix chain 'B' and resid 1116 through 1118 No H-bonds generated for 'chain 'B' and resid 1116 through 1118' Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 366 through 370 Processing helix chain 'C' and resid 405 through 408 removed outlier: 4.323A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 405 through 408' Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 619 through 628 removed outlier: 3.670A pdb=" N ALA C 623 " --> pdb=" O GLU C 619 " (cutoff:3.500A) Processing helix chain 'C' and resid 630 through 637 removed outlier: 3.695A pdb=" N ARG C 634 " --> pdb=" O THR C 630 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.511A pdb=" N SER C 750 " --> pdb=" O SER C 746 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU C 754 " --> pdb=" O SER C 750 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.662A pdb=" N THR C 768 " --> pdb=" O LYS C 764 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLY C 769 " --> pdb=" O ARG C 765 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ILE C 770 " --> pdb=" O ALA C 766 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ALA C 771 " --> pdb=" O LEU C 767 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 827 removed outlier: 3.507A pdb=" N ASN C 824 " --> pdb=" O ASP C 820 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LYS C 825 " --> pdb=" O LEU C 821 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N THR C 827 " --> pdb=" O PHE C 823 " (cutoff:3.500A) Processing helix chain 'C' and resid 849 through 856 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 890 removed outlier: 3.541A pdb=" N GLY C 889 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.574A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 918 removed outlier: 3.651A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.529A pdb=" N THR C 941 " --> pdb=" O SER C 937 " (cutoff:3.500A) Processing helix chain 'C' and resid 946 through 965 removed outlier: 3.610A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 983 removed outlier: 3.637A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1034 removed outlier: 4.741A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA C1016 " --> pdb=" O LEU C1012 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLU C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU C1034 " --> pdb=" O SER C1030 " (cutoff:3.500A) Processing helix chain 'C' and resid 1116 through 1118 No H-bonds generated for 'chain 'C' and resid 1116 through 1118' Processing helix chain 'C' and resid 1140 through 1145 removed outlier: 4.573A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU C1145 " --> pdb=" O LEU C1141 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1140 through 1145' Processing helix chain 'D' and resid 28 through 30 No H-bonds generated for 'chain 'D' and resid 28 through 30' Processing helix chain 'D' and resid 62 through 65 removed outlier: 3.745A pdb=" N LYS D 65 " --> pdb=" O ASP D 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 62 through 65' Processing helix chain 'D' and resid 87 through 91 removed outlier: 3.538A pdb=" N THR D 91 " --> pdb=" O ALA D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 145 Processing helix chain 'D' and resid 169 through 171 No H-bonds generated for 'chain 'D' and resid 169 through 171' Processing helix chain 'D' and resid 200 through 202 No H-bonds generated for 'chain 'D' and resid 200 through 202' Processing helix chain 'E' and resid 30 through 34 Processing helix chain 'E' and resid 81 through 85 Processing helix chain 'E' and resid 125 through 130 Processing helix chain 'E' and resid 185 through 191 Processing helix chain 'E' and resid 211 through 216 removed outlier: 3.900A pdb=" N CYS E 215 " --> pdb=" O ALA E 211 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N SER E 216 " --> pdb=" O PRO E 212 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 211 through 216' Processing helix chain 'H' and resid 28 through 30 No H-bonds generated for 'chain 'H' and resid 28 through 30' Processing helix chain 'H' and resid 62 through 65 Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'H' and resid 169 through 171 No H-bonds generated for 'chain 'H' and resid 169 through 171' Processing helix chain 'H' and resid 200 through 202 No H-bonds generated for 'chain 'H' and resid 200 through 202' Processing helix chain 'L' and resid 30 through 34 Processing helix chain 'L' and resid 81 through 85 removed outlier: 3.563A pdb=" N ASP L 84 " --> pdb=" O GLN L 81 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLU L 85 " --> pdb=" O ALA L 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 81 through 85' Processing helix chain 'L' and resid 125 through 131 Processing helix chain 'L' and resid 185 through 191 Processing helix chain 'L' and resid 211 through 216 removed outlier: 3.928A pdb=" N CYS L 215 " --> pdb=" O ALA L 211 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N SER L 216 " --> pdb=" O PRO L 212 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 211 through 216' Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 3.540A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA A 263 " --> pdb=" O VAL A 67 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.681A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 83 through 85 Processing sheet with id=AA5, first strand: chain 'A' and resid 93 through 94 Processing sheet with id=AA6, first strand: chain 'A' and resid 101 through 102 Processing sheet with id=AA7, first strand: chain 'A' and resid 116 through 117 removed outlier: 3.650A pdb=" N VAL A 130 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 193 through 197 removed outlier: 3.532A pdb=" N LYS A 195 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N ILE A 203 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 311 through 319 removed outlier: 3.573A pdb=" N THR A 599 " --> pdb=" O GLY A 311 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 325 through 326 removed outlier: 3.535A pdb=" N ILE A 326 " --> pdb=" O ASN A 540 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 356 through 357 Processing sheet with id=AB3, first strand: chain 'A' and resid 378 through 380 Processing sheet with id=AB4, first strand: chain 'A' and resid 453 through 454 Processing sheet with id=AB5, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB6, first strand: chain 'A' and resid 553 through 554 Processing sheet with id=AB7, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.579A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.615A pdb=" N ILE A 714 " --> pdb=" O LYS A1073 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 718 through 727 removed outlier: 3.921A pdb=" N SER A 721 " --> pdb=" O THR A1066 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.324A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N CYS A1082 " --> pdb=" O VAL A1133 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 27 through 30 removed outlier: 3.848A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA B 264 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ALA B 93 " --> pdb=" O TYR B 266 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N LEU B 189 " --> pdb=" O THR B 208 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.562A pdb=" N THR B 51 " --> pdb=" O PHE B 275 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N PHE B 275 " --> pdb=" O THR B 51 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LYS B 278 " --> pdb=" O ASP B 287 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC5, first strand: chain 'B' and resid 142 through 146 removed outlier: 3.711A pdb=" N HIS B 146 " --> pdb=" O LEU B 244 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.499A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLN B 613 " --> pdb=" O GLY B 594 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL B 610 " --> pdb=" O ILE B 651 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 324 through 326 Processing sheet with id=AC8, first strand: chain 'B' and resid 356 through 358 removed outlier: 3.734A pdb=" N ILE B 358 " --> pdb=" O VAL B 395 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER B 514 " --> pdb=" O TYR B 396 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ASP B 398 " --> pdb=" O VAL B 512 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD1, first strand: chain 'B' and resid 654 through 660 removed outlier: 3.836A pdb=" N GLU B 654 " --> pdb=" O ILE B 692 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N THR B 696 " --> pdb=" O VAL B 656 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N ASN B 658 " --> pdb=" O THR B 696 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLN B 675 " --> pdb=" O SER B 691 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 711 through 713 removed outlier: 3.651A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N THR B1105 " --> pdb=" O VAL B1094 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 717 through 719 removed outlier: 3.803A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 722 through 728 removed outlier: 3.534A pdb=" N GLU B 725 " --> pdb=" O PHE B1062 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD6, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 3.896A pdb=" N SER B1123 " --> pdb=" O ALA B1087 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N CYS B1082 " --> pdb=" O VAL B1133 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 27 through 28 Processing sheet with id=AD8, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.552A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LYS C 278 " --> pdb=" O ASP C 287 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.823A pdb=" N LEU C 84 " --> pdb=" O PHE C 238 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 93 through 96 removed outlier: 3.505A pdb=" N GLU C 191 " --> pdb=" O LYS C 206 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYS C 195 " --> pdb=" O LYS C 202 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 118 through 120 Processing sheet with id=AE3, first strand: chain 'C' and resid 156 through 157 removed outlier: 3.737A pdb=" N GLU C 156 " --> pdb=" O ASP C 142 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ASP C 142 " --> pdb=" O GLU C 156 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 311 through 319 removed outlier: 7.190A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLN C 613 " --> pdb=" O GLY C 594 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N CYS C 649 " --> pdb=" O TYR C 612 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 324 through 327 removed outlier: 3.558A pdb=" N GLY C 550 " --> pdb=" O VAL C 539 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLY C 548 " --> pdb=" O PHE C 541 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N THR C 553 " --> pdb=" O ASP C 586 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 356 through 358 removed outlier: 3.940A pdb=" N ILE C 358 " --> pdb=" O VAL C 395 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ASP C 398 " --> pdb=" O VAL C 512 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N GLY C 431 " --> pdb=" O TYR C 380 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N TYR C 380 " --> pdb=" O GLY C 431 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N VAL C 433 " --> pdb=" O LYS C 378 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N LYS C 378 " --> pdb=" O VAL C 433 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE8, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.494A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.756A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N SER C 691 " --> pdb=" O GLN C 675 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLN C 675 " --> pdb=" O SER C 691 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.463A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLU C 725 " --> pdb=" O PHE C1062 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N PHE C1052 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.463A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLU C 725 " --> pdb=" O PHE C1062 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AF3, first strand: chain 'C' and resid 1081 through 1083 Processing sheet with id=AF4, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AF5, first strand: chain 'D' and resid 11 through 12 removed outlier: 3.913A pdb=" N VAL D 12 " --> pdb=" O THR D 123 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N GLY D 33 " --> pdb=" O GLY D 99 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N MET D 34 " --> pdb=" O VAL D 50 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N VAL D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N TYR D 59 " --> pdb=" O VAL D 50 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'D' and resid 11 through 12 removed outlier: 3.913A pdb=" N VAL D 12 " --> pdb=" O THR D 123 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N VAL D 115 " --> pdb=" O ARG D 98 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'D' and resid 133 through 137 removed outlier: 3.713A pdb=" N GLY D 152 " --> pdb=" O LEU D 137 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N TYR D 189 " --> pdb=" O ASP D 157 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL D 194 " --> pdb=" O HIS D 177 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N HIS D 177 " --> pdb=" O VAL D 194 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'D' and resid 133 through 137 removed outlier: 3.713A pdb=" N GLY D 152 " --> pdb=" O LEU D 137 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N TYR D 189 " --> pdb=" O ASP D 157 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N SER D 190 " --> pdb=" O VAL D 182 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N VAL D 182 " --> pdb=" O SER D 190 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'D' and resid 164 through 167 removed outlier: 3.564A pdb=" N VAL D 211 " --> pdb=" O VAL D 220 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N VAL D 220 " --> pdb=" O VAL D 211 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N HIS D 213 " --> pdb=" O THR D 218 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N THR D 218 " --> pdb=" O HIS D 213 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'E' and resid 4 through 6 Processing sheet with id=AG2, first strand: chain 'E' and resid 9 through 12 removed outlier: 5.894A pdb=" N PHE E 10 " --> pdb=" O THR E 108 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N GLN E 39 " --> pdb=" O THR E 48 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N THR E 48 " --> pdb=" O GLN E 39 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR E 55 " --> pdb=" O TYR E 51 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'E' and resid 9 through 12 removed outlier: 5.894A pdb=" N PHE E 10 " --> pdb=" O THR E 108 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU E 92 " --> pdb=" O VAL E 100 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ILE E 98 " --> pdb=" O MET E 94 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'E' and resid 118 through 122 removed outlier: 3.503A pdb=" N SER E 141 " --> pdb=" O SER E 118 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N VAL E 137 " --> pdb=" O PHE E 122 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N TYR E 176 " --> pdb=" O ASP E 142 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'E' and resid 118 through 122 removed outlier: 3.503A pdb=" N SER E 141 " --> pdb=" O SER E 118 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N VAL E 137 " --> pdb=" O PHE E 122 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N TYR E 176 " --> pdb=" O ASP E 142 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'E' and resid 157 through 159 removed outlier: 4.764A pdb=" N TRP E 152 " --> pdb=" O VAL E 159 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LYS E 153 " --> pdb=" O SER E 196 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER E 196 " --> pdb=" O LYS E 153 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL E 199 " --> pdb=" O VAL E 206 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL E 206 " --> pdb=" O VAL E 199 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AG8, first strand: chain 'H' and resid 11 through 12 removed outlier: 4.309A pdb=" N GLY H 33 " --> pdb=" O GLY H 99 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N MET H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N VAL H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL H 50 " --> pdb=" O TYR H 59 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N TYR H 59 " --> pdb=" O VAL H 50 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.959A pdb=" N VAL H 115 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'H' and resid 133 through 137 removed outlier: 3.551A pdb=" N CYS H 153 " --> pdb=" O SER H 193 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N TYR H 189 " --> pdb=" O ASP H 157 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'H' and resid 164 through 167 removed outlier: 4.045A pdb=" N TYR H 207 " --> pdb=" O VAL H 224 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'L' and resid 4 through 6 removed outlier: 3.526A pdb=" N GLY L 23 " --> pdb=" O THR L 5 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'L' and resid 55 through 56 removed outlier: 6.616A pdb=" N TRP L 37 " --> pdb=" O LEU L 49 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'L' and resid 55 through 56 removed outlier: 6.616A pdb=" N TRP L 37 " --> pdb=" O LEU L 49 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'L' and resid 118 through 122 removed outlier: 3.513A pdb=" N VAL L 137 " --> pdb=" O PHE L 122 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N TYR L 181 " --> pdb=" O GLU L 164 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLU L 164 " --> pdb=" O TYR L 181 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'L' and resid 118 through 122 removed outlier: 3.513A pdb=" N VAL L 137 " --> pdb=" O PHE L 122 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N TYR L 176 " --> pdb=" O ASP L 142 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'L' and resid 157 through 159 removed outlier: 4.259A pdb=" N TRP L 152 " --> pdb=" O VAL L 159 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LYS L 153 " --> pdb=" O SER L 196 " (cutoff:3.500A) 1138 hydrogen bonds defined for protein. 3012 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: 9.81 Time building geometry restraints manager: 4.35 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: 10699 1.34 - 1.47: 8696 1.47 - 1.59: 14917 1.59 - 1.71: 1 1.71 - 1.84: 186 Bond restraints: 34499 Sorted by residual: bond pdb=" C1 NAG B1308 " pdb=" O5 NAG B1308 " ideal model delta sigma weight residual 1.406 1.491 -0.085 2.00e-02 2.50e+03 1.80e+01 bond pdb=" C1 NAG C1304 " pdb=" O5 NAG C1304 " ideal model delta sigma weight residual 1.406 1.486 -0.080 2.00e-02 2.50e+03 1.60e+01 bond pdb=" C1 NAG C1303 " pdb=" O5 NAG C1303 " ideal model delta sigma weight residual 1.406 1.474 -0.068 2.00e-02 2.50e+03 1.15e+01 bond pdb=" C1 NAG A1306 " pdb=" O5 NAG A1306 " ideal model delta sigma weight residual 1.406 1.459 -0.053 2.00e-02 2.50e+03 7.11e+00 bond pdb=" C1 NAG N 1 " pdb=" O5 NAG N 1 " ideal model delta sigma weight residual 1.406 1.456 -0.050 2.00e-02 2.50e+03 6.25e+00 ... (remaining 34494 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.62: 46829 3.62 - 7.23: 133 7.23 - 10.85: 12 10.85 - 14.47: 1 14.47 - 18.08: 3 Bond angle restraints: 46978 Sorted by residual: angle pdb=" CA CYS C 391 " pdb=" CB CYS C 391 " pdb=" SG CYS C 391 " ideal model delta sigma weight residual 114.40 132.29 -17.89 2.30e+00 1.89e-01 6.05e+01 angle pdb=" CA CYS C 525 " pdb=" CB CYS C 525 " pdb=" SG CYS C 525 " ideal model delta sigma weight residual 114.40 131.75 -17.35 2.30e+00 1.89e-01 5.69e+01 angle pdb=" C LEU C 390 " pdb=" N CYS C 391 " pdb=" CA CYS C 391 " ideal model delta sigma weight residual 122.44 113.50 8.94 1.45e+00 4.76e-01 3.80e+01 angle pdb=" N THR A 76 " pdb=" CA THR A 76 " pdb=" C THR A 76 " ideal model delta sigma weight residual 114.56 108.65 5.91 1.27e+00 6.20e-01 2.17e+01 angle pdb=" C GLY C 526 " pdb=" N PRO C 527 " pdb=" CD PRO C 527 " ideal model delta sigma weight residual 125.00 106.92 18.08 4.10e+00 5.95e-02 1.94e+01 ... (remaining 46973 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.75: 18229 17.75 - 35.50: 1548 35.50 - 53.25: 229 53.25 - 70.99: 56 70.99 - 88.74: 31 Dihedral angle restraints: 20093 sinusoidal: 7767 harmonic: 12326 Sorted by residual: dihedral pdb=" CA CYS C 525 " pdb=" C CYS C 525 " pdb=" N GLY C 526 " pdb=" CA GLY C 526 " ideal model delta harmonic sigma weight residual -180.00 -126.83 -53.17 0 5.00e+00 4.00e-02 1.13e+02 dihedral pdb=" CB CYS C 391 " pdb=" SG CYS C 391 " pdb=" SG CYS C 525 " pdb=" CB CYS C 525 " ideal model delta sinusoidal sigma weight residual -86.00 1.31 -87.31 1 1.00e+01 1.00e-02 9.15e+01 dihedral pdb=" CB CYS A 840 " pdb=" SG CYS A 840 " pdb=" SG CYS A 851 " pdb=" CB CYS A 851 " ideal model delta sinusoidal sigma weight residual 93.00 172.75 -79.75 1 1.00e+01 1.00e-02 7.89e+01 ... (remaining 20090 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.123: 5410 0.123 - 0.246: 49 0.246 - 0.369: 4 0.369 - 0.492: 1 0.492 - 0.615: 2 Chirality restraints: 5466 Sorted by residual: chirality pdb=" C1 NAG B1304 " pdb=" ND2 ASN B 657 " pdb=" C2 NAG B1304 " pdb=" O5 NAG B1304 " both_signs ideal model delta sigma weight residual False -2.40 -1.79 -0.61 2.00e-01 2.50e+01 9.45e+00 chirality pdb=" C1 NAG C1308 " pdb=" ND2 ASN C 234 " pdb=" C2 NAG C1308 " pdb=" O5 NAG C1308 " both_signs ideal model delta sigma weight residual False -2.40 -1.79 -0.61 2.00e-01 2.50e+01 9.24e+00 chirality pdb=" C1 NAG T 1 " pdb=" ND2 ASN C 331 " pdb=" C2 NAG T 1 " pdb=" O5 NAG T 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.96 -0.44 2.00e-01 2.50e+01 4.79e+00 ... (remaining 5463 not shown) Planarity restraints: 6028 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY C 526 " -0.112 5.00e-02 4.00e+02 1.70e-01 4.65e+01 pdb=" N PRO C 527 " 0.295 5.00e-02 4.00e+02 pdb=" CA PRO C 527 " -0.102 5.00e-02 4.00e+02 pdb=" CD PRO C 527 " -0.081 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 717 " 0.050 2.00e-02 2.50e+03 4.68e-02 2.74e+01 pdb=" CG ASN A 717 " -0.054 2.00e-02 2.50e+03 pdb=" OD1 ASN A 717 " 0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN A 717 " -0.054 2.00e-02 2.50e+03 pdb=" C1 NAG F 1 " 0.051 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 717 " 0.049 2.00e-02 2.50e+03 4.54e-02 2.57e+01 pdb=" CG ASN B 717 " -0.048 2.00e-02 2.50e+03 pdb=" OD1 ASN B 717 " 0.000 2.00e-02 2.50e+03 pdb=" ND2 ASN B 717 " -0.054 2.00e-02 2.50e+03 pdb=" C1 NAG K 1 " 0.052 2.00e-02 2.50e+03 ... (remaining 6025 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 871 2.69 - 3.24: 33208 3.24 - 3.79: 50915 3.79 - 4.35: 64785 4.35 - 4.90: 106320 Nonbonded interactions: 256099 Sorted by model distance: nonbonded pdb=" OG1 THR B 323 " pdb=" OE1 GLU B 324 " model vdw 2.132 3.040 nonbonded pdb=" O THR C 208 " pdb=" NH2 ARG C 214 " model vdw 2.191 3.120 nonbonded pdb=" O THR B 208 " pdb=" NH1 ARG B 214 " model vdw 2.202 3.120 nonbonded pdb=" OE1 GLN D 184 " pdb=" OG SER D 190 " model vdw 2.205 3.040 nonbonded pdb=" O CYS C 15 " pdb=" N ASN C 17 " model vdw 2.206 3.120 ... (remaining 256094 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 676 or resid 689 through 1309)) selection = (chain 'B' and (resid 14 through 213 or resid 215 through 676 or resid 689 throu \ gh 1309)) selection = (chain 'C' and (resid 14 through 213 or resid 215 through 676 or resid 689 throu \ gh 1309)) } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'L' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'K' 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 11.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.060 Extract box with map and model: 0.930 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 36.650 Find NCS groups from input model: 1.290 Set up NCS constraints: 0.200 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:1.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 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 0.107 34601 Z= 0.155 Angle : 0.694 21.174 47236 Z= 0.331 Chirality : 0.048 0.615 5466 Planarity : 0.005 0.170 5988 Dihedral : 13.407 88.742 12051 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.43 % Allowed : 7.03 % Favored : 92.54 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.68 % Cis-general : 0.00 % Twisted Proline : 0.45 % 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 are not related in a simple way. whole: -0.96 (0.13), residues: 4222 helix: 1.69 (0.21), residues: 728 sheet: -0.13 (0.17), residues: 958 loop : -1.62 (0.12), residues: 2536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 237 TYR 0.017 0.001 TYR L 38 PHE 0.032 0.001 PHE A 238 TRP 0.028 0.001 TRP B 258 HIS 0.004 0.000 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.15 (34499) covalent geometry : angle 0.63809 / 0.32 (46978) SS BOND : bond 0.00393 / 0.29 ( 48) SS BOND : angle 1.93180 / 1.23 ( 96) hydrogen bonds : bond 0.23435 / 15.67 ( 1071) hydrogen bonds : angle 8.50243 / 5.77 ( 3012) link_BETA1-4 : bond 0.00607 / 0.39 ( 14) link_BETA1-4 : angle 2.07473 / 1.33 ( 42) link_NAG-ASN : bond 0.00848 / 0.55 ( 40) link_NAG-ASN : angle 5.07728 / 3.23 ( 120) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8444 Ramachandran restraints generated. 4222 Oldfield, 0 Emsley, 4222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8444 Ramachandran restraints generated. 4222 Oldfield, 0 Emsley, 4222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 3667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 1.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 490 PHE cc_start: 0.8642 (t80) cc_final: 0.8226 (t80) REVERT: C 177 MET cc_start: 0.6535 (mpp) cc_final: 0.6226 (mmm) REVERT: C 988 GLU cc_start: 0.8906 (mm-30) cc_final: 0.8608 (mp0) REVERT: E 170 LYS cc_start: 0.7497 (pttt) cc_final: 0.7273 (mttt) REVERT: L 94 MET cc_start: 0.9008 (mmp) cc_final: 0.8530 (mmm) outliers start: 0 outliers final: 0 residues processed: 127 average time/residue: 0.2522 time to fit residues: 51.3896 Evaluate side-chains 76 residues out of total 3667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 1.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 421 random chunks: chunk 197 optimal weight: 9.9990 chunk 388 optimal weight: 0.8980 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 6.9990 chunk 401 optimal weight: 6.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 8.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 544 ASN A 784 GLN ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 GLN ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 580 GLN B 625 HIS B 762 GLN ** B 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN B1036 GLN ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 35 HIS ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.057319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.035893 restraints weight = 333302.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.036141 restraints weight = 194997.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.035959 restraints weight = 135911.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.036080 restraints weight = 113000.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.036238 restraints weight = 97332.699| |-----------------------------------------------------------------------------| r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.1175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.095 34601 Z= 0.153 Angle : 0.663 18.975 47236 Z= 0.329 Chirality : 0.045 0.315 5466 Planarity : 0.005 0.170 5988 Dihedral : 4.545 48.509 4571 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.38 % Allowed : 7.30 % Favored : 92.33 % Rotamer: Outliers : 0.30 % Allowed : 6.79 % Favored : 92.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.68 % 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 are not related in a simple way. whole: -0.88 (0.13), residues: 4222 helix: 1.77 (0.21), residues: 728 sheet: -0.11 (0.17), residues: 978 loop : -1.58 (0.12), residues: 2516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 408 TYR 0.024 0.001 TYR L 51 PHE 0.030 0.001 PHE A 759 TRP 0.022 0.001 TRP A 633 HIS 0.006 0.001 HIS C 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.15 (34499) covalent geometry : angle 0.63744 / 0.32 (46978) SS BOND : bond 0.00324 / 0.23 ( 48) SS BOND : angle 1.50168 / 0.99 ( 96) hydrogen bonds : bond 0.04274 / 2.84 ( 1071) hydrogen bonds : angle 6.39108 / 4.35 ( 3012) link_BETA1-4 : bond 0.00467 / 0.25 ( 14) link_BETA1-4 : angle 1.48470 / 0.99 ( 42) link_NAG-ASN : bond 0.00562 / 0.36 ( 40) link_NAG-ASN : angle 3.37311 / 2.44 ( 120) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8444 Ramachandran restraints generated. 4222 Oldfield, 0 Emsley, 4222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8444 Ramachandran restraints generated. 4222 Oldfield, 0 Emsley, 4222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 3667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 78 time to evaluate : 1.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 490 PHE cc_start: 0.8763 (t80) cc_final: 0.8502 (t80) REVERT: A 633 TRP cc_start: 0.8171 (p90) cc_final: 0.7753 (p90) REVERT: A 697 MET cc_start: 0.8765 (pmm) cc_final: 0.8479 (pmm) REVERT: A 780 GLU cc_start: 0.9355 (tp30) cc_final: 0.9021 (tp30) REVERT: A 1050 MET cc_start: 0.8889 (ptp) cc_final: 0.8238 (mtm) REVERT: B 900 MET cc_start: 0.9225 (mmm) cc_final: 0.9005 (mmm) REVERT: C 118 LEU cc_start: 0.9425 (mm) cc_final: 0.8906 (mp) REVERT: C 177 MET cc_start: 0.6735 (mpp) cc_final: 0.6418 (mmm) REVERT: C 740 MET cc_start: 0.8914 (tpp) cc_final: 0.8644 (tpt) REVERT: C 759 PHE cc_start: 0.8869 (m-80) cc_final: 0.8605 (m-80) REVERT: C 900 MET cc_start: 0.9422 (mmm) cc_final: 0.9116 (mmp) REVERT: C 988 GLU cc_start: 0.9459 (mm-30) cc_final: 0.9099 (mp0) REVERT: C 1050 MET cc_start: 0.8395 (pmm) cc_final: 0.7923 (pmm) REVERT: L 94 MET cc_start: 0.8748 (mmp) cc_final: 0.8309 (mmm) outliers start: 11 outliers final: 4 residues processed: 86 average time/residue: 0.2423 time to fit residues: 34.3000 Evaluate side-chains 71 residues out of total 3667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 67 time to evaluate : 1.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 717 ASN Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 822 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 421 random chunks: chunk 277 optimal weight: 1.9990 chunk 127 optimal weight: 9.9990 chunk 398 optimal weight: 20.0000 chunk 91 optimal weight: 0.8980 chunk 176 optimal weight: 3.9990 chunk 238 optimal weight: 10.0000 chunk 172 optimal weight: 9.9990 chunk 339 optimal weight: 4.9990 chunk 85 optimal weight: 6.9990 chunk 196 optimal weight: 6.9990 chunk 80 optimal weight: 0.5980 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 448 ASN ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1106 GLN B 239 GLN ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 6 GLN ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.056169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.035842 restraints weight = 334393.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.036803 restraints weight = 189569.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.037430 restraints weight = 133336.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.037841 restraints weight = 106462.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.038105 restraints weight = 92170.877| |-----------------------------------------------------------------------------| r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.1612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.091 34601 Z= 0.146 Angle : 0.609 18.688 47236 Z= 0.302 Chirality : 0.044 0.306 5466 Planarity : 0.004 0.170 5988 Dihedral : 4.431 49.595 4571 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.40 % Allowed : 7.20 % Favored : 92.40 % Rotamer: Outliers : 0.49 % Allowed : 9.22 % Favored : 90.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.68 % 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 are not related in a simple way. whole: -0.80 (0.13), residues: 4222 helix: 1.87 (0.21), residues: 721 sheet: -0.07 (0.17), residues: 972 loop : -1.52 (0.12), residues: 2529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 357 TYR 0.018 0.001 TYR B 269 PHE 0.016 0.001 PHE A 759 TRP 0.011 0.001 TRP C 436 HIS 0.006 0.001 HIS C 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.15 (34499) covalent geometry : angle 0.58678 / 0.30 (46978) SS BOND : bond 0.00300 / 0.22 ( 48) SS BOND : angle 1.37234 / 0.92 ( 96) hydrogen bonds : bond 0.03945 / 2.61 ( 1071) hydrogen bonds : angle 5.85413 / 4.00 ( 3012) link_BETA1-4 : bond 0.00234 / 0.16 ( 14) link_BETA1-4 : angle 1.39179 / 0.93 ( 42) link_NAG-ASN : bond 0.00528 / 0.32 ( 40) link_NAG-ASN : angle 2.96852 / 2.21 ( 120) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8444 Ramachandran restraints generated. 4222 Oldfield, 0 Emsley, 4222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8444 Ramachandran restraints generated. 4222 Oldfield, 0 Emsley, 4222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 3667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 71 time to evaluate : 1.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 490 PHE cc_start: 0.8618 (t80) cc_final: 0.8255 (t80) REVERT: A 633 TRP cc_start: 0.8390 (p90) cc_final: 0.8056 (p90) REVERT: A 697 MET cc_start: 0.8889 (pmm) cc_final: 0.8608 (pmm) REVERT: A 780 GLU cc_start: 0.9376 (tp30) cc_final: 0.9028 (tp30) REVERT: A 869 MET cc_start: 0.9336 (mtp) cc_final: 0.9030 (ptp) REVERT: B 697 MET cc_start: 0.9109 (mmp) cc_final: 0.8866 (mmp) REVERT: B 717 ASN cc_start: 0.8793 (OUTLIER) cc_final: 0.8389 (m-40) REVERT: B 869 MET cc_start: 0.9333 (ptp) cc_final: 0.9109 (ptp) REVERT: C 177 MET cc_start: 0.6745 (mpp) cc_final: 0.6409 (mmm) REVERT: C 697 MET cc_start: 0.9140 (mmm) cc_final: 0.8569 (mmm) REVERT: C 740 MET cc_start: 0.9053 (tpp) cc_final: 0.8631 (tpt) REVERT: C 742 ILE cc_start: 0.9525 (OUTLIER) cc_final: 0.9062 (tp) REVERT: C 900 MET cc_start: 0.9439 (mmm) cc_final: 0.9165 (mmp) REVERT: C 988 GLU cc_start: 0.9346 (mm-30) cc_final: 0.8985 (mp0) REVERT: C 1050 MET cc_start: 0.8440 (pmm) cc_final: 0.8121 (pmm) REVERT: L 94 MET cc_start: 0.8702 (mmp) cc_final: 0.8257 (mmm) outliers start: 18 outliers final: 9 residues processed: 87 average time/residue: 0.2399 time to fit residues: 34.9495 Evaluate side-chains 76 residues out of total 3667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 65 time to evaluate : 1.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 717 ASN Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 717 ASN Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 742 ILE Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain L residue 109 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 421 random chunks: chunk 48 optimal weight: 30.0000 chunk 337 optimal weight: 20.0000 chunk 235 optimal weight: 9.9990 chunk 75 optimal weight: 7.9990 chunk 323 optimal weight: 8.9990 chunk 89 optimal weight: 6.9990 chunk 328 optimal weight: 5.9990 chunk 322 optimal weight: 3.9990 chunk 92 optimal weight: 8.9990 chunk 10 optimal weight: 10.0000 chunk 175 optimal weight: 8.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 556 ASN ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 52 GLN B 239 GLN ** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1036 GLN ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 ASN ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 580 GLN C1101 HIS C1106 GLN ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** 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 = 0.3626 r_free = 0.3626 target = 0.054186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.034059 restraints weight = 344086.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.034931 restraints weight = 201432.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.035502 restraints weight = 144471.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.035869 restraints weight = 116992.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.036073 restraints weight = 102439.125| |-----------------------------------------------------------------------------| r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.2585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.098 34601 Z= 0.344 Angle : 0.787 19.803 47236 Z= 0.394 Chirality : 0.046 0.293 5466 Planarity : 0.005 0.172 5988 Dihedral : 5.043 48.146 4571 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 16.59 Ramachandran Plot: Outliers : 0.38 % Allowed : 9.21 % Favored : 90.41 % Rotamer: Outliers : 1.39 % Allowed : 12.27 % Favored : 86.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.68 % 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 are not related in a simple way. whole: -1.20 (0.13), residues: 4222 helix: 1.11 (0.19), residues: 730 sheet: -0.41 (0.17), residues: 935 loop : -1.59 (0.12), residues: 2557 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 357 TYR 0.031 0.002 TYR B 269 PHE 0.026 0.002 PHE A 759 TRP 0.017 0.002 TRP A1102 HIS 0.008 0.001 HIS C 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00721 / 0.34 (34499) covalent geometry : angle 0.76549 / 0.39 (46978) SS BOND : bond 0.00402 / 0.28 ( 48) SS BOND : angle 1.45872 / 0.97 ( 96) hydrogen bonds : bond 0.04509 / 2.99 ( 1071) hydrogen bonds : angle 6.23769 / 4.27 ( 3012) link_BETA1-4 : bond 0.00530 / 0.30 ( 14) link_BETA1-4 : angle 2.07993 / 1.49 ( 42) link_NAG-ASN : bond 0.00847 / 0.49 ( 40) link_NAG-ASN : angle 3.31095 / 2.38 ( 120) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8444 Ramachandran restraints generated. 4222 Oldfield, 0 Emsley, 4222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8444 Ramachandran restraints generated. 4222 Oldfield, 0 Emsley, 4222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 3667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 68 time to evaluate : 1.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 490 PHE cc_start: 0.8411 (t80) cc_final: 0.7923 (t80) REVERT: A 553 THR cc_start: 0.9123 (OUTLIER) cc_final: 0.8917 (p) REVERT: A 697 MET cc_start: 0.8852 (pmm) cc_final: 0.8603 (pmm) REVERT: A 869 MET cc_start: 0.9404 (mtp) cc_final: 0.9066 (ptp) REVERT: A 1050 MET cc_start: 0.9023 (ptp) cc_final: 0.8399 (mtm) REVERT: B 414 GLN cc_start: 0.8112 (OUTLIER) cc_final: 0.6799 (pm20) REVERT: C 331 ASN cc_start: 0.8901 (OUTLIER) cc_final: 0.8673 (m-40) REVERT: C 740 MET cc_start: 0.9233 (tpp) cc_final: 0.8785 (tpp) REVERT: C 900 MET cc_start: 0.9447 (mmm) cc_final: 0.9180 (mmp) REVERT: C 1018 ILE cc_start: 0.9732 (OUTLIER) cc_final: 0.9341 (mm) REVERT: C 1050 MET cc_start: 0.8967 (pmm) cc_final: 0.8289 (pmm) REVERT: L 94 MET cc_start: 0.8729 (mmp) cc_final: 0.8299 (mmm) outliers start: 51 outliers final: 20 residues processed: 116 average time/residue: 0.2097 time to fit residues: 41.6358 Evaluate side-chains 85 residues out of total 3667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 61 time to evaluate : 1.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 717 ASN Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 414 GLN Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 1008 VAL Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1118 ASP Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain L residue 51 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 421 random chunks: chunk 139 optimal weight: 6.9990 chunk 47 optimal weight: 20.0000 chunk 28 optimal weight: 4.9990 chunk 250 optimal weight: 2.9990 chunk 186 optimal weight: 3.9990 chunk 294 optimal weight: 8.9990 chunk 306 optimal weight: 0.9980 chunk 199 optimal weight: 1.9990 chunk 225 optimal weight: 3.9990 chunk 154 optimal weight: 20.0000 chunk 239 optimal weight: 5.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 901 GLN ** A1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1048 HIS A1083 HIS B 239 GLN ** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 965 GLN ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1023 ASN C1106 GLN ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 39 GLN ** 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 = 0.3651 r_free = 0.3651 target = 0.054842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.034777 restraints weight = 343484.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.035712 restraints weight = 195246.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.036306 restraints weight = 137694.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.036709 restraints weight = 110671.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.036923 restraints weight = 96037.373| |-----------------------------------------------------------------------------| r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.2605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.091 34601 Z= 0.159 Angle : 0.640 18.368 47236 Z= 0.316 Chirality : 0.044 0.285 5466 Planarity : 0.005 0.168 5988 Dihedral : 4.743 47.568 4571 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.38 % Allowed : 7.25 % Favored : 92.37 % Rotamer: Outliers : 1.17 % Allowed : 13.91 % Favored : 84.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.68 % 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 are not related in a simple way. whole: -0.97 (0.13), residues: 4222 helix: 1.56 (0.20), residues: 728 sheet: -0.31 (0.17), residues: 965 loop : -1.51 (0.12), residues: 2529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 357 TYR 0.016 0.001 TYR D 109 PHE 0.018 0.001 PHE A 400 TRP 0.007 0.001 TRP L 152 HIS 0.005 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.16 (34499) covalent geometry : angle 0.62126 / 0.31 (46978) SS BOND : bond 0.00495 / 0.37 ( 48) SS BOND : angle 1.34818 / 0.92 ( 96) hydrogen bonds : bond 0.03721 / 2.47 ( 1071) hydrogen bonds : angle 5.78866 / 3.97 ( 3012) link_BETA1-4 : bond 0.00242 / 0.18 ( 14) link_BETA1-4 : angle 1.36499 / 0.93 ( 42) link_NAG-ASN : bond 0.00477 / 0.29 ( 40) link_NAG-ASN : angle 2.85120 / 2.13 ( 120) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8444 Ramachandran restraints generated. 4222 Oldfield, 0 Emsley, 4222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8444 Ramachandran restraints generated. 4222 Oldfield, 0 Emsley, 4222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 3667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 62 time to evaluate : 1.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 490 PHE cc_start: 0.8470 (t80) cc_final: 0.8001 (t80) REVERT: A 697 MET cc_start: 0.8894 (pmm) cc_final: 0.8627 (pmm) REVERT: A 1050 MET cc_start: 0.8925 (ptp) cc_final: 0.8335 (mtm) REVERT: B 408 ARG cc_start: 0.9358 (OUTLIER) cc_final: 0.8665 (pmt-80) REVERT: B 414 GLN cc_start: 0.8006 (OUTLIER) cc_final: 0.6016 (pm20) REVERT: B 528 LYS cc_start: 0.5591 (OUTLIER) cc_final: 0.4935 (mtmm) REVERT: B 965 GLN cc_start: 0.9274 (OUTLIER) cc_final: 0.9040 (tp-100) REVERT: C 331 ASN cc_start: 0.8794 (OUTLIER) cc_final: 0.8571 (m-40) REVERT: C 740 MET cc_start: 0.9205 (tpp) cc_final: 0.8707 (tpt) REVERT: C 900 MET cc_start: 0.9440 (mmm) cc_final: 0.9106 (mmp) REVERT: C 1050 MET cc_start: 0.8805 (pmm) cc_final: 0.8278 (pmm) REVERT: L 94 MET cc_start: 0.8512 (mmp) cc_final: 0.7960 (mmm) outliers start: 43 outliers final: 22 residues processed: 103 average time/residue: 0.2099 time to fit residues: 37.5971 Evaluate side-chains 85 residues out of total 3667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 58 time to evaluate : 1.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 717 ASN Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 414 GLN Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 965 GLN Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 138 ASP Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain L residue 109 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 421 random chunks: chunk 244 optimal weight: 10.0000 chunk 234 optimal weight: 20.0000 chunk 287 optimal weight: 7.9990 chunk 177 optimal weight: 10.0000 chunk 369 optimal weight: 9.9990 chunk 148 optimal weight: 0.5980 chunk 337 optimal weight: 20.0000 chunk 243 optimal weight: 5.9990 chunk 30 optimal weight: 8.9990 chunk 378 optimal weight: 4.9990 chunk 45 optimal weight: 9.9990 overall best weight: 5.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 66 HIS ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN A1108 ASN B 239 GLN ** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 245 HIS C 901 GLN ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 40 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 39 GLN ** 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 = 0.3629 r_free = 0.3629 target = 0.053993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.033654 restraints weight = 346333.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.034474 restraints weight = 206056.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.035020 restraints weight = 148898.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.035388 restraints weight = 121757.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.035577 restraints weight = 106826.135| |-----------------------------------------------------------------------------| r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.3251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.091 34601 Z= 0.290 Angle : 0.741 18.955 47236 Z= 0.369 Chirality : 0.045 0.280 5466 Planarity : 0.005 0.169 5988 Dihedral : 5.035 46.285 4571 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 17.01 Ramachandran Plot: Outliers : 0.36 % Allowed : 9.43 % Favored : 90.22 % Rotamer: Outliers : 1.83 % Allowed : 14.59 % Favored : 83.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.68 % 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 are not related in a simple way. whole: -1.25 (0.13), residues: 4222 helix: 1.11 (0.20), residues: 730 sheet: -0.48 (0.17), residues: 904 loop : -1.61 (0.12), residues: 2588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 357 TYR 0.023 0.002 TYR B 269 PHE 0.019 0.002 PHE A 759 TRP 0.018 0.002 TRP C 104 HIS 0.008 0.001 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00612 / 0.29 (34499) covalent geometry : angle 0.72236 / 0.36 (46978) SS BOND : bond 0.00413 / 0.29 ( 48) SS BOND : angle 1.41032 / 0.95 ( 96) hydrogen bonds : bond 0.04186 / 2.78 ( 1071) hydrogen bonds : angle 6.04259 / 4.15 ( 3012) link_BETA1-4 : bond 0.00377 / 0.19 ( 14) link_BETA1-4 : angle 1.74249 / 1.25 ( 42) link_NAG-ASN : bond 0.00704 / 0.41 ( 40) link_NAG-ASN : angle 3.03302 / 2.19 ( 120) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8444 Ramachandran restraints generated. 4222 Oldfield, 0 Emsley, 4222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8444 Ramachandran restraints generated. 4222 Oldfield, 0 Emsley, 4222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 3667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 60 time to evaluate : 1.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 LEU cc_start: 0.9337 (OUTLIER) cc_final: 0.9070 (pp) REVERT: A 490 PHE cc_start: 0.8362 (t80) cc_final: 0.7861 (t80) REVERT: A 492 LEU cc_start: 0.9265 (mp) cc_final: 0.8973 (mp) REVERT: A 697 MET cc_start: 0.8952 (pmm) cc_final: 0.8663 (pmm) REVERT: A 869 MET cc_start: 0.9393 (mtp) cc_final: 0.9117 (ptp) REVERT: A 1050 MET cc_start: 0.9005 (ptp) cc_final: 0.8235 (mtm) REVERT: B 182 LYS cc_start: 0.7521 (mttt) cc_final: 0.7191 (mtmt) REVERT: B 408 ARG cc_start: 0.9396 (OUTLIER) cc_final: 0.8715 (pmt-80) REVERT: B 414 GLN cc_start: 0.8037 (OUTLIER) cc_final: 0.5951 (pm20) REVERT: B 528 LYS cc_start: 0.6094 (OUTLIER) cc_final: 0.5564 (mtmm) REVERT: C 331 ASN cc_start: 0.8910 (OUTLIER) cc_final: 0.8612 (m-40) REVERT: C 740 MET cc_start: 0.9279 (tpp) cc_final: 0.8847 (tpp) REVERT: C 900 MET cc_start: 0.9442 (mmm) cc_final: 0.9165 (mmp) REVERT: C 1018 ILE cc_start: 0.9728 (OUTLIER) cc_final: 0.9364 (mm) REVERT: C 1050 MET cc_start: 0.9013 (pmm) cc_final: 0.8076 (pmm) outliers start: 67 outliers final: 34 residues processed: 126 average time/residue: 0.2034 time to fit residues: 44.6424 Evaluate side-chains 97 residues out of total 3667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 57 time to evaluate : 1.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 717 ASN Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 414 GLN Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 138 ASP Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1118 ASP Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain L residue 101 PHE Chi-restraints excluded: chain L residue 109 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 421 random chunks: chunk 16 optimal weight: 10.0000 chunk 239 optimal weight: 8.9990 chunk 368 optimal weight: 30.0000 chunk 48 optimal weight: 0.2980 chunk 361 optimal weight: 0.2980 chunk 223 optimal weight: 5.9990 chunk 24 optimal weight: 6.9990 chunk 141 optimal weight: 3.9990 chunk 122 optimal weight: 1.9990 chunk 290 optimal weight: 5.9990 chunk 45 optimal weight: 20.0000 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN A1010 GLN B 239 GLN ** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 784 GLN ** B 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 965 GLN ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 198 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.055890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.034862 restraints weight = 290360.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.035603 restraints weight = 186599.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.036070 restraints weight = 143742.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.036394 restraints weight = 122718.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.036519 restraints weight = 111228.021| |-----------------------------------------------------------------------------| r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.3223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.091 34601 Z= 0.152 Angle : 0.651 18.127 47236 Z= 0.320 Chirality : 0.045 0.283 5466 Planarity : 0.005 0.168 5988 Dihedral : 4.799 46.137 4571 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.36 % Allowed : 7.58 % Favored : 92.07 % Rotamer: Outliers : 1.47 % Allowed : 15.57 % Favored : 82.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.68 % 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 are not related in a simple way. whole: -1.05 (0.13), residues: 4222 helix: 1.52 (0.20), residues: 726 sheet: -0.34 (0.17), residues: 899 loop : -1.56 (0.12), residues: 2597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 357 TYR 0.015 0.001 TYR D 109 PHE 0.028 0.001 PHE E 10 TRP 0.009 0.001 TRP C 104 HIS 0.006 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.15 (34499) covalent geometry : angle 0.63063 / 0.31 (46978) SS BOND : bond 0.00422 / 0.27 ( 48) SS BOND : angle 1.84082 / 1.04 ( 96) hydrogen bonds : bond 0.03599 / 2.38 ( 1071) hydrogen bonds : angle 5.68563 / 3.92 ( 3012) link_BETA1-4 : bond 0.00198 / 0.13 ( 14) link_BETA1-4 : angle 1.37246 / 0.94 ( 42) link_NAG-ASN : bond 0.00456 / 0.28 ( 40) link_NAG-ASN : angle 2.76727 / 2.07 ( 120) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8444 Ramachandran restraints generated. 4222 Oldfield, 0 Emsley, 4222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8444 Ramachandran restraints generated. 4222 Oldfield, 0 Emsley, 4222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 3667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 61 time to evaluate : 1.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 490 PHE cc_start: 0.8469 (t80) cc_final: 0.8035 (t80) REVERT: A 492 LEU cc_start: 0.9269 (mp) cc_final: 0.9035 (mp) REVERT: A 697 MET cc_start: 0.8921 (pmm) cc_final: 0.8563 (pmm) REVERT: A 869 MET cc_start: 0.9326 (mtp) cc_final: 0.9054 (ptp) REVERT: A 1031 GLU cc_start: 0.8767 (OUTLIER) cc_final: 0.8484 (mm-30) REVERT: A 1050 MET cc_start: 0.8979 (ptp) cc_final: 0.8433 (mtm) REVERT: B 182 LYS cc_start: 0.7381 (mttt) cc_final: 0.7030 (mtmt) REVERT: B 408 ARG cc_start: 0.9326 (OUTLIER) cc_final: 0.8688 (pmt-80) REVERT: B 414 GLN cc_start: 0.7656 (OUTLIER) cc_final: 0.5494 (pm20) REVERT: C 242 LEU cc_start: 0.9335 (mm) cc_final: 0.9022 (pp) REVERT: C 331 ASN cc_start: 0.8799 (OUTLIER) cc_final: 0.8534 (m-40) REVERT: C 740 MET cc_start: 0.9227 (tpp) cc_final: 0.8811 (tpp) REVERT: C 900 MET cc_start: 0.9478 (mmm) cc_final: 0.9144 (mmp) REVERT: C 1050 MET cc_start: 0.8856 (pmm) cc_final: 0.8278 (pmm) REVERT: D 113 MET cc_start: 0.8258 (tmm) cc_final: 0.7862 (tmm) outliers start: 54 outliers final: 36 residues processed: 113 average time/residue: 0.2004 time to fit residues: 39.7747 Evaluate side-chains 100 residues out of total 3667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 60 time to evaluate : 1.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 717 ASN Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 414 GLN Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 945 LEU Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 138 ASP Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 844 ILE Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain L residue 101 PHE Chi-restraints excluded: chain L residue 109 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 421 random chunks: chunk 383 optimal weight: 10.0000 chunk 356 optimal weight: 30.0000 chunk 176 optimal weight: 6.9990 chunk 265 optimal weight: 30.0000 chunk 396 optimal weight: 30.0000 chunk 381 optimal weight: 0.0050 chunk 153 optimal weight: 20.0000 chunk 407 optimal weight: 30.0000 chunk 268 optimal weight: 0.0770 chunk 138 optimal weight: 1.9990 chunk 208 optimal weight: 4.9990 overall best weight: 2.8158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 99 ASN ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 487 ASN ** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 49 HIS C 901 GLN ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.055923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.034794 restraints weight = 277979.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.034794 restraints weight = 197828.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.034794 restraints weight = 197828.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.034794 restraints weight = 197828.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.034794 restraints weight = 197828.303| |-----------------------------------------------------------------------------| r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.3370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.092 34601 Z= 0.159 Angle : 0.634 17.990 47236 Z= 0.313 Chirality : 0.044 0.282 5466 Planarity : 0.005 0.167 5988 Dihedral : 4.680 44.995 4571 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.36 % Allowed : 8.41 % Favored : 91.24 % Rotamer: Outliers : 1.55 % Allowed : 15.84 % Favored : 82.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.68 % 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 are not related in a simple way. whole: -1.02 (0.13), residues: 4222 helix: 1.56 (0.20), residues: 730 sheet: -0.38 (0.17), residues: 927 loop : -1.53 (0.12), residues: 2565 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 357 TYR 0.017 0.001 TYR D 109 PHE 0.019 0.001 PHE E 10 TRP 0.009 0.001 TRP C 104 HIS 0.005 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.16 (34499) covalent geometry : angle 0.61668 / 0.31 (46978) SS BOND : bond 0.00364 / 0.25 ( 48) SS BOND : angle 1.48027 / 0.91 ( 96) hydrogen bonds : bond 0.03504 / 2.32 ( 1071) hydrogen bonds : angle 5.57065 / 3.85 ( 3012) link_BETA1-4 : bond 0.00171 / 0.12 ( 14) link_BETA1-4 : angle 1.37034 / 0.95 ( 42) link_NAG-ASN : bond 0.00435 / 0.26 ( 40) link_NAG-ASN : angle 2.59369 / 1.92 ( 120) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8444 Ramachandran restraints generated. 4222 Oldfield, 0 Emsley, 4222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8444 Ramachandran restraints generated. 4222 Oldfield, 0 Emsley, 4222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 3667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 59 time to evaluate : 1.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 490 PHE cc_start: 0.8451 (t80) cc_final: 0.8136 (t80) REVERT: A 697 MET cc_start: 0.8959 (pmm) cc_final: 0.8625 (pmm) REVERT: A 869 MET cc_start: 0.9256 (mtp) cc_final: 0.8988 (ptp) REVERT: A 1031 GLU cc_start: 0.8942 (OUTLIER) cc_final: 0.8649 (mm-30) REVERT: A 1050 MET cc_start: 0.8973 (ptp) cc_final: 0.8405 (mtm) REVERT: B 182 LYS cc_start: 0.7697 (mttt) cc_final: 0.7386 (mtmt) REVERT: B 414 GLN cc_start: 0.7787 (OUTLIER) cc_final: 0.6370 (pm20) REVERT: C 226 LEU cc_start: 0.9382 (OUTLIER) cc_final: 0.9159 (mm) REVERT: C 242 LEU cc_start: 0.9367 (mm) cc_final: 0.9039 (pp) REVERT: C 331 ASN cc_start: 0.8851 (OUTLIER) cc_final: 0.8567 (m-40) REVERT: C 432 CYS cc_start: 0.7988 (OUTLIER) cc_final: 0.7338 (p) REVERT: C 740 MET cc_start: 0.9295 (tpp) cc_final: 0.8901 (tpp) REVERT: C 900 MET cc_start: 0.9524 (mmm) cc_final: 0.9205 (mmp) REVERT: C 1050 MET cc_start: 0.8890 (pmm) cc_final: 0.8291 (pmm) REVERT: D 113 MET cc_start: 0.8225 (tmm) cc_final: 0.7845 (tmm) outliers start: 57 outliers final: 41 residues processed: 114 average time/residue: 0.1927 time to fit residues: 39.0850 Evaluate side-chains 103 residues out of total 3667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 57 time to evaluate : 1.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 717 ASN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 414 GLN Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 945 LEU Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 49 HIS Chi-restraints excluded: chain C residue 138 ASP Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 844 ILE Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain H residue 113 MET Chi-restraints excluded: chain L residue 109 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 421 random chunks: chunk 164 optimal weight: 0.8980 chunk 281 optimal weight: 0.8980 chunk 234 optimal weight: 6.9990 chunk 178 optimal weight: 9.9990 chunk 385 optimal weight: 20.0000 chunk 358 optimal weight: 50.0000 chunk 251 optimal weight: 2.9990 chunk 311 optimal weight: 5.9990 chunk 127 optimal weight: 10.0000 chunk 170 optimal weight: 8.9990 chunk 346 optimal weight: 7.9990 overall best weight: 3.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 487 ASN ** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 49 HIS ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.054296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.033727 restraints weight = 339634.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.034590 restraints weight = 201528.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.035146 restraints weight = 146029.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.035463 restraints weight = 119358.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.035731 restraints weight = 105359.833| |-----------------------------------------------------------------------------| r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.3539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 34601 Z= 0.187 Angle : 0.649 18.024 47236 Z= 0.321 Chirality : 0.044 0.281 5466 Planarity : 0.005 0.168 5988 Dihedral : 4.712 44.756 4571 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.36 % Allowed : 8.27 % Favored : 91.38 % Rotamer: Outliers : 1.58 % Allowed : 16.20 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.68 % 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 are not related in a simple way. whole: -1.06 (0.13), residues: 4222 helix: 1.52 (0.20), residues: 730 sheet: -0.42 (0.17), residues: 901 loop : -1.54 (0.12), residues: 2591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 357 TYR 0.017 0.001 TYR D 109 PHE 0.018 0.001 PHE E 10 TRP 0.010 0.001 TRP C 104 HIS 0.015 0.001 HIS C 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.19 (34499) covalent geometry : angle 0.63315 / 0.32 (46978) SS BOND : bond 0.00357 / 0.25 ( 48) SS BOND : angle 1.42683 / 0.90 ( 96) hydrogen bonds : bond 0.03588 / 2.38 ( 1071) hydrogen bonds : angle 5.58525 / 3.87 ( 3012) link_BETA1-4 : bond 0.00149 / 0.09 ( 14) link_BETA1-4 : angle 1.42111 / 0.98 ( 42) link_NAG-ASN : bond 0.00437 / 0.25 ( 40) link_NAG-ASN : angle 2.57168 / 1.88 ( 120) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8444 Ramachandran restraints generated. 4222 Oldfield, 0 Emsley, 4222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8444 Ramachandran restraints generated. 4222 Oldfield, 0 Emsley, 4222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 3667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 58 time to evaluate : 1.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 490 PHE cc_start: 0.8396 (t80) cc_final: 0.8024 (t80) REVERT: A 492 LEU cc_start: 0.9245 (mp) cc_final: 0.8863 (mt) REVERT: A 697 MET cc_start: 0.8996 (pmm) cc_final: 0.8635 (pmm) REVERT: A 869 MET cc_start: 0.9359 (mtp) cc_final: 0.9071 (ptp) REVERT: A 1031 GLU cc_start: 0.8803 (OUTLIER) cc_final: 0.8525 (mm-30) REVERT: A 1050 MET cc_start: 0.8999 (ptp) cc_final: 0.8332 (mtm) REVERT: B 182 LYS cc_start: 0.7546 (mttt) cc_final: 0.7220 (mtmt) REVERT: B 414 GLN cc_start: 0.7772 (OUTLIER) cc_final: 0.6319 (pm20) REVERT: C 226 LEU cc_start: 0.9207 (OUTLIER) cc_final: 0.8971 (mm) REVERT: C 242 LEU cc_start: 0.9387 (mm) cc_final: 0.9063 (pp) REVERT: C 331 ASN cc_start: 0.8875 (OUTLIER) cc_final: 0.8575 (m-40) REVERT: C 432 CYS cc_start: 0.7978 (OUTLIER) cc_final: 0.7370 (p) REVERT: C 740 MET cc_start: 0.9265 (tpp) cc_final: 0.8859 (tpp) REVERT: C 900 MET cc_start: 0.9466 (mmm) cc_final: 0.9127 (mmp) REVERT: C 1050 MET cc_start: 0.8890 (pmm) cc_final: 0.8230 (pmm) REVERT: D 113 MET cc_start: 0.8250 (tmm) cc_final: 0.7913 (tmm) REVERT: L 94 MET cc_start: 0.8694 (mmp) cc_final: 0.8151 (mmm) outliers start: 58 outliers final: 45 residues processed: 115 average time/residue: 0.1952 time to fit residues: 39.5870 Evaluate side-chains 107 residues out of total 3667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 57 time to evaluate : 1.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 717 ASN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 414 GLN Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 49 HIS Chi-restraints excluded: chain C residue 138 ASP Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 844 ILE Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain H residue 113 MET Chi-restraints excluded: chain L residue 101 PHE Chi-restraints excluded: chain L residue 109 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 421 random chunks: chunk 67 optimal weight: 5.9990 chunk 6 optimal weight: 0.8980 chunk 24 optimal weight: 5.9990 chunk 380 optimal weight: 20.0000 chunk 233 optimal weight: 8.9990 chunk 65 optimal weight: 6.9990 chunk 175 optimal weight: 0.8980 chunk 162 optimal weight: 7.9990 chunk 92 optimal weight: 8.9990 chunk 159 optimal weight: 8.9990 chunk 68 optimal weight: 4.9990 overall best weight: 3.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 487 ASN ** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.054203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.033855 restraints weight = 343199.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.034710 restraints weight = 202203.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.035252 restraints weight = 146316.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.035628 restraints weight = 119667.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.035829 restraints weight = 104743.468| |-----------------------------------------------------------------------------| r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.3707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 34601 Z= 0.195 Angle : 0.657 18.162 47236 Z= 0.325 Chirality : 0.044 0.279 5466 Planarity : 0.005 0.168 5988 Dihedral : 4.732 43.982 4571 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.38 % Allowed : 8.36 % Favored : 91.26 % Rotamer: Outliers : 1.42 % Allowed : 16.39 % Favored : 82.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.68 % 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 are not related in a simple way. whole: -1.08 (0.13), residues: 4222 helix: 1.47 (0.20), residues: 729 sheet: -0.46 (0.17), residues: 891 loop : -1.53 (0.12), residues: 2602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 357 TYR 0.017 0.001 TYR D 109 PHE 0.017 0.001 PHE E 10 TRP 0.012 0.001 TRP C 104 HIS 0.024 0.001 HIS C 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.19 (34499) covalent geometry : angle 0.64131 / 0.32 (46978) SS BOND : bond 0.00363 / 0.25 ( 48) SS BOND : angle 1.41401 / 0.90 ( 96) hydrogen bonds : bond 0.03580 / 2.37 ( 1071) hydrogen bonds : angle 5.59534 / 3.88 ( 3012) link_BETA1-4 : bond 0.00120 / 0.07 ( 14) link_BETA1-4 : angle 1.42963 / 0.99 ( 42) link_NAG-ASN : bond 0.00440 / 0.25 ( 40) link_NAG-ASN : angle 2.54699 / 1.85 ( 120) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8444 Ramachandran restraints generated. 4222 Oldfield, 0 Emsley, 4222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8444 Ramachandran restraints generated. 4222 Oldfield, 0 Emsley, 4222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 3667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 56 time to evaluate : 1.136 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 697 MET cc_start: 0.8996 (pmm) cc_final: 0.8662 (pmm) REVERT: A 869 MET cc_start: 0.9372 (mtp) cc_final: 0.9088 (ptp) REVERT: A 1031 GLU cc_start: 0.8819 (OUTLIER) cc_final: 0.8544 (mm-30) REVERT: A 1050 MET cc_start: 0.9007 (ptp) cc_final: 0.8358 (mtm) REVERT: B 182 LYS cc_start: 0.7543 (mttt) cc_final: 0.7210 (mtmt) REVERT: B 414 GLN cc_start: 0.7735 (OUTLIER) cc_final: 0.6277 (pm20) REVERT: C 226 LEU cc_start: 0.9202 (OUTLIER) cc_final: 0.8967 (mm) REVERT: C 242 LEU cc_start: 0.9416 (mm) cc_final: 0.9081 (pp) REVERT: C 331 ASN cc_start: 0.8895 (OUTLIER) cc_final: 0.8583 (m-40) REVERT: C 432 CYS cc_start: 0.8011 (OUTLIER) cc_final: 0.7408 (p) REVERT: C 740 MET cc_start: 0.9316 (tpp) cc_final: 0.8912 (tpp) REVERT: C 900 MET cc_start: 0.9455 (mmm) cc_final: 0.9105 (mmp) REVERT: C 1050 MET cc_start: 0.8914 (pmm) cc_final: 0.8211 (pmm) REVERT: D 113 MET cc_start: 0.8244 (tmm) cc_final: 0.7936 (tmm) REVERT: L 94 MET cc_start: 0.8701 (mmp) cc_final: 0.8173 (mmm) outliers start: 52 outliers final: 45 residues processed: 107 average time/residue: 0.1973 time to fit residues: 37.1284 Evaluate side-chains 105 residues out of total 3667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 55 time to evaluate : 1.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 717 ASN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 414 GLN Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 138 ASP Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 844 ILE Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain H residue 113 MET Chi-restraints excluded: chain L residue 101 PHE Chi-restraints excluded: chain L residue 109 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 421 random chunks: chunk 231 optimal weight: 0.9990 chunk 333 optimal weight: 10.0000 chunk 203 optimal weight: 6.9990 chunk 380 optimal weight: 20.0000 chunk 124 optimal weight: 0.0770 chunk 396 optimal weight: 10.0000 chunk 189 optimal weight: 0.0970 chunk 114 optimal weight: 9.9990 chunk 130 optimal weight: 9.9990 chunk 285 optimal weight: 6.9990 chunk 26 optimal weight: 0.8980 overall best weight: 1.8140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 487 ASN ** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 836 GLN ** B 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 39 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.055987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.035128 restraints weight = 276404.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.035815 restraints weight = 183269.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.036275 restraints weight = 143169.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.036561 restraints weight = 123043.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.036737 restraints weight = 111919.186| |-----------------------------------------------------------------------------| r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.3695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.096 34601 Z= 0.128 Angle : 0.617 17.857 47236 Z= 0.303 Chirality : 0.044 0.376 5466 Planarity : 0.005 0.167 5988 Dihedral : 4.583 43.536 4571 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.38 % Allowed : 7.41 % Favored : 92.21 % Rotamer: Outliers : 1.36 % Allowed : 16.53 % Favored : 82.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.68 % 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 are not related in a simple way. whole: -0.96 (0.13), residues: 4222 helix: 1.68 (0.21), residues: 729 sheet: -0.39 (0.17), residues: 948 loop : -1.50 (0.12), residues: 2545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 454 TYR 0.017 0.001 TYR D 109 PHE 0.017 0.001 PHE A 400 TRP 0.008 0.001 TRP H 47 HIS 0.006 0.001 HIS A 625 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 (34499) covalent geometry : angle 0.60188 / 0.30 (46978) SS BOND : bond 0.00324 / 0.23 ( 48) SS BOND : angle 1.35106 / 0.87 ( 96) hydrogen bonds : bond 0.03332 / 2.21 ( 1071) hydrogen bonds : angle 5.38248 / 3.74 ( 3012) link_BETA1-4 : bond 0.00241 / 0.17 ( 14) link_BETA1-4 : angle 1.32990 / 0.91 ( 42) link_NAG-ASN : bond 0.00408 / 0.27 ( 40) link_NAG-ASN : angle 2.39533 / 1.76 ( 120) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7673.47 seconds wall clock time: 133 minutes 12.87 seconds (7992.87 seconds total)