Starting phenix.real_space_refine on Mon Jul 6 11:23:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7wob_32647/07_2026/7wob_32647.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wob_32647/07_2026/7wob_32647.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7wob_32647/07_2026/7wob_32647.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wob_32647/07_2026/7wob_32647.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7wob_32647/07_2026/7wob_32647.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7wob_32647/07_2026/7wob_32647.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7wob_32647/07_2026/7wob_32647.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wob_32647/07_2026/7wob_32647.map" } resolution = 3.25 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 144 5.16 5 C 22315 2.51 5 N 5867 2.21 5 O 6808 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 56 residue(s): 0.03s 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: 35134 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 8338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1076, 8338 Classifications: {'peptide': 1076} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 53, 'TRANS': 1022} Chain breaks: 3 Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 6, 'ARG:plan': 1, 'ASP:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 39 Chain: "C" Number of atoms: 8338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1076, 8338 Classifications: {'peptide': 1076} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 53, 'TRANS': 1022} Chain breaks: 3 Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 6, 'ARG:plan': 1, 'ASP:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 39 Chain: "E" Number of atoms: 8338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1076, 8338 Classifications: {'peptide': 1076} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 53, 'TRANS': 1022} Chain breaks: 3 Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 6, 'ARG:plan': 1, 'ASP:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 39 Chain: "D" Number of atoms: 1560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1560 Classifications: {'peptide': 204} Link IDs: {'PTRANS': 12, 'TRANS': 191} Chain breaks: 2 Chain: "B" Number of atoms: 1636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1636 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 199} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "F" Number of atoms: 1560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1560 Classifications: {'peptide': 204} Link IDs: {'PTRANS': 12, 'TRANS': 191} Chain breaks: 2 Chain: "G" Number of atoms: 1636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1636 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 199} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "H" Number of atoms: 1560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1560 Classifications: {'peptide': 204} Link IDs: {'PTRANS': 12, 'TRANS': 191} Chain breaks: 2 Chain: "I" Number of atoms: 1636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1636 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 199} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "A" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen chiralities: 13 Chain: "C" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen chiralities: 13 Chain: "E" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen chiralities: 12 Time building chain proxies: 7.11, per 1000 atoms: 0.20 Number of scatterers: 35134 At special positions: 0 Unit cell: (207.46, 193.52, 223.04, 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 144 16.00 O 6808 8.00 N 5867 7.00 C 22315 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=54, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS E 15 " - pdb=" SG CYS E 136 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 166 " distance=2.03 Simple disulfide: pdb=" SG CYS E 291 " - pdb=" SG CYS E 301 " distance=2.03 Simple disulfide: pdb=" SG CYS E 336 " - pdb=" SG CYS E 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 432 " distance=2.03 Simple disulfide: pdb=" SG CYS E 391 " - pdb=" SG CYS E 525 " distance=2.03 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " distance=2.03 Simple disulfide: pdb=" SG CYS E 538 " - pdb=" SG CYS E 590 " distance=2.03 Simple disulfide: pdb=" SG CYS E 617 " - pdb=" SG CYS E 649 " distance=2.03 Simple disulfide: pdb=" SG CYS E 662 " - pdb=" SG CYS E 671 " distance=2.03 Simple disulfide: pdb=" SG CYS E 738 " - pdb=" SG CYS E 760 " distance=2.03 Simple disulfide: pdb=" SG CYS E 743 " - pdb=" SG CYS E 749 " distance=2.03 Simple disulfide: pdb=" SG CYS E1032 " - pdb=" SG CYS E1043 " distance=2.03 Simple disulfide: pdb=" SG CYS E1082 " - pdb=" SG CYS E1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 147 " - pdb=" SG CYS D 203 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 89 " distance=2.03 Simple disulfide: pdb=" SG CYS B 135 " - pdb=" SG CYS B 195 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 147 " - pdb=" SG CYS F 203 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 89 " distance=2.03 Simple disulfide: pdb=" SG CYS G 135 " - pdb=" SG CYS G 195 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 147 " - pdb=" SG CYS H 203 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 89 " distance=2.03 Simple disulfide: pdb=" SG CYS I 135 " - pdb=" SG CYS I 195 " 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 NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 165 " " NAG A1303 " - " ASN A 234 " " NAG A1304 " - " ASN A 282 " " NAG A1305 " - " ASN A 331 " " NAG A1306 " - " ASN A 343 " " NAG A1307 " - " ASN A 616 " " NAG A1308 " - " ASN A 709 " " NAG A1309 " - " ASN A 717 " " NAG A1310 " - " ASN A 801 " " NAG A1311 " - " ASN A1074 " " NAG A1312 " - " ASN A1098 " " NAG A1313 " - " ASN A1134 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 165 " " NAG C1303 " - " ASN C 234 " " NAG C1304 " - " ASN C 282 " " NAG C1305 " - " ASN C 331 " " NAG C1306 " - " ASN C 343 " " NAG C1307 " - " ASN C 616 " " NAG C1308 " - " ASN C 709 " " NAG C1309 " - " ASN C 717 " " NAG C1310 " - " ASN C 801 " " NAG C1311 " - " ASN C1074 " " NAG C1312 " - " ASN C1098 " " NAG C1313 " - " ASN C1134 " " NAG E1301 " - " ASN E 61 " " NAG E1302 " - " ASN E 165 " " NAG E1303 " - " ASN E 234 " " NAG E1304 " - " ASN E 282 " " NAG E1305 " - " ASN E 331 " " NAG E1306 " - " ASN E 616 " " NAG E1307 " - " ASN E 709 " " NAG E1308 " - " ASN E 717 " " NAG E1309 " - " ASN E 801 " " NAG E1310 " - " ASN E1074 " " NAG E1311 " - " ASN E1098 " " NAG E1312 " - " ASN E1134 " Time building additional restraints: 2.57 Conformation dependent library (CDL) restraints added in 1.3 seconds 8856 Ramachandran restraints generated. 4428 Oldfield, 0 Emsley, 4428 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8352 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 83 sheets defined 16.6% alpha, 21.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.25 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 403 through 407 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.698A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N PHE A 782 " --> pdb=" O THR A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.501A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 897 through 907 Processing helix chain 'A' and resid 912 through 941 removed outlier: 4.199A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N LYS A 921 " --> pdb=" O TYR A 917 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N LEU A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.543A pdb=" N GLN A 949 " --> pdb=" O LEU A 945 " (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 984 removed outlier: 3.594A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.653A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 3.897A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 337 through 343 removed outlier: 4.001A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 386 through 390 removed outlier: 3.798A pdb=" N LEU C 390 " --> pdb=" O LEU C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 407 removed outlier: 3.906A pdb=" N GLU C 406 " --> pdb=" O ARG C 403 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 403 through 407' Processing helix chain 'C' and resid 502 through 506 removed outlier: 3.815A pdb=" N GLN C 506 " --> pdb=" O VAL C 503 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 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: 3.651A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 4.031A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 912 through 941 removed outlier: 4.224A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N LYS C 921 " --> pdb=" O TYR C 917 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N LEU C 922 " --> pdb=" O GLU C 918 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.000A pdb=" N GLN C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 5.276A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1146 removed outlier: 3.765A pdb=" N LEU C1145 " --> pdb=" O LEU C1141 " (cutoff:3.500A) Processing helix chain 'E' and resid 294 through 303 Processing helix chain 'E' and resid 365 through 370 Processing helix chain 'E' and resid 386 through 390 removed outlier: 3.778A pdb=" N ASP E 389 " --> pdb=" O LYS E 386 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU E 390 " --> pdb=" O LEU E 387 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 386 through 390' Processing helix chain 'E' and resid 403 through 407 removed outlier: 3.761A pdb=" N GLU E 406 " --> pdb=" O ARG E 403 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N VAL E 407 " --> pdb=" O GLY E 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 403 through 407' Processing helix chain 'E' and resid 502 through 506 removed outlier: 3.793A pdb=" N TYR E 505 " --> pdb=" O GLY E 502 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLN E 506 " --> pdb=" O VAL E 503 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 502 through 506' Processing helix chain 'E' and resid 737 through 742 Processing helix chain 'E' and resid 746 through 754 removed outlier: 3.685A pdb=" N LEU E 754 " --> pdb=" O SER E 750 " (cutoff:3.500A) Processing helix chain 'E' and resid 759 through 783 removed outlier: 3.599A pdb=" N VAL E 781 " --> pdb=" O ASN E 777 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N PHE E 782 " --> pdb=" O THR E 778 " (cutoff:3.500A) Processing helix chain 'E' and resid 816 through 826 Processing helix chain 'E' and resid 866 through 884 Processing helix chain 'E' and resid 897 through 908 Processing helix chain 'E' and resid 912 through 941 removed outlier: 4.324A pdb=" N LEU E 916 " --> pdb=" O THR E 912 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N LYS E 921 " --> pdb=" O TYR E 917 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N LEU E 922 " --> pdb=" O GLU E 918 " (cutoff:3.500A) Processing helix chain 'E' and resid 946 through 965 Processing helix chain 'E' and resid 966 through 968 No H-bonds generated for 'chain 'E' and resid 966 through 968' Processing helix chain 'E' and resid 976 through 984 Processing helix chain 'E' and resid 985 through 1033 removed outlier: 4.721A pdb=" N VAL E 991 " --> pdb=" O PRO E 987 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N GLN E 992 " --> pdb=" O GLU E 988 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 165 Processing helix chain 'B' and resid 122 through 126 removed outlier: 3.567A pdb=" N GLN B 125 " --> pdb=" O SER B 122 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N LEU B 126 " --> pdb=" O ASP B 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 122 through 126' Processing helix chain 'G' and resid 29 through 32 removed outlier: 4.335A pdb=" N ARG G 32 " --> pdb=" O ILE G 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 29 through 32' Processing helix chain 'G' and resid 80 through 84 removed outlier: 3.543A pdb=" N PHE G 84 " --> pdb=" O PRO G 81 " (cutoff:3.500A) Processing helix chain 'G' and resid 122 through 127 removed outlier: 3.675A pdb=" N LYS G 127 " --> pdb=" O ASP G 123 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 removed outlier: 4.009A pdb=" N THR H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 160 through 165 Processing helix chain 'I' and resid 80 through 84 Processing helix chain 'I' and resid 186 through 190 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 3.895A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 36 through 37 removed outlier: 7.524A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 8.889A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N TYR A 200 " --> pdb=" O ILE A 197 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL A 193 " --> pdb=" O TYR A 204 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYS A 206 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLU A 191 " --> pdb=" O LYS A 206 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 42 through 43 Processing sheet with id=AA4, first strand: chain 'A' and resid 50 through 51 Processing sheet with id=AA5, first strand: chain 'A' and resid 54 through 55 Processing sheet with id=AA6, first strand: chain 'A' and resid 83 through 85 Processing sheet with id=AA7, first strand: chain 'A' and resid 116 through 118 Processing sheet with id=AA8, first strand: chain 'A' and resid 152 through 154 Processing sheet with id=AA9, first strand: chain 'A' and resid 311 through 319 removed outlier: 7.232A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 325 through 327 removed outlier: 6.686A pdb=" N ILE A 326 " --> pdb=" O ASN A 542 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLY A 548 " --> pdb=" O PHE A 541 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.807A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB4, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.579A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 565 through 566 removed outlier: 7.227A pdb=" N PHE A 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.081A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.536A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLN A 675 " --> pdb=" O SER A 691 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N SER A 673 " --> pdb=" O ILE A 693 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 702 through 703 Processing sheet with id=AB8, first strand: chain 'A' and resid 712 through 728 removed outlier: 6.868A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 712 through 728 removed outlier: 6.868A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.372A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 788 through 790 removed outlier: 5.965A pdb=" N ILE A 788 " --> pdb=" O ASN E 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 5.481A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N CYS A1082 " --> pdb=" O VAL A1133 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 27 through 30 removed outlier: 3.724A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU C 189 " --> pdb=" O THR C 208 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLU C 191 " --> pdb=" O LYS C 206 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL C 193 " --> pdb=" O TYR C 204 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU C 229 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 51 through 55 Processing sheet with id=AC6, first strand: chain 'C' and resid 83 through 85 Processing sheet with id=AC7, first strand: chain 'C' and resid 152 through 153 Processing sheet with id=AC8, first strand: chain 'C' and resid 278 through 279 removed outlier: 6.658A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.173A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 376 through 378 Processing sheet with id=AD2, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AD3, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.843A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 538 through 539 removed outlier: 3.695A pdb=" N THR C 588 " --> pdb=" O VAL C 551 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 565 through 566 removed outlier: 6.632A pdb=" N PHE C 565 " --> pdb=" O PHE E 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.871A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.423A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 702 through 703 Processing sheet with id=AD8, first strand: chain 'C' and resid 711 through 722 removed outlier: 6.814A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 725 through 728 Processing sheet with id=AE1, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.256A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 1081 through 1082 removed outlier: 5.140A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER C1123 " --> pdb=" O ALA C1087 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 28 through 30 Processing sheet with id=AE4, first strand: chain 'E' and resid 47 through 48 removed outlier: 3.997A pdb=" N VAL E 47 " --> pdb=" O TYR E 279 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N ASP E 287 " --> pdb=" O LYS E 278 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 54 through 55 removed outlier: 3.551A pdb=" N PHE E 55 " --> pdb=" O GLN E 271 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'E' and resid 65 through 68 removed outlier: 3.659A pdb=" N PHE E 65 " --> pdb=" O TYR E 265 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'E' and resid 83 through 85 removed outlier: 3.514A pdb=" N LEU E 241 " --> pdb=" O GLY E 103 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLY E 103 " --> pdb=" O LEU E 241 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'E' and resid 224 through 230 removed outlier: 3.592A pdb=" N GLU E 224 " --> pdb=" O SER E 205 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ILE E 203 " --> pdb=" O LEU E 226 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N ASP E 228 " --> pdb=" O PHE E 201 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N PHE E 201 " --> pdb=" O ASP E 228 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N TYR E 204 " --> pdb=" O VAL E 193 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL E 193 " --> pdb=" O TYR E 204 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'E' and resid 127 through 129 removed outlier: 4.292A pdb=" N ILE E 128 " --> pdb=" O TYR E 170 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'E' and resid 135 through 140 removed outlier: 10.827A pdb=" N ASP E 138 " --> pdb=" O TYR E 160 " (cutoff:3.500A) removed outlier: 8.853A pdb=" N TYR E 160 " --> pdb=" O ASP E 138 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N PHE E 140 " --> pdb=" O ARG E 158 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'E' and resid 151 through 153 removed outlier: 3.591A pdb=" N SER E 151 " --> pdb=" O HIS E 146 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N HIS E 146 " --> pdb=" O SER E 151 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'E' and resid 311 through 319 removed outlier: 5.388A pdb=" N ILE E 312 " --> pdb=" O THR E 599 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N THR E 599 " --> pdb=" O ILE E 312 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N GLN E 314 " --> pdb=" O VAL E 597 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N VAL E 597 " --> pdb=" O GLN E 314 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER E 316 " --> pdb=" O VAL E 595 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N GLY E 594 " --> pdb=" O GLN E 613 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'E' and resid 325 through 327 removed outlier: 3.574A pdb=" N GLY E 548 " --> pdb=" O PHE E 541 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'E' and resid 357 through 358 removed outlier: 3.688A pdb=" N SER E 514 " --> pdb=" O TYR E 396 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TRP E 436 " --> pdb=" O ARG E 509 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA E 435 " --> pdb=" O THR E 376 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'E' and resid 452 through 453 Processing sheet with id=AF7, first strand: chain 'E' and resid 654 through 655 removed outlier: 6.131A pdb=" N GLU E 654 " --> pdb=" O ALA E 694 " (cutoff:3.500A) removed outlier: 8.514A pdb=" N THR E 696 " --> pdb=" O GLU E 654 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N SER E 691 " --> pdb=" O GLN E 675 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLN E 675 " --> pdb=" O SER E 691 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER E 673 " --> pdb=" O ILE E 693 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ILE E 670 " --> pdb=" O ILE E 666 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'E' and resid 711 through 722 removed outlier: 7.072A pdb=" N GLN E1071 " --> pdb=" O THR E 716 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N PHE E 718 " --> pdb=" O PRO E1069 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N ILE E 720 " --> pdb=" O TYR E1067 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N TYR E1067 " --> pdb=" O ILE E 720 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N VAL E 722 " --> pdb=" O VAL E1065 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N VAL E1065 " --> pdb=" O VAL E 722 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N TYR E1067 " --> pdb=" O HIS E1048 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N HIS E1048 " --> pdb=" O TYR E1067 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'E' and resid 711 through 722 removed outlier: 7.072A pdb=" N GLN E1071 " --> pdb=" O THR E 716 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N PHE E 718 " --> pdb=" O PRO E1069 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N ILE E 720 " --> pdb=" O TYR E1067 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N TYR E1067 " --> pdb=" O ILE E 720 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N VAL E 722 " --> pdb=" O VAL E1065 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N VAL E1065 " --> pdb=" O VAL E 722 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'E' and resid 725 through 728 Processing sheet with id=AG2, first strand: chain 'E' and resid 733 through 735 removed outlier: 4.098A pdb=" N LYS E 733 " --> pdb=" O LEU E 861 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'E' and resid 1120 through 1125 removed outlier: 3.671A pdb=" N SER E1123 " --> pdb=" O ALA E1087 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N ALA E1087 " --> pdb=" O SER E1123 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE E1081 " --> pdb=" O HIS E1088 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'D' and resid 5 through 6 removed outlier: 3.695A pdb=" N VAL D 18 " --> pdb=" O LEU D 83 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU D 83 " --> pdb=" O VAL D 18 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR D 78 " --> pdb=" O ASP D 73 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'D' and resid 57 through 60 removed outlier: 3.570A pdb=" N ARG D 50 " --> pdb=" O HIS D 59 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N TRP D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ARG D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLY D 49 " --> pdb=" O TRP D 36 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'D' and resid 144 through 148 removed outlier: 4.021A pdb=" N SER D 187 " --> pdb=" O CYS D 147 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'D' and resid 157 through 160 removed outlier: 3.527A pdb=" N THR D 158 " --> pdb=" O ASN D 206 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'B' and resid 4 through 6 removed outlier: 3.539A pdb=" N PHE B 72 " --> pdb=" O CYS B 23 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'B' and resid 10 through 13 removed outlier: 3.561A pdb=" N LEU B 13 " --> pdb=" O GLU B 106 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N TRP B 36 " --> pdb=" O LEU B 48 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER B 54 " --> pdb=" O TYR B 50 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'B' and resid 10 through 13 removed outlier: 3.561A pdb=" N LEU B 13 " --> pdb=" O GLU B 106 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N THR B 98 " --> pdb=" O GLN B 91 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'B' and resid 115 through 118 removed outlier: 3.501A pdb=" N SER B 115 " --> pdb=" O ASN B 138 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ASN B 138 " --> pdb=" O SER B 115 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N TYR B 174 " --> pdb=" O ASN B 139 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'B' and resid 147 through 150 Processing sheet with id=AH4, first strand: chain 'F' and resid 4 through 6 removed outlier: 3.743A pdb=" N VAL F 20 " --> pdb=" O MET F 81 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N MET F 81 " --> pdb=" O VAL F 20 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'F' and resid 57 through 60 removed outlier: 3.545A pdb=" N ILE F 57 " --> pdb=" O ILE F 52 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLU F 46 " --> pdb=" O ARG F 38 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ARG F 38 " --> pdb=" O GLU F 46 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N TRP F 36 " --> pdb=" O MET F 48 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N ARG F 50 " --> pdb=" O PHE F 34 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N PHE F 34 " --> pdb=" O ARG F 50 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA F 92 " --> pdb=" O VAL F 116 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'F' and resid 127 through 129 removed outlier: 4.046A pdb=" N LYS F 150 " --> pdb=" O SER F 127 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N CYS F 147 " --> pdb=" O SER F 187 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N SER F 187 " --> pdb=" O CYS F 147 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL F 188 " --> pdb=" O HIS F 171 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'F' and resid 157 through 159 Processing sheet with id=AH8, first strand: chain 'G' and resid 10 through 13 removed outlier: 3.789A pdb=" N LEU G 11 " --> pdb=" O LYS G 104 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU G 13 " --> pdb=" O GLU G 106 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'G' and resid 19 through 20 removed outlier: 3.546A pdb=" N ALA G 19 " --> pdb=" O ILE G 76 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'G' and resid 54 through 55 removed outlier: 6.590A pdb=" N TRP G 36 " --> pdb=" O LEU G 48 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N TYR G 50 " --> pdb=" O LEU G 34 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N LEU G 34 " --> pdb=" O TYR G 50 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'G' and resid 118 through 119 Processing sheet with id=AI3, first strand: chain 'G' and resid 146 through 149 removed outlier: 4.234A pdb=" N LYS G 146 " --> pdb=" O THR G 198 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR G 198 " --> pdb=" O LYS G 146 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLN G 148 " --> pdb=" O GLU G 196 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU G 196 " --> pdb=" O GLN G 148 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI3 Processing sheet with id=AI4, first strand: chain 'H' and resid 20 through 23 Processing sheet with id=AI5, first strand: chain 'H' and resid 46 through 51 removed outlier: 5.981A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N PHE H 34 " --> pdb=" O ILE H 51 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N VAL H 37 " --> pdb=" O PHE H 95 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'H' and resid 170 through 172 removed outlier: 3.666A pdb=" N HIS H 171 " --> pdb=" O VAL H 188 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N VAL H 188 " --> pdb=" O HIS H 171 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI6 Processing sheet with id=AI7, first strand: chain 'I' and resid 12 through 13 Processing sheet with id=AI8, first strand: chain 'I' and resid 19 through 24 removed outlier: 3.645A pdb=" N ALA I 19 " --> pdb=" O ILE I 76 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N CYS I 23 " --> pdb=" O PHE I 72 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N PHE I 72 " --> pdb=" O CYS I 23 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'I' and resid 36 through 37 removed outlier: 7.027A pdb=" N TRP I 36 " --> pdb=" O LEU I 48 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'I' and resid 86 through 87 Processing sheet with id=AJ2, first strand: chain 'I' and resid 146 through 148 992 hydrogen bonds defined for protein. 2673 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.53 Time building geometry restraints manager: 3.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 11275 1.34 - 1.46: 8654 1.46 - 1.58: 15838 1.58 - 1.70: 0 1.70 - 1.82: 180 Bond restraints: 35947 Sorted by residual: bond pdb=" C PHE D 153 " pdb=" N PRO D 154 " ideal model delta sigma weight residual 1.332 1.362 -0.030 1.12e-02 7.97e+03 7.25e+00 bond pdb=" C PHE F 153 " pdb=" N PRO F 154 " ideal model delta sigma weight residual 1.332 1.360 -0.028 1.12e-02 7.97e+03 6.34e+00 bond pdb=" C1 NAG A1301 " pdb=" O5 NAG A1301 " ideal model delta sigma weight residual 1.406 1.443 -0.037 2.00e-02 2.50e+03 3.33e+00 bond pdb=" C1 NAG A1304 " pdb=" O5 NAG A1304 " ideal model delta sigma weight residual 1.406 1.438 -0.032 2.00e-02 2.50e+03 2.63e+00 bond pdb=" C1 NAG C1302 " pdb=" O5 NAG C1302 " ideal model delta sigma weight residual 1.406 1.438 -0.032 2.00e-02 2.50e+03 2.49e+00 ... (remaining 35942 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.24: 47577 1.24 - 2.48: 1072 2.48 - 3.72: 246 3.72 - 4.96: 31 4.96 - 6.20: 15 Bond angle restraints: 48941 Sorted by residual: angle pdb=" N GLN I 125 " pdb=" CA GLN I 125 " pdb=" C GLN I 125 " ideal model delta sigma weight residual 114.56 110.71 3.85 1.27e+00 6.20e-01 9.21e+00 angle pdb=" C PRO D 154 " pdb=" N GLU D 155 " pdb=" CA GLU D 155 " ideal model delta sigma weight residual 120.26 124.30 -4.04 1.34e+00 5.57e-01 9.11e+00 angle pdb=" N LYS E 97 " pdb=" CA LYS E 97 " pdb=" C LYS E 97 " ideal model delta sigma weight residual 114.56 110.87 3.69 1.27e+00 6.20e-01 8.45e+00 angle pdb=" C ASP E 290 " pdb=" N CYS E 291 " pdb=" CA CYS E 291 " ideal model delta sigma weight residual 121.54 126.29 -4.75 1.91e+00 2.74e-01 6.19e+00 angle pdb=" C ASP A 290 " pdb=" N CYS A 291 " pdb=" CA CYS A 291 " ideal model delta sigma weight residual 121.54 126.27 -4.73 1.91e+00 2.74e-01 6.13e+00 ... (remaining 48936 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.82: 20120 16.82 - 33.63: 783 33.63 - 50.45: 161 50.45 - 67.26: 38 67.26 - 84.08: 9 Dihedral angle restraints: 21111 sinusoidal: 8115 harmonic: 12996 Sorted by residual: dihedral pdb=" CA LYS A 150 " pdb=" C LYS A 150 " pdb=" N SER A 151 " pdb=" CA SER A 151 " ideal model delta harmonic sigma weight residual -180.00 -156.86 -23.14 0 5.00e+00 4.00e-02 2.14e+01 dihedral pdb=" CA THR C 73 " pdb=" C THR C 73 " pdb=" N ASN C 74 " pdb=" CA ASN C 74 " ideal model delta harmonic sigma weight residual 180.00 158.94 21.06 0 5.00e+00 4.00e-02 1.77e+01 dihedral pdb=" CA CYS E 379 " pdb=" CB CYS E 379 " pdb=" SG CYS E 379 " pdb=" SG CYS E 432 " ideal model delta sinusoidal sigma weight residual 79.00 5.89 73.11 1 2.00e+01 2.50e-03 1.70e+01 ... (remaining 21108 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 4872 0.058 - 0.116: 751 0.116 - 0.174: 26 0.174 - 0.232: 0 0.232 - 0.290: 1 Chirality restraints: 5650 Sorted by residual: chirality pdb=" C1 NAG A1301 " pdb=" ND2 ASN A 61 " pdb=" C2 NAG A1301 " pdb=" O5 NAG A1301 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-01 2.50e+01 2.10e+00 chirality pdb=" C2 NAG E1312 " pdb=" C1 NAG E1312 " pdb=" C3 NAG E1312 " pdb=" N2 NAG E1312 " both_signs ideal model delta sigma weight residual False -2.49 -2.33 -0.17 2.00e-01 2.50e+01 6.95e-01 chirality pdb=" C1 NAG A1305 " pdb=" ND2 ASN A 331 " pdb=" C2 NAG A1305 " pdb=" O5 NAG A1305 " both_signs ideal model delta sigma weight residual False -2.40 -2.25 -0.15 2.00e-01 2.50e+01 5.81e-01 ... (remaining 5647 not shown) Planarity restraints: 6325 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA G 44 " 0.023 5.00e-02 4.00e+02 3.51e-02 1.98e+00 pdb=" N PRO G 45 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO G 45 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO G 45 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 985 " 0.022 5.00e-02 4.00e+02 3.31e-02 1.75e+00 pdb=" N PRO A 986 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO A 986 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 986 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP C 985 " -0.020 5.00e-02 4.00e+02 3.05e-02 1.48e+00 pdb=" N PRO C 986 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO C 986 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO C 986 " -0.017 5.00e-02 4.00e+02 ... (remaining 6322 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 6048 2.77 - 3.31: 32441 3.31 - 3.84: 57642 3.84 - 4.37: 66237 4.37 - 4.90: 116494 Nonbonded interactions: 278862 Sorted by model distance: nonbonded pdb=" OG1 THR E1100 " pdb=" O7 NAG E1311 " model vdw 2.243 3.040 nonbonded pdb=" O GLN E 498 " pdb=" ND2 ASN E 501 " model vdw 2.256 3.120 nonbonded pdb=" O ASN A 99 " pdb=" NH1 ARG A 102 " model vdw 2.282 3.120 nonbonded pdb=" OD1 ASN B 138 " pdb=" OG SER B 175 " model vdw 2.283 3.040 nonbonded pdb=" OG SER A 735 " pdb=" OG1 THR A 859 " model vdw 2.288 3.040 ... (remaining 278857 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 1312) selection = (chain 'C' and resid 14 through 1312) selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'G' selection = chain 'I' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.890 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 31.880 Find NCS groups from input model: 1.000 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 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 : 0.002 0.049 36039 Z= 0.122 Angle : 0.472 8.594 49163 Z= 0.251 Chirality : 0.041 0.290 5650 Planarity : 0.003 0.035 6287 Dihedral : 9.198 84.077 12597 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 4.57 % Allowed : 7.23 % Favored : 88.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.68 (0.11), residues: 4428 helix: 0.82 (0.20), residues: 649 sheet: -2.81 (0.15), residues: 936 loop : -3.32 (0.09), residues: 2843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 273 TYR 0.007 0.000 TYR E 265 PHE 0.010 0.001 PHE E 562 TRP 0.008 0.001 TRP A 152 HIS 0.002 0.000 HIS C 655 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.12 (35947) covalent geometry : angle 0.46837 / 0.25 (48941) SS BOND : bond 0.00133 / 0.09 ( 54) SS BOND : angle 0.59404 / 0.41 ( 108) hydrogen bonds : bond 0.22092 / 14.79 ( 978) hydrogen bonds : angle 8.53569 / 5.92 ( 2673) link_NAG-ASN : bond 0.00310 / 0.17 ( 38) link_NAG-ASN : angle 1.30611 / 0.79 ( 114) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8856 Ramachandran restraints generated. 4428 Oldfield, 0 Emsley, 4428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8856 Ramachandran restraints generated. 4428 Oldfield, 0 Emsley, 4428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1039 residues out of total 3885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 175 poor density : 864 time to evaluate : 1.380 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: 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 179 LEU cc_start: 0.6855 (mt) cc_final: 0.6637 (tt) REVERT: A 249 LEU cc_start: 0.8291 (mt) cc_final: 0.8083 (mp) REVERT: A 878 LEU cc_start: 0.8486 (OUTLIER) cc_final: 0.8274 (mt) REVERT: A 1127 ASP cc_start: 0.7426 (p0) cc_final: 0.7046 (p0) REVERT: A 1144 GLU cc_start: 0.7251 (mm-30) cc_final: 0.7037 (mm-30) REVERT: C 368 LEU cc_start: 0.8835 (mt) cc_final: 0.8258 (mt) REVERT: C 458 LYS cc_start: 0.7727 (OUTLIER) cc_final: 0.7106 (mttp) REVERT: C 495 TYR cc_start: 0.7788 (OUTLIER) cc_final: 0.6613 (t80) REVERT: C 904 TYR cc_start: 0.7468 (m-10) cc_final: 0.7136 (m-10) REVERT: E 150 LYS cc_start: 0.7710 (OUTLIER) cc_final: 0.6748 (ttpt) REVERT: E 277 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.8357 (pp) REVERT: E 747 THR cc_start: 0.8217 (m) cc_final: 0.7922 (p) REVERT: E 878 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8209 (mt) REVERT: E 934 ILE cc_start: 0.8077 (mm) cc_final: 0.7717 (mm) REVERT: B 119 PHE cc_start: 0.4986 (m-80) cc_final: 0.4372 (m-80) REVERT: B 126 LEU cc_start: 0.5409 (mt) cc_final: 0.4892 (tt) REVERT: B 174 TYR cc_start: 0.5439 (m-80) cc_final: 0.5223 (m-10) REVERT: F 80 TYR cc_start: 0.7939 (m-10) cc_final: 0.7730 (m-10) REVERT: I 88 TYR cc_start: 0.6280 (m-80) cc_final: 0.6029 (m-10) REVERT: I 155 LEU cc_start: 0.6228 (OUTLIER) cc_final: 0.5866 (tp) outliers start: 175 outliers final: 24 residues processed: 981 average time/residue: 0.2285 time to fit residues: 354.2750 Evaluate side-chains 460 residues out of total 3885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 429 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 PHE Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain E residue 150 LYS Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 489 TYR Chi-restraints excluded: chain E residue 712 ILE Chi-restraints excluded: chain E residue 878 LEU Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain F residue 157 VAL Chi-restraints excluded: chain F residue 167 THR Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain I residue 155 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 432 optimal weight: 0.3980 chunk 197 optimal weight: 6.9990 chunk 388 optimal weight: 8.9990 chunk 215 optimal weight: 0.0170 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 2.9990 chunk 401 optimal weight: 30.0000 chunk 424 optimal weight: 6.9990 overall best weight: 3.0824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 14 GLN A 23 GLN A 49 HIS ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 173 GLN A 207 HIS A 245 HIS A 439 ASN A 498 GLN A 540 ASN A 644 GLN A 774 GLN A 784 GLN A 872 GLN A 926 GLN A 954 GLN A 992 GLN A1005 GLN A1048 HIS ** A1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 23 GLN C 66 HIS C 134 GLN C 148 ASN C 149 ASN C 218 GLN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN C 414 GLN C 439 ASN C 440 ASN ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 498 GLN C 690 GLN C 762 GLN C 804 GLN C 913 GLN C1048 HIS E 14 GLN E 23 GLN E 148 ASN E 149 ASN E 196 ASN E 207 HIS E 218 GLN E 334 ASN E 343 ASN E 354 ASN E 450 ASN E 506 GLN E 580 GLN E 690 GLN E 755 GLN E 762 GLN E 784 GLN E 907 ASN E 969 ASN E1002 GLN E1005 GLN E1048 HIS E1106 GLN ** E1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 3 GLN D 39 GLN D 62 GLN D 112 GLN ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 153 ASN ** B 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 1 GLN F 6 GLN F 39 GLN F 112 GLN F 171 HIS G 27 GLN G 31 ASN G 148 GLN G 159 ASN G 161 GLN H 1 GLN H 3 GLN H 39 GLN H 65 GLN H 112 GLN ** H 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 206 ASN I 43 GLN I 90 GLN ** I 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 156 GLN ** I 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 81 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.104281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.075153 restraints weight = 95868.118| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 2.35 r_work: 0.3084 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.3305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 36039 Z= 0.255 Angle : 0.733 13.811 49163 Z= 0.364 Chirality : 0.048 0.263 5650 Planarity : 0.005 0.056 6287 Dihedral : 4.960 54.401 4855 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.36 % Favored : 91.64 % Rotamer: Outliers : 3.94 % Allowed : 12.09 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.17 (0.11), residues: 4428 helix: 1.12 (0.20), residues: 635 sheet: -2.32 (0.15), residues: 1033 loop : -2.98 (0.10), residues: 2760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C1014 TYR 0.025 0.002 TYR A 91 PHE 0.028 0.003 PHE B 47 TRP 0.028 0.002 TRP A 152 HIS 0.009 0.002 HIS C1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00609 / 0.25 (35947) covalent geometry : angle 0.71687 / 0.36 (48941) SS BOND : bond 0.00614 / 0.40 ( 54) SS BOND : angle 2.60217 / 1.71 ( 108) hydrogen bonds : bond 0.04923 / 3.27 ( 978) hydrogen bonds : angle 6.25476 / 4.33 ( 2673) link_NAG-ASN : bond 0.00697 / 0.40 ( 38) link_NAG-ASN : angle 2.18870 / 1.25 ( 114) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8856 Ramachandran restraints generated. 4428 Oldfield, 0 Emsley, 4428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8856 Ramachandran restraints generated. 4428 Oldfield, 0 Emsley, 4428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 596 residues out of total 3885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 151 poor density : 445 time to evaluate : 1.143 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 PHE cc_start: 0.7379 (m-80) cc_final: 0.7011 (m-80) REVERT: A 249 LEU cc_start: 0.8411 (mt) cc_final: 0.8073 (mp) REVERT: A 1144 GLU cc_start: 0.7977 (mm-30) cc_final: 0.7661 (mm-30) REVERT: C 119 ILE cc_start: 0.9320 (OUTLIER) cc_final: 0.9061 (mt) REVERT: C 177 MET cc_start: 0.6700 (mtt) cc_final: 0.6410 (mtt) REVERT: C 362 VAL cc_start: 0.9313 (t) cc_final: 0.9062 (p) REVERT: C 374 PHE cc_start: 0.8076 (m-80) cc_final: 0.7766 (m-80) REVERT: C 458 LYS cc_start: 0.8217 (OUTLIER) cc_final: 0.7439 (mttp) REVERT: C 493 GLN cc_start: 0.7814 (tt0) cc_final: 0.7597 (tt0) REVERT: C 817 PHE cc_start: 0.8061 (t80) cc_final: 0.7844 (t80) REVERT: C 1050 MET cc_start: 0.8842 (ptm) cc_final: 0.8638 (ptm) REVERT: E 141 LEU cc_start: 0.8041 (mm) cc_final: 0.7835 (mt) REVERT: E 150 LYS cc_start: 0.7683 (OUTLIER) cc_final: 0.6750 (ttpt) REVERT: E 198 ASP cc_start: 0.7716 (t0) cc_final: 0.7457 (t0) REVERT: E 258 TRP cc_start: 0.8543 (p-90) cc_final: 0.8286 (p-90) REVERT: E 277 LEU cc_start: 0.9177 (OUTLIER) cc_final: 0.8901 (pp) REVERT: E 406 GLU cc_start: 0.7135 (mt-10) cc_final: 0.6637 (mt-10) REVERT: E 735 SER cc_start: 0.8885 (t) cc_final: 0.8452 (p) REVERT: E 747 THR cc_start: 0.8813 (m) cc_final: 0.8417 (p) REVERT: E 756 TYR cc_start: 0.8949 (m-80) cc_final: 0.8700 (m-80) REVERT: E 934 ILE cc_start: 0.8502 (mm) cc_final: 0.8069 (mm) REVERT: E 988 GLU cc_start: 0.7976 (mp0) cc_final: 0.7768 (mp0) REVERT: E 1130 ILE cc_start: 0.8521 (pt) cc_final: 0.8263 (mt) REVERT: D 30 ILE cc_start: 0.8931 (mm) cc_final: 0.8713 (mp) REVERT: B 6 GLN cc_start: 0.7064 (mm110) cc_final: 0.6803 (mm-40) REVERT: B 17 GLU cc_start: 0.7976 (mp0) cc_final: 0.7487 (tt0) REVERT: F 27 ASP cc_start: 0.8246 (t0) cc_final: 0.7952 (t0) REVERT: F 32 TYR cc_start: 0.7931 (m-10) cc_final: 0.7673 (m-10) REVERT: F 48 MET cc_start: 0.8004 (mtp) cc_final: 0.7316 (mpp) REVERT: F 59 HIS cc_start: 0.8407 (m170) cc_final: 0.8192 (m-70) REVERT: F 112 GLN cc_start: 0.7291 (OUTLIER) cc_final: 0.7083 (pm20) REVERT: F 151 ASP cc_start: 0.6096 (t0) cc_final: 0.5684 (t0) REVERT: G 18 ARG cc_start: 0.7501 (ptm160) cc_final: 0.7276 (ptm160) REVERT: G 87 TYR cc_start: 0.7862 (m-80) cc_final: 0.7562 (m-10) REVERT: G 104 LYS cc_start: 0.7594 (pptt) cc_final: 0.6796 (pptt) REVERT: G 108 LYS cc_start: 0.7966 (tttm) cc_final: 0.7605 (ttpt) REVERT: G 166 GLU cc_start: 0.4616 (OUTLIER) cc_final: 0.4280 (pt0) REVERT: H 67 ARG cc_start: 0.6541 (ptt180) cc_final: 0.6089 (ptt180) REVERT: H 124 LYS cc_start: 0.7465 (mmmm) cc_final: 0.7244 (mmmm) REVERT: H 171 HIS cc_start: 0.4535 (OUTLIER) cc_final: 0.3110 (t-90) REVERT: I 31 ASN cc_start: 0.7342 (p0) cc_final: 0.6939 (p0) REVERT: I 87 TYR cc_start: 0.6026 (m-10) cc_final: 0.5801 (m-10) REVERT: I 88 TYR cc_start: 0.7363 (m-80) cc_final: 0.6549 (m-10) outliers start: 151 outliers final: 84 residues processed: 565 average time/residue: 0.2226 time to fit residues: 200.5703 Evaluate side-chains 451 residues out of total 3885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 360 time to evaluate : 1.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 218 GLN Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 150 LYS Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 238 PHE Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 422 ASN Chi-restraints excluded: chain E residue 489 TYR Chi-restraints excluded: chain E residue 546 LEU Chi-restraints excluded: chain E residue 599 THR Chi-restraints excluded: chain E residue 712 ILE Chi-restraints excluded: chain E residue 719 THR Chi-restraints excluded: chain E residue 721 SER Chi-restraints excluded: chain E residue 751 ASN Chi-restraints excluded: chain E residue 858 LEU Chi-restraints excluded: chain E residue 878 LEU Chi-restraints excluded: chain E residue 939 SER Chi-restraints excluded: chain E residue 984 LEU Chi-restraints excluded: chain E residue 1114 ILE Chi-restraints excluded: chain E residue 1116 THR Chi-restraints excluded: chain E residue 1129 VAL Chi-restraints excluded: chain E residue 1136 THR Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain F residue 70 ILE Chi-restraints excluded: chain F residue 112 GLN Chi-restraints excluded: chain F residue 157 VAL Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 167 THR Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain G residue 59 ILE Chi-restraints excluded: chain G residue 166 GLU Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 149 VAL Chi-restraints excluded: chain H residue 171 HIS Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 21 LEU Chi-restraints excluded: chain I residue 38 GLN Chi-restraints excluded: chain I residue 80 GLU Chi-restraints excluded: chain I residue 180 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 201 optimal weight: 0.7980 chunk 64 optimal weight: 7.9990 chunk 82 optimal weight: 0.8980 chunk 409 optimal weight: 9.9990 chunk 316 optimal weight: 4.9990 chunk 424 optimal weight: 0.9980 chunk 177 optimal weight: 1.9990 chunk 318 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 40 optimal weight: 6.9990 chunk 130 optimal weight: 9.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 GLN ** A1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS C 218 GLN C 448 ASN C 450 ASN C 913 GLN E 245 HIS ** E 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 762 GLN E 907 ASN E 969 ASN ** E1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 3 GLN D 31 ASN B 6 GLN ** B 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 112 GLN ** G 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.104911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.076313 restraints weight = 95271.092| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 2.38 r_work: 0.3094 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.3617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 36039 Z= 0.138 Angle : 0.589 10.459 49163 Z= 0.293 Chirality : 0.044 0.279 5650 Planarity : 0.004 0.055 6287 Dihedral : 4.668 52.767 4845 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 3.60 % Allowed : 13.18 % Favored : 83.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.75 (0.12), residues: 4428 helix: 1.60 (0.21), residues: 629 sheet: -1.97 (0.15), residues: 1050 loop : -2.76 (0.10), residues: 2749 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG I 24 TYR 0.016 0.001 TYR B 141 PHE 0.049 0.002 PHE E 65 TRP 0.014 0.001 TRP H 106 HIS 0.008 0.001 HIS B 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 (35947) covalent geometry : angle 0.57832 / 0.29 (48941) SS BOND : bond 0.00515 / 0.39 ( 54) SS BOND : angle 1.76387 / 1.18 ( 108) hydrogen bonds : bond 0.03897 / 2.60 ( 978) hydrogen bonds : angle 5.76854 / 4.00 ( 2673) link_NAG-ASN : bond 0.00545 / 0.30 ( 38) link_NAG-ASN : angle 1.71949 / 0.98 ( 114) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8856 Ramachandran restraints generated. 4428 Oldfield, 0 Emsley, 4428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8856 Ramachandran restraints generated. 4428 Oldfield, 0 Emsley, 4428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 501 residues out of total 3885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 363 time to evaluate : 1.348 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: symmetry clash revert: symmetry clash REVERT: A 249 LEU cc_start: 0.8368 (mt) cc_final: 0.8122 (mp) REVERT: A 774 GLN cc_start: 0.8419 (OUTLIER) cc_final: 0.8166 (mp-120) REVERT: A 1144 GLU cc_start: 0.7960 (mm-30) cc_final: 0.7656 (mm-30) REVERT: C 362 VAL cc_start: 0.9332 (t) cc_final: 0.9088 (p) REVERT: C 458 LYS cc_start: 0.8244 (OUTLIER) cc_final: 0.7439 (mttp) REVERT: C 493 GLN cc_start: 0.7930 (tt0) cc_final: 0.7666 (tt0) REVERT: C 574 ASP cc_start: 0.8163 (t70) cc_final: 0.7686 (t0) REVERT: C 778 THR cc_start: 0.9503 (OUTLIER) cc_final: 0.9101 (p) REVERT: C 900 MET cc_start: 0.8641 (mtt) cc_final: 0.8382 (mtt) REVERT: E 133 PHE cc_start: 0.6779 (OUTLIER) cc_final: 0.6367 (p90) REVERT: E 150 LYS cc_start: 0.7688 (OUTLIER) cc_final: 0.6813 (ttpt) REVERT: E 198 ASP cc_start: 0.7848 (t0) cc_final: 0.7474 (t0) REVERT: E 277 LEU cc_start: 0.9189 (OUTLIER) cc_final: 0.8872 (pp) REVERT: E 489 TYR cc_start: 0.8567 (OUTLIER) cc_final: 0.7636 (p90) REVERT: E 747 THR cc_start: 0.8768 (m) cc_final: 0.8377 (p) REVERT: E 934 ILE cc_start: 0.8469 (mm) cc_final: 0.8038 (mm) REVERT: D 155 GLU cc_start: 0.6534 (pm20) cc_final: 0.6252 (pm20) REVERT: B 6 GLN cc_start: 0.7033 (mm-40) cc_final: 0.6787 (mm-40) REVERT: B 126 LEU cc_start: 0.5971 (OUTLIER) cc_final: 0.5502 (tp) REVERT: F 27 ASP cc_start: 0.8284 (t0) cc_final: 0.8048 (t0) REVERT: F 81 MET cc_start: 0.6747 (tmm) cc_final: 0.6502 (tmm) REVERT: F 185 LEU cc_start: 0.6869 (mt) cc_final: 0.6655 (mt) REVERT: G 18 ARG cc_start: 0.7426 (ptm160) cc_final: 0.7065 (ttp-170) REVERT: G 20 THR cc_start: 0.7707 (OUTLIER) cc_final: 0.7493 (m) REVERT: G 87 TYR cc_start: 0.7846 (m-80) cc_final: 0.7520 (m-10) REVERT: G 141 TYR cc_start: 0.6167 (t80) cc_final: 0.5669 (t80) REVERT: H 51 ILE cc_start: 0.8202 (OUTLIER) cc_final: 0.7979 (mm) REVERT: H 104 GLN cc_start: 0.7072 (pt0) cc_final: 0.6847 (pt0) REVERT: H 124 LYS cc_start: 0.7545 (mmmm) cc_final: 0.7251 (mmmm) REVERT: H 171 HIS cc_start: 0.4443 (OUTLIER) cc_final: 0.3165 (t-90) REVERT: I 88 TYR cc_start: 0.7283 (m-80) cc_final: 0.6559 (m-10) outliers start: 138 outliers final: 86 residues processed: 479 average time/residue: 0.2140 time to fit residues: 164.6879 Evaluate side-chains 431 residues out of total 3885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 334 time to evaluate : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 774 GLN Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 218 GLN Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 133 PHE Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 150 LYS Chi-restraints excluded: chain E residue 197 ILE Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 422 ASN Chi-restraints excluded: chain E residue 489 TYR Chi-restraints excluded: chain E residue 508 TYR Chi-restraints excluded: chain E residue 525 CYS Chi-restraints excluded: chain E residue 546 LEU Chi-restraints excluded: chain E residue 599 THR Chi-restraints excluded: chain E residue 712 ILE Chi-restraints excluded: chain E residue 719 THR Chi-restraints excluded: chain E residue 721 SER Chi-restraints excluded: chain E residue 858 LEU Chi-restraints excluded: chain E residue 878 LEU Chi-restraints excluded: chain E residue 939 SER Chi-restraints excluded: chain E residue 964 LYS Chi-restraints excluded: chain E residue 984 LEU Chi-restraints excluded: chain E residue 1114 ILE Chi-restraints excluded: chain E residue 1116 THR Chi-restraints excluded: chain E residue 1136 THR Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain F residue 54 ILE Chi-restraints excluded: chain F residue 70 ILE Chi-restraints excluded: chain F residue 112 GLN Chi-restraints excluded: chain F residue 157 VAL Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 161 TRP Chi-restraints excluded: chain F residue 167 THR Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 106 TRP Chi-restraints excluded: chain H residue 149 VAL Chi-restraints excluded: chain H residue 171 HIS Chi-restraints excluded: chain H residue 185 LEU Chi-restraints excluded: chain I residue 17 GLU Chi-restraints excluded: chain I residue 38 GLN Chi-restraints excluded: chain I residue 180 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 321 optimal weight: 0.9990 chunk 181 optimal weight: 0.7980 chunk 248 optimal weight: 8.9990 chunk 272 optimal weight: 0.2980 chunk 439 optimal weight: 20.0000 chunk 378 optimal weight: 20.0000 chunk 136 optimal weight: 6.9990 chunk 215 optimal weight: 0.0070 chunk 177 optimal weight: 3.9990 chunk 161 optimal weight: 0.4980 chunk 398 optimal weight: 10.0000 overall best weight: 0.5200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 134 GLN A 334 ASN A 755 GLN A 901 GLN A1135 ASN C 207 HIS E 245 HIS ** E1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 3 GLN ** B 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 112 GLN ** G 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 190 HIS ** 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 = 0.3882 r_free = 0.3882 target = 0.103785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.076891 restraints weight = 97034.892| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 2.44 r_work: 0.3106 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.3754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.067 36039 Z= 0.102 Angle : 0.547 10.345 49163 Z= 0.271 Chirality : 0.043 0.291 5650 Planarity : 0.004 0.051 6287 Dihedral : 4.561 53.150 4845 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 3.42 % Allowed : 13.73 % Favored : 82.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.46 (0.12), residues: 4428 helix: 1.93 (0.21), residues: 629 sheet: -1.70 (0.15), residues: 1059 loop : -2.63 (0.11), residues: 2740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG I 24 TYR 0.019 0.001 TYR B 141 PHE 0.040 0.001 PHE E 65 TRP 0.010 0.001 TRP H 106 HIS 0.007 0.001 HIS C 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.10 (35947) covalent geometry : angle 0.53778 / 0.27 (48941) SS BOND : bond 0.00391 / 0.29 ( 54) SS BOND : angle 1.43075 / 0.96 ( 108) hydrogen bonds : bond 0.03380 / 2.26 ( 978) hydrogen bonds : angle 5.44442 / 3.77 ( 2673) link_NAG-ASN : bond 0.00445 / 0.26 ( 38) link_NAG-ASN : angle 1.65546 / 0.96 ( 114) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8856 Ramachandran restraints generated. 4428 Oldfield, 0 Emsley, 4428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8856 Ramachandran restraints generated. 4428 Oldfield, 0 Emsley, 4428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 492 residues out of total 3885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 361 time to evaluate : 1.393 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 PHE cc_start: 0.5356 (m-80) cc_final: 0.5153 (m-10) REVERT: A 249 LEU cc_start: 0.8348 (mt) cc_final: 0.8110 (mp) REVERT: A 994 ASP cc_start: 0.8172 (m-30) cc_final: 0.7906 (t70) REVERT: A 1144 GLU cc_start: 0.7978 (mm-30) cc_final: 0.7770 (mm-30) REVERT: C 362 VAL cc_start: 0.9312 (t) cc_final: 0.9076 (p) REVERT: C 458 LYS cc_start: 0.8263 (OUTLIER) cc_final: 0.7474 (mttp) REVERT: C 493 GLN cc_start: 0.7969 (tt0) cc_final: 0.7733 (tt0) REVERT: C 574 ASP cc_start: 0.8161 (t70) cc_final: 0.7677 (t0) REVERT: E 133 PHE cc_start: 0.6809 (OUTLIER) cc_final: 0.6390 (p90) REVERT: E 150 LYS cc_start: 0.7682 (OUTLIER) cc_final: 0.6828 (ttpt) REVERT: E 198 ASP cc_start: 0.7844 (t0) cc_final: 0.7441 (t0) REVERT: E 277 LEU cc_start: 0.9190 (OUTLIER) cc_final: 0.8869 (pp) REVERT: E 489 TYR cc_start: 0.8625 (OUTLIER) cc_final: 0.7865 (p90) REVERT: E 490 PHE cc_start: 0.7037 (m-80) cc_final: 0.6297 (m-80) REVERT: E 546 LEU cc_start: 0.8197 (OUTLIER) cc_final: 0.7965 (mm) REVERT: E 747 THR cc_start: 0.8752 (m) cc_final: 0.8363 (p) REVERT: E 878 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8380 (mt) REVERT: E 934 ILE cc_start: 0.8377 (mm) cc_final: 0.7935 (mm) REVERT: D 10 GLU cc_start: 0.7330 (mt-10) cc_final: 0.7087 (mm-30) REVERT: D 32 TYR cc_start: 0.7916 (m-80) cc_final: 0.7479 (m-80) REVERT: D 155 GLU cc_start: 0.6520 (pm20) cc_final: 0.6289 (pm20) REVERT: B 6 GLN cc_start: 0.6988 (mm-40) cc_final: 0.6769 (mm-40) REVERT: B 126 LEU cc_start: 0.6108 (OUTLIER) cc_final: 0.5698 (tp) REVERT: B 210 PHE cc_start: 0.4221 (t80) cc_final: 0.3889 (t80) REVERT: F 28 THR cc_start: 0.8487 (OUTLIER) cc_final: 0.8169 (p) REVERT: F 81 MET cc_start: 0.6651 (tmm) cc_final: 0.6402 (tmm) REVERT: F 124 LYS cc_start: 0.6529 (pttt) cc_final: 0.5182 (pttt) REVERT: G 87 TYR cc_start: 0.7855 (m-80) cc_final: 0.7524 (m-10) REVERT: G 141 TYR cc_start: 0.6251 (t80) cc_final: 0.5834 (t80) REVERT: H 124 LYS cc_start: 0.7615 (mmmm) cc_final: 0.7207 (mmmm) REVERT: H 171 HIS cc_start: 0.4372 (OUTLIER) cc_final: 0.3296 (t-90) REVERT: H 177 LEU cc_start: 0.8498 (mt) cc_final: 0.7663 (tt) REVERT: I 31 ASN cc_start: 0.7152 (p0) cc_final: 0.5786 (p0) REVERT: I 32 ARG cc_start: 0.7339 (tpp-160) cc_final: 0.7109 (tpp80) REVERT: I 33 HIS cc_start: 0.6949 (m170) cc_final: 0.6628 (m170) REVERT: I 88 TYR cc_start: 0.7323 (m-80) cc_final: 0.6494 (m-10) REVERT: I 148 GLN cc_start: 0.6782 (mp10) cc_final: 0.6561 (mp10) REVERT: I 190 HIS cc_start: 0.3185 (OUTLIER) cc_final: 0.2386 (t-90) outliers start: 131 outliers final: 84 residues processed: 466 average time/residue: 0.2350 time to fit residues: 175.9797 Evaluate side-chains 424 residues out of total 3885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 329 time to evaluate : 1.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 133 PHE Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 218 GLN Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain E residue 104 TRP Chi-restraints excluded: chain E residue 133 PHE Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 150 LYS Chi-restraints excluded: chain E residue 197 ILE Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 238 PHE Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 483 VAL Chi-restraints excluded: chain E residue 489 TYR Chi-restraints excluded: chain E residue 508 TYR Chi-restraints excluded: chain E residue 525 CYS Chi-restraints excluded: chain E residue 546 LEU Chi-restraints excluded: chain E residue 599 THR Chi-restraints excluded: chain E residue 656 VAL Chi-restraints excluded: chain E residue 712 ILE Chi-restraints excluded: chain E residue 721 SER Chi-restraints excluded: chain E residue 858 LEU Chi-restraints excluded: chain E residue 878 LEU Chi-restraints excluded: chain E residue 939 SER Chi-restraints excluded: chain E residue 984 LEU Chi-restraints excluded: chain E residue 1116 THR Chi-restraints excluded: chain E residue 1129 VAL Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 54 ILE Chi-restraints excluded: chain F residue 70 ILE Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 167 THR Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain G residue 64 SER Chi-restraints excluded: chain H residue 81 MET Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 149 VAL Chi-restraints excluded: chain H residue 171 HIS Chi-restraints excluded: chain H residue 185 LEU Chi-restraints excluded: chain H residue 200 THR Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 17 GLU Chi-restraints excluded: chain I residue 38 GLN Chi-restraints excluded: chain I residue 180 LEU Chi-restraints excluded: chain I residue 190 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 132 optimal weight: 5.9990 chunk 87 optimal weight: 8.9990 chunk 89 optimal weight: 3.9990 chunk 147 optimal weight: 10.0000 chunk 372 optimal weight: 7.9990 chunk 164 optimal weight: 5.9990 chunk 314 optimal weight: 5.9990 chunk 34 optimal weight: 7.9990 chunk 270 optimal weight: 5.9990 chunk 257 optimal weight: 20.0000 chunk 315 optimal weight: 1.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 540 ASN A 901 GLN ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1119 ASN ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 218 GLN C 239 GLN C 613 GLN C 804 GLN C 935 GLN C1002 GLN E 30 ASN E 271 GLN ** E1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 3 GLN B 39 GLN B 125 GLN ** B 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 200 GLN F 112 GLN G 33 HIS ** G 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.099632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.070817 restraints weight = 96967.645| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 2.42 r_work: 0.2986 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2864 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.4558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.085 36039 Z= 0.357 Angle : 0.758 13.375 49163 Z= 0.380 Chirality : 0.051 0.323 5650 Planarity : 0.005 0.051 6287 Dihedral : 5.388 55.694 4844 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.82 % Favored : 90.18 % Rotamer: Outliers : 4.28 % Allowed : 14.17 % Favored : 81.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.69 (0.12), residues: 4428 helix: 1.10 (0.20), residues: 628 sheet: -1.76 (0.15), residues: 1087 loop : -2.66 (0.11), residues: 2713 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG I 24 TYR 0.027 0.002 TYR C 265 PHE 0.033 0.003 PHE B 47 TRP 0.018 0.002 TRP E 886 HIS 0.031 0.002 HIS C 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00859 / 0.36 (35947) covalent geometry : angle 0.74564 / 0.38 (48941) SS BOND : bond 0.00874 / 0.62 ( 54) SS BOND : angle 2.18096 / 1.44 ( 108) hydrogen bonds : bond 0.05258 / 3.50 ( 978) hydrogen bonds : angle 5.94537 / 4.09 ( 2673) link_NAG-ASN : bond 0.00766 / 0.45 ( 38) link_NAG-ASN : angle 2.16805 / 1.30 ( 114) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8856 Ramachandran restraints generated. 4428 Oldfield, 0 Emsley, 4428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8856 Ramachandran restraints generated. 4428 Oldfield, 0 Emsley, 4428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 492 residues out of total 3885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 164 poor density : 328 time to evaluate : 1.433 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: symmetry clash revert: symmetry clash REVERT: A 135 PHE cc_start: 0.7324 (m-80) cc_final: 0.7008 (m-80) REVERT: A 231 ILE cc_start: 0.8585 (OUTLIER) cc_final: 0.8362 (pt) REVERT: A 249 LEU cc_start: 0.8418 (mt) cc_final: 0.8133 (mp) REVERT: A 858 LEU cc_start: 0.9257 (OUTLIER) cc_final: 0.8982 (mt) REVERT: A 1144 GLU cc_start: 0.8090 (mm-30) cc_final: 0.7828 (mm-30) REVERT: C 119 ILE cc_start: 0.9283 (OUTLIER) cc_final: 0.9063 (mt) REVERT: C 177 MET cc_start: 0.7089 (mtp) cc_final: 0.6853 (mtt) REVERT: C 374 PHE cc_start: 0.8262 (m-80) cc_final: 0.7969 (m-80) REVERT: C 458 LYS cc_start: 0.8265 (OUTLIER) cc_final: 0.7610 (mttp) REVERT: C 493 GLN cc_start: 0.8080 (tt0) cc_final: 0.7819 (tt0) REVERT: C 778 THR cc_start: 0.9475 (OUTLIER) cc_final: 0.9158 (p) REVERT: C 995 ARG cc_start: 0.8762 (OUTLIER) cc_final: 0.8400 (mtt-85) REVERT: C 1091 ARG cc_start: 0.8819 (OUTLIER) cc_final: 0.7795 (mtm-85) REVERT: E 150 LYS cc_start: 0.7737 (OUTLIER) cc_final: 0.6986 (ttpt) REVERT: E 197 ILE cc_start: 0.8932 (OUTLIER) cc_final: 0.8678 (mp) REVERT: E 277 LEU cc_start: 0.9239 (OUTLIER) cc_final: 0.9021 (pp) REVERT: E 460 ASN cc_start: 0.7853 (m-40) cc_final: 0.7615 (m110) REVERT: E 934 ILE cc_start: 0.8774 (mm) cc_final: 0.8561 (mm) REVERT: D 32 TYR cc_start: 0.8354 (m-80) cc_final: 0.7796 (m-80) REVERT: D 50 ARG cc_start: 0.8873 (OUTLIER) cc_final: 0.8552 (ttt180) REVERT: B 125 GLN cc_start: 0.3533 (OUTLIER) cc_final: 0.2216 (tp40) REVERT: B 155 LEU cc_start: 0.6084 (mm) cc_final: 0.5504 (pp) REVERT: F 28 THR cc_start: 0.8373 (OUTLIER) cc_final: 0.8132 (p) REVERT: F 81 MET cc_start: 0.6636 (tmm) cc_final: 0.6379 (tmm) REVERT: F 112 GLN cc_start: 0.7198 (OUTLIER) cc_final: 0.6784 (pm20) REVERT: H 171 HIS cc_start: 0.4543 (OUTLIER) cc_final: 0.3294 (t-90) REVERT: I 31 ASN cc_start: 0.7210 (p0) cc_final: 0.6029 (p0) REVERT: I 33 HIS cc_start: 0.7034 (m170) cc_final: 0.6806 (m170) REVERT: I 78 ARG cc_start: 0.8102 (mmp80) cc_final: 0.7420 (mmp80) REVERT: I 80 GLU cc_start: 0.8279 (OUTLIER) cc_final: 0.8030 (mp0) REVERT: I 88 TYR cc_start: 0.7382 (m-80) cc_final: 0.6571 (m-10) REVERT: I 148 GLN cc_start: 0.6731 (mp10) cc_final: 0.6529 (mp10) REVERT: I 190 HIS cc_start: 0.2905 (OUTLIER) cc_final: 0.2286 (t-90) outliers start: 164 outliers final: 105 residues processed: 475 average time/residue: 0.2440 time to fit residues: 184.3619 Evaluate side-chains 421 residues out of total 3885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 299 time to evaluate : 1.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 765 ARG Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 218 GLN Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 735 SER Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 995 ARG Chi-restraints excluded: chain C residue 1091 ARG Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 104 TRP Chi-restraints excluded: chain E residue 121 ASN Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 150 LYS Chi-restraints excluded: chain E residue 182 LYS Chi-restraints excluded: chain E residue 197 ILE Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 238 PHE Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 312 ILE Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 422 ASN Chi-restraints excluded: chain E residue 489 TYR Chi-restraints excluded: chain E residue 525 CYS Chi-restraints excluded: chain E residue 546 LEU Chi-restraints excluded: chain E residue 599 THR Chi-restraints excluded: chain E residue 656 VAL Chi-restraints excluded: chain E residue 705 VAL Chi-restraints excluded: chain E residue 712 ILE Chi-restraints excluded: chain E residue 719 THR Chi-restraints excluded: chain E residue 721 SER Chi-restraints excluded: chain E residue 735 SER Chi-restraints excluded: chain E residue 751 ASN Chi-restraints excluded: chain E residue 858 LEU Chi-restraints excluded: chain E residue 878 LEU Chi-restraints excluded: chain E residue 939 SER Chi-restraints excluded: chain E residue 964 LYS Chi-restraints excluded: chain E residue 984 LEU Chi-restraints excluded: chain E residue 1114 ILE Chi-restraints excluded: chain E residue 1116 THR Chi-restraints excluded: chain E residue 1122 VAL Chi-restraints excluded: chain E residue 1129 VAL Chi-restraints excluded: chain E residue 1136 THR Chi-restraints excluded: chain D residue 50 ARG Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 125 GLN Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 54 ILE Chi-restraints excluded: chain F residue 70 ILE Chi-restraints excluded: chain F residue 112 GLN Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 167 THR Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 189 VAL Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain G residue 64 SER Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 106 TRP Chi-restraints excluded: chain H residue 149 VAL Chi-restraints excluded: chain H residue 171 HIS Chi-restraints excluded: chain H residue 185 LEU Chi-restraints excluded: chain H residue 200 THR Chi-restraints excluded: chain I residue 1 GLU Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 17 GLU Chi-restraints excluded: chain I residue 21 LEU Chi-restraints excluded: chain I residue 38 GLN Chi-restraints excluded: chain I residue 80 GLU Chi-restraints excluded: chain I residue 190 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 370 optimal weight: 7.9990 chunk 185 optimal weight: 0.6980 chunk 422 optimal weight: 10.0000 chunk 317 optimal weight: 0.9980 chunk 127 optimal weight: 0.1980 chunk 434 optimal weight: 30.0000 chunk 357 optimal weight: 0.9990 chunk 313 optimal weight: 0.9980 chunk 104 optimal weight: 2.9990 chunk 414 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 690 GLN ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS C 613 GLN C1002 GLN E 245 HIS E 969 ASN ** E1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 3 GLN B 125 GLN ** B 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 112 GLN ** G 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 190 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.102088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.073530 restraints weight = 95750.055| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 2.41 r_work: 0.3052 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2931 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.4487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 36039 Z= 0.119 Angle : 0.583 13.495 49163 Z= 0.292 Chirality : 0.044 0.275 5650 Planarity : 0.004 0.048 6287 Dihedral : 5.019 54.273 4844 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 3.32 % Allowed : 15.58 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.36 (0.12), residues: 4428 helix: 1.81 (0.21), residues: 615 sheet: -1.51 (0.15), residues: 1050 loop : -2.54 (0.11), residues: 2763 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG I 62 TYR 0.020 0.001 TYR B 50 PHE 0.032 0.001 PHE D 153 TRP 0.011 0.001 TRP E 886 HIS 0.023 0.001 HIS B 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 (35947) covalent geometry : angle 0.57567 / 0.29 (48941) SS BOND : bond 0.00501 / 0.37 ( 54) SS BOND : angle 1.64791 / 1.11 ( 108) hydrogen bonds : bond 0.03724 / 2.48 ( 978) hydrogen bonds : angle 5.52925 / 3.81 ( 2673) link_NAG-ASN : bond 0.01237 / 0.66 ( 38) link_NAG-ASN : angle 1.37882 / 0.90 ( 114) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8856 Ramachandran restraints generated. 4428 Oldfield, 0 Emsley, 4428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8856 Ramachandran restraints generated. 4428 Oldfield, 0 Emsley, 4428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 3885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 330 time to evaluate : 1.511 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 231 ILE cc_start: 0.8597 (OUTLIER) cc_final: 0.8358 (pt) REVERT: A 249 LEU cc_start: 0.8310 (mt) cc_final: 0.8060 (mp) REVERT: A 332 ILE cc_start: 0.8734 (OUTLIER) cc_final: 0.8384 (tt) REVERT: A 774 GLN cc_start: 0.8469 (OUTLIER) cc_final: 0.8218 (mp-120) REVERT: A 858 LEU cc_start: 0.9133 (OUTLIER) cc_final: 0.8908 (mt) REVERT: A 1144 GLU cc_start: 0.8087 (mm-30) cc_final: 0.7835 (mm-30) REVERT: C 119 ILE cc_start: 0.9288 (OUTLIER) cc_final: 0.9064 (mt) REVERT: C 374 PHE cc_start: 0.8215 (m-80) cc_final: 0.7959 (m-80) REVERT: C 458 LYS cc_start: 0.8328 (OUTLIER) cc_final: 0.7633 (mttp) REVERT: C 493 GLN cc_start: 0.8067 (tt0) cc_final: 0.7855 (tt0) REVERT: C 995 ARG cc_start: 0.8614 (OUTLIER) cc_final: 0.8149 (mtt90) REVERT: E 150 LYS cc_start: 0.7747 (OUTLIER) cc_final: 0.7016 (ttpt) REVERT: E 277 LEU cc_start: 0.9197 (OUTLIER) cc_final: 0.8883 (pp) REVERT: E 369 TYR cc_start: 0.8135 (t80) cc_final: 0.7931 (t80) REVERT: E 490 PHE cc_start: 0.7302 (m-80) cc_final: 0.6992 (m-80) REVERT: E 934 ILE cc_start: 0.8661 (mm) cc_final: 0.8335 (mm) REVERT: B 126 LEU cc_start: 0.6007 (OUTLIER) cc_final: 0.5569 (tp) REVERT: B 155 LEU cc_start: 0.5953 (OUTLIER) cc_final: 0.5357 (pp) REVERT: F 28 THR cc_start: 0.8369 (OUTLIER) cc_final: 0.8157 (p) REVERT: F 59 HIS cc_start: 0.8353 (m170) cc_final: 0.8147 (m-70) REVERT: F 81 MET cc_start: 0.6570 (tmm) cc_final: 0.6282 (tmm) REVERT: G 141 TYR cc_start: 0.6150 (t80) cc_final: 0.5633 (t80) REVERT: H 19 LYS cc_start: 0.8583 (mmtt) cc_final: 0.8358 (mmtt) REVERT: H 171 HIS cc_start: 0.4444 (OUTLIER) cc_final: 0.3249 (t-90) REVERT: H 177 LEU cc_start: 0.8333 (mt) cc_final: 0.7515 (tt) REVERT: I 31 ASN cc_start: 0.7040 (p0) cc_final: 0.5607 (p0) REVERT: I 33 HIS cc_start: 0.6913 (m170) cc_final: 0.6712 (m170) REVERT: I 88 TYR cc_start: 0.7329 (m-80) cc_final: 0.6494 (m-10) REVERT: I 190 HIS cc_start: 0.3139 (OUTLIER) cc_final: 0.2590 (t70) outliers start: 127 outliers final: 91 residues processed: 434 average time/residue: 0.2398 time to fit residues: 166.7354 Evaluate side-chains 412 residues out of total 3885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 307 time to evaluate : 1.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 774 GLN Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 133 PHE Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 218 GLN Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 995 ARG Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain E residue 104 TRP Chi-restraints excluded: chain E residue 150 LYS Chi-restraints excluded: chain E residue 182 LYS Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 238 PHE Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 312 ILE Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 489 TYR Chi-restraints excluded: chain E residue 508 TYR Chi-restraints excluded: chain E residue 525 CYS Chi-restraints excluded: chain E residue 546 LEU Chi-restraints excluded: chain E residue 599 THR Chi-restraints excluded: chain E residue 656 VAL Chi-restraints excluded: chain E residue 712 ILE Chi-restraints excluded: chain E residue 721 SER Chi-restraints excluded: chain E residue 858 LEU Chi-restraints excluded: chain E residue 878 LEU Chi-restraints excluded: chain E residue 939 SER Chi-restraints excluded: chain E residue 984 LEU Chi-restraints excluded: chain E residue 1116 THR Chi-restraints excluded: chain E residue 1128 VAL Chi-restraints excluded: chain E residue 1129 VAL Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 54 ILE Chi-restraints excluded: chain F residue 70 ILE Chi-restraints excluded: chain F residue 112 GLN Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 167 THR Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain G residue 64 SER Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 106 TRP Chi-restraints excluded: chain H residue 149 VAL Chi-restraints excluded: chain H residue 171 HIS Chi-restraints excluded: chain H residue 185 LEU Chi-restraints excluded: chain H residue 200 THR Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 17 GLU Chi-restraints excluded: chain I residue 38 GLN Chi-restraints excluded: chain I residue 180 LEU Chi-restraints excluded: chain I residue 190 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 187 optimal weight: 5.9990 chunk 427 optimal weight: 9.9990 chunk 375 optimal weight: 20.0000 chunk 66 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 365 optimal weight: 9.9990 chunk 299 optimal weight: 4.9990 chunk 158 optimal weight: 6.9990 chunk 241 optimal weight: 0.9990 chunk 69 optimal weight: 4.9990 chunk 298 optimal weight: 4.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS C 218 GLN E 245 HIS E 762 GLN ** E1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 3 GLN ** B 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 112 GLN ** G 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.101180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.072829 restraints weight = 96545.523| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 2.29 r_work: 0.3035 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2912 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.4682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 36039 Z= 0.224 Angle : 0.644 13.467 49163 Z= 0.321 Chirality : 0.047 0.535 5650 Planarity : 0.004 0.049 6287 Dihedral : 5.164 56.106 4844 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.08 % Favored : 90.92 % Rotamer: Outliers : 3.78 % Allowed : 15.11 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.42 (0.12), residues: 4428 helix: 1.52 (0.21), residues: 627 sheet: -1.53 (0.15), residues: 1086 loop : -2.55 (0.11), residues: 2715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG I 62 TYR 0.020 0.002 TYR C 265 PHE 0.037 0.002 PHE A 140 TRP 0.011 0.001 TRP C 64 HIS 0.014 0.001 HIS C 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00537 / 0.22 (35947) covalent geometry : angle 0.63308 / 0.32 (48941) SS BOND : bond 0.00556 / 0.40 ( 54) SS BOND : angle 2.09374 / 1.40 ( 108) hydrogen bonds : bond 0.04284 / 2.85 ( 978) hydrogen bonds : angle 5.59119 / 3.85 ( 2673) link_NAG-ASN : bond 0.00408 / 0.25 ( 38) link_NAG-ASN : angle 1.60651 / 0.99 ( 114) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8856 Ramachandran restraints generated. 4428 Oldfield, 0 Emsley, 4428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8856 Ramachandran restraints generated. 4428 Oldfield, 0 Emsley, 4428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 3885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 324 time to evaluate : 1.447 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 PHE cc_start: 0.6834 (t80) cc_final: 0.6421 (t80) REVERT: A 231 ILE cc_start: 0.8584 (OUTLIER) cc_final: 0.8354 (pt) REVERT: A 249 LEU cc_start: 0.8324 (mt) cc_final: 0.8067 (mp) REVERT: A 774 GLN cc_start: 0.8582 (OUTLIER) cc_final: 0.8196 (mp-120) REVERT: A 858 LEU cc_start: 0.9223 (OUTLIER) cc_final: 0.8981 (mt) REVERT: A 1144 GLU cc_start: 0.8027 (mm-30) cc_final: 0.7775 (mm-30) REVERT: C 119 ILE cc_start: 0.9340 (OUTLIER) cc_final: 0.9101 (mt) REVERT: C 374 PHE cc_start: 0.8204 (m-80) cc_final: 0.7889 (m-80) REVERT: C 458 LYS cc_start: 0.8288 (OUTLIER) cc_final: 0.7648 (mttp) REVERT: C 778 THR cc_start: 0.9485 (OUTLIER) cc_final: 0.9134 (p) REVERT: C 995 ARG cc_start: 0.8681 (OUTLIER) cc_final: 0.8211 (mtt90) REVERT: C 1091 ARG cc_start: 0.8752 (OUTLIER) cc_final: 0.7744 (mtm-85) REVERT: E 150 LYS cc_start: 0.7771 (OUTLIER) cc_final: 0.7037 (ttpt) REVERT: E 277 LEU cc_start: 0.9185 (OUTLIER) cc_final: 0.8909 (pp) REVERT: E 934 ILE cc_start: 0.8724 (mm) cc_final: 0.8449 (mm) REVERT: B 155 LEU cc_start: 0.6211 (OUTLIER) cc_final: 0.5736 (pp) REVERT: F 28 THR cc_start: 0.8371 (OUTLIER) cc_final: 0.8168 (p) REVERT: F 36 TRP cc_start: 0.7392 (m100) cc_final: 0.6786 (m100) REVERT: F 81 MET cc_start: 0.6544 (tmm) cc_final: 0.6199 (tmm) REVERT: G 141 TYR cc_start: 0.6233 (t80) cc_final: 0.5776 (t80) REVERT: H 171 HIS cc_start: 0.4470 (OUTLIER) cc_final: 0.3226 (t-90) REVERT: H 177 LEU cc_start: 0.8430 (mt) cc_final: 0.7614 (tt) REVERT: I 31 ASN cc_start: 0.7106 (p0) cc_final: 0.5642 (p0) REVERT: I 88 TYR cc_start: 0.7341 (m-80) cc_final: 0.6689 (m-10) REVERT: I 148 GLN cc_start: 0.6523 (mp10) cc_final: 0.6319 (mp10) REVERT: I 196 GLU cc_start: 0.8466 (mt-10) cc_final: 0.8159 (tt0) outliers start: 145 outliers final: 113 residues processed: 445 average time/residue: 0.2398 time to fit residues: 171.0814 Evaluate side-chains 434 residues out of total 3885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 308 time to evaluate : 1.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 765 ARG Chi-restraints excluded: chain A residue 774 GLN Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 146 HIS Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 218 GLN Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 735 SER Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 995 ARG Chi-restraints excluded: chain C residue 1091 ARG Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain E residue 104 TRP Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 150 LYS Chi-restraints excluded: chain E residue 182 LYS Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 238 PHE Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 312 ILE Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 489 TYR Chi-restraints excluded: chain E residue 508 TYR Chi-restraints excluded: chain E residue 525 CYS Chi-restraints excluded: chain E residue 546 LEU Chi-restraints excluded: chain E residue 599 THR Chi-restraints excluded: chain E residue 656 VAL Chi-restraints excluded: chain E residue 705 VAL Chi-restraints excluded: chain E residue 712 ILE Chi-restraints excluded: chain E residue 719 THR Chi-restraints excluded: chain E residue 721 SER Chi-restraints excluded: chain E residue 735 SER Chi-restraints excluded: chain E residue 751 ASN Chi-restraints excluded: chain E residue 858 LEU Chi-restraints excluded: chain E residue 878 LEU Chi-restraints excluded: chain E residue 939 SER Chi-restraints excluded: chain E residue 964 LYS Chi-restraints excluded: chain E residue 984 LEU Chi-restraints excluded: chain E residue 1072 GLU Chi-restraints excluded: chain E residue 1116 THR Chi-restraints excluded: chain E residue 1122 VAL Chi-restraints excluded: chain E residue 1128 VAL Chi-restraints excluded: chain E residue 1129 VAL Chi-restraints excluded: chain E residue 1136 THR Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 54 ILE Chi-restraints excluded: chain F residue 70 ILE Chi-restraints excluded: chain F residue 112 GLN Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 167 THR Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain G residue 64 SER Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 106 TRP Chi-restraints excluded: chain H residue 119 SER Chi-restraints excluded: chain H residue 149 VAL Chi-restraints excluded: chain H residue 171 HIS Chi-restraints excluded: chain H residue 185 LEU Chi-restraints excluded: chain H residue 200 THR Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 17 GLU Chi-restraints excluded: chain I residue 38 GLN Chi-restraints excluded: chain I residue 180 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 92 optimal weight: 3.9990 chunk 125 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 60 optimal weight: 0.3980 chunk 149 optimal weight: 4.9990 chunk 132 optimal weight: 1.9990 chunk 127 optimal weight: 0.9990 chunk 387 optimal weight: 7.9990 chunk 179 optimal weight: 0.6980 chunk 9 optimal weight: 2.9990 chunk 374 optimal weight: 8.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 388 ASN ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS C 218 GLN E 969 ASN D 3 GLN ** B 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 112 GLN ** G 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.102366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.074588 restraints weight = 96255.447| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 2.35 r_work: 0.3068 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.4673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 36039 Z= 0.122 Angle : 0.580 12.346 49163 Z= 0.289 Chirality : 0.044 0.438 5650 Planarity : 0.004 0.049 6287 Dihedral : 4.960 55.856 4842 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 3.32 % Allowed : 15.90 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.22 (0.12), residues: 4428 helix: 1.85 (0.21), residues: 621 sheet: -1.37 (0.15), residues: 1075 loop : -2.46 (0.11), residues: 2732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG I 62 TYR 0.020 0.001 TYR B 141 PHE 0.030 0.001 PHE A 140 TRP 0.016 0.001 TRP F 161 HIS 0.017 0.001 HIS C 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.12 (35947) covalent geometry : angle 0.57211 / 0.29 (48941) SS BOND : bond 0.00435 / 0.32 ( 54) SS BOND : angle 1.65507 / 1.12 ( 108) hydrogen bonds : bond 0.03612 / 2.41 ( 978) hydrogen bonds : angle 5.36173 / 3.70 ( 2673) link_NAG-ASN : bond 0.00379 / 0.20 ( 38) link_NAG-ASN : angle 1.31890 / 0.86 ( 114) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8856 Ramachandran restraints generated. 4428 Oldfield, 0 Emsley, 4428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8856 Ramachandran restraints generated. 4428 Oldfield, 0 Emsley, 4428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 3885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 336 time to evaluate : 1.416 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 231 ILE cc_start: 0.8578 (OUTLIER) cc_final: 0.8351 (pt) REVERT: A 249 LEU cc_start: 0.8251 (mt) cc_final: 0.7991 (mp) REVERT: A 332 ILE cc_start: 0.8589 (OUTLIER) cc_final: 0.8214 (tt) REVERT: A 774 GLN cc_start: 0.8438 (OUTLIER) cc_final: 0.8174 (mp-120) REVERT: A 858 LEU cc_start: 0.9132 (OUTLIER) cc_final: 0.8915 (mt) REVERT: A 994 ASP cc_start: 0.8230 (m-30) cc_final: 0.7985 (t70) REVERT: C 119 ILE cc_start: 0.9239 (OUTLIER) cc_final: 0.9029 (mt) REVERT: C 362 VAL cc_start: 0.9405 (t) cc_final: 0.9199 (p) REVERT: C 374 PHE cc_start: 0.8171 (m-80) cc_final: 0.7908 (m-80) REVERT: C 458 LYS cc_start: 0.8330 (OUTLIER) cc_final: 0.7635 (mttp) REVERT: C 995 ARG cc_start: 0.8588 (OUTLIER) cc_final: 0.8353 (mtm-85) REVERT: C 1091 ARG cc_start: 0.8684 (OUTLIER) cc_final: 0.7683 (mtm-85) REVERT: E 150 LYS cc_start: 0.7791 (OUTLIER) cc_final: 0.7060 (ttpt) REVERT: E 277 LEU cc_start: 0.9173 (OUTLIER) cc_final: 0.8867 (pp) REVERT: E 490 PHE cc_start: 0.7231 (m-80) cc_final: 0.6881 (m-80) REVERT: E 492 LEU cc_start: 0.8155 (mt) cc_final: 0.7912 (mp) REVERT: E 934 ILE cc_start: 0.8674 (mm) cc_final: 0.8345 (mm) REVERT: B 155 LEU cc_start: 0.6092 (OUTLIER) cc_final: 0.5654 (pp) REVERT: F 28 THR cc_start: 0.8372 (OUTLIER) cc_final: 0.8146 (p) REVERT: F 36 TRP cc_start: 0.7375 (m100) cc_final: 0.6678 (m100) REVERT: F 81 MET cc_start: 0.6530 (tmm) cc_final: 0.6200 (tmm) REVERT: G 17 GLU cc_start: 0.7757 (mp0) cc_final: 0.7354 (mp0) REVERT: G 18 ARG cc_start: 0.6874 (ttt180) cc_final: 0.6494 (ttt-90) REVERT: G 55 ARG cc_start: 0.8073 (ttm110) cc_final: 0.7781 (ttp-110) REVERT: G 141 TYR cc_start: 0.6200 (t80) cc_final: 0.5984 (t80) REVERT: H 171 HIS cc_start: 0.4366 (OUTLIER) cc_final: 0.3204 (t-90) REVERT: H 177 LEU cc_start: 0.8418 (mt) cc_final: 0.7723 (tt) REVERT: I 31 ASN cc_start: 0.6832 (p0) cc_final: 0.6133 (p0) REVERT: I 88 TYR cc_start: 0.7349 (m-80) cc_final: 0.6616 (m-10) REVERT: I 196 GLU cc_start: 0.8531 (mt-10) cc_final: 0.8216 (tt0) REVERT: I 212 ARG cc_start: 0.5713 (mtp85) cc_final: 0.5150 (mmt-90) outliers start: 127 outliers final: 97 residues processed: 437 average time/residue: 0.2449 time to fit residues: 170.1588 Evaluate side-chains 431 residues out of total 3885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 321 time to evaluate : 1.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 765 ARG Chi-restraints excluded: chain A residue 774 GLN Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 133 PHE Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 218 GLN Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 995 ARG Chi-restraints excluded: chain C residue 1091 ARG Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain E residue 104 TRP Chi-restraints excluded: chain E residue 150 LYS Chi-restraints excluded: chain E residue 182 LYS Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 238 PHE Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 312 ILE Chi-restraints excluded: chain E residue 489 TYR Chi-restraints excluded: chain E residue 508 TYR Chi-restraints excluded: chain E residue 525 CYS Chi-restraints excluded: chain E residue 546 LEU Chi-restraints excluded: chain E residue 599 THR Chi-restraints excluded: chain E residue 656 VAL Chi-restraints excluded: chain E residue 705 VAL Chi-restraints excluded: chain E residue 712 ILE Chi-restraints excluded: chain E residue 719 THR Chi-restraints excluded: chain E residue 721 SER Chi-restraints excluded: chain E residue 858 LEU Chi-restraints excluded: chain E residue 878 LEU Chi-restraints excluded: chain E residue 939 SER Chi-restraints excluded: chain E residue 1072 GLU Chi-restraints excluded: chain E residue 1116 THR Chi-restraints excluded: chain E residue 1128 VAL Chi-restraints excluded: chain E residue 1129 VAL Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 54 ILE Chi-restraints excluded: chain F residue 112 GLN Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 167 THR Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 106 TRP Chi-restraints excluded: chain H residue 149 VAL Chi-restraints excluded: chain H residue 171 HIS Chi-restraints excluded: chain H residue 185 LEU Chi-restraints excluded: chain H residue 200 THR Chi-restraints excluded: chain I residue 1 GLU Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 17 GLU Chi-restraints excluded: chain I residue 38 GLN Chi-restraints excluded: chain I residue 80 GLU Chi-restraints excluded: chain I residue 180 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 332 optimal weight: 2.9990 chunk 272 optimal weight: 6.9990 chunk 40 optimal weight: 6.9990 chunk 212 optimal weight: 3.9990 chunk 176 optimal weight: 3.9990 chunk 358 optimal weight: 10.0000 chunk 86 optimal weight: 6.9990 chunk 253 optimal weight: 6.9990 chunk 247 optimal weight: 10.0000 chunk 421 optimal weight: 20.0000 chunk 165 optimal weight: 0.3980 overall best weight: 3.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS C 218 GLN ** E1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 3 GLN D 162 ASN ** B 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 112 GLN ** G 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.099941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.071380 restraints weight = 95900.143| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 2.33 r_work: 0.3003 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2878 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.4960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.084 36039 Z= 0.283 Angle : 0.700 14.519 49163 Z= 0.351 Chirality : 0.048 0.395 5650 Planarity : 0.005 0.052 6287 Dihedral : 5.361 59.035 4841 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.14 % Favored : 89.86 % Rotamer: Outliers : 3.55 % Allowed : 15.77 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.42 (0.12), residues: 4428 helix: 1.30 (0.21), residues: 633 sheet: -1.51 (0.15), residues: 1078 loop : -2.50 (0.11), residues: 2717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG I 24 TYR 0.022 0.002 TYR C 265 PHE 0.030 0.002 PHE B 210 TRP 0.015 0.002 TRP A 64 HIS 0.021 0.002 HIS C 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00684 / 0.28 (35947) covalent geometry : angle 0.69013 / 0.35 (48941) SS BOND : bond 0.00641 / 0.45 ( 54) SS BOND : angle 2.10198 / 1.40 ( 108) hydrogen bonds : bond 0.04697 / 3.13 ( 978) hydrogen bonds : angle 5.65506 / 3.89 ( 2673) link_NAG-ASN : bond 0.00451 / 0.29 ( 38) link_NAG-ASN : angle 1.63821 / 1.06 ( 114) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8856 Ramachandran restraints generated. 4428 Oldfield, 0 Emsley, 4428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8856 Ramachandran restraints generated. 4428 Oldfield, 0 Emsley, 4428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 467 residues out of total 3885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 331 time to evaluate : 1.401 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: symmetry clash revert: symmetry clash REVERT: A 774 GLN cc_start: 0.8653 (OUTLIER) cc_final: 0.8213 (mp-120) REVERT: A 858 LEU cc_start: 0.9241 (OUTLIER) cc_final: 0.8984 (mt) REVERT: A 994 ASP cc_start: 0.8328 (m-30) cc_final: 0.8113 (t70) REVERT: C 69 HIS cc_start: 0.7221 (OUTLIER) cc_final: 0.6546 (p-80) REVERT: C 458 LYS cc_start: 0.8336 (OUTLIER) cc_final: 0.7727 (mttp) REVERT: C 995 ARG cc_start: 0.8754 (OUTLIER) cc_final: 0.8428 (mtm-85) REVERT: C 1091 ARG cc_start: 0.8788 (OUTLIER) cc_final: 0.7768 (mtm-85) REVERT: E 150 LYS cc_start: 0.7714 (OUTLIER) cc_final: 0.7020 (ttpt) REVERT: E 277 LEU cc_start: 0.9202 (OUTLIER) cc_final: 0.8947 (pp) REVERT: E 490 PHE cc_start: 0.7400 (m-80) cc_final: 0.7075 (m-80) REVERT: E 934 ILE cc_start: 0.8759 (mm) cc_final: 0.8540 (mm) REVERT: B 59 ILE cc_start: 0.7812 (mp) cc_final: 0.7304 (mm) REVERT: B 155 LEU cc_start: 0.6415 (OUTLIER) cc_final: 0.6149 (pp) REVERT: F 36 TRP cc_start: 0.7389 (m100) cc_final: 0.6929 (m100) REVERT: F 81 MET cc_start: 0.6553 (tmm) cc_final: 0.6212 (tmm) REVERT: G 17 GLU cc_start: 0.7836 (mp0) cc_final: 0.7465 (mp0) REVERT: G 55 ARG cc_start: 0.8215 (ttm110) cc_final: 0.7994 (ttp-110) REVERT: G 104 LYS cc_start: 0.7834 (pptt) cc_final: 0.7138 (ptmt) REVERT: G 141 TYR cc_start: 0.6340 (t80) cc_final: 0.6030 (t80) REVERT: H 171 HIS cc_start: 0.4620 (OUTLIER) cc_final: 0.3300 (t-90) REVERT: H 177 LEU cc_start: 0.8479 (mt) cc_final: 0.7689 (tt) REVERT: I 31 ASN cc_start: 0.6889 (p0) cc_final: 0.6246 (p0) REVERT: I 88 TYR cc_start: 0.7399 (m-80) cc_final: 0.6710 (m-10) REVERT: I 166 GLU cc_start: 0.6144 (mt-10) cc_final: 0.5913 (mt-10) REVERT: I 212 ARG cc_start: 0.6036 (mtp85) cc_final: 0.5381 (mmt-90) outliers start: 136 outliers final: 107 residues processed: 441 average time/residue: 0.2414 time to fit residues: 170.1886 Evaluate side-chains 430 residues out of total 3885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 313 time to evaluate : 1.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 765 ARG Chi-restraints excluded: chain A residue 774 GLN Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 218 GLN Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 453 TYR Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 995 ARG Chi-restraints excluded: chain C residue 1091 ARG Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 150 LYS Chi-restraints excluded: chain E residue 182 LYS Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 238 PHE Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 312 ILE Chi-restraints excluded: chain E residue 422 ASN Chi-restraints excluded: chain E residue 489 TYR Chi-restraints excluded: chain E residue 508 TYR Chi-restraints excluded: chain E residue 525 CYS Chi-restraints excluded: chain E residue 546 LEU Chi-restraints excluded: chain E residue 599 THR Chi-restraints excluded: chain E residue 656 VAL Chi-restraints excluded: chain E residue 705 VAL Chi-restraints excluded: chain E residue 712 ILE Chi-restraints excluded: chain E residue 719 THR Chi-restraints excluded: chain E residue 721 SER Chi-restraints excluded: chain E residue 751 ASN Chi-restraints excluded: chain E residue 858 LEU Chi-restraints excluded: chain E residue 878 LEU Chi-restraints excluded: chain E residue 939 SER Chi-restraints excluded: chain E residue 1072 GLU Chi-restraints excluded: chain E residue 1116 THR Chi-restraints excluded: chain E residue 1128 VAL Chi-restraints excluded: chain E residue 1129 VAL Chi-restraints excluded: chain E residue 1136 THR Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain F residue 54 ILE Chi-restraints excluded: chain F residue 112 GLN Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 167 THR Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 106 TRP Chi-restraints excluded: chain H residue 119 SER Chi-restraints excluded: chain H residue 149 VAL Chi-restraints excluded: chain H residue 171 HIS Chi-restraints excluded: chain H residue 185 LEU Chi-restraints excluded: chain H residue 200 THR Chi-restraints excluded: chain I residue 1 GLU Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 17 GLU Chi-restraints excluded: chain I residue 38 GLN Chi-restraints excluded: chain I residue 80 GLU Chi-restraints excluded: chain I residue 180 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 277 optimal weight: 0.9980 chunk 386 optimal weight: 0.7980 chunk 57 optimal weight: 10.0000 chunk 249 optimal weight: 6.9990 chunk 156 optimal weight: 4.9990 chunk 404 optimal weight: 5.9990 chunk 263 optimal weight: 10.0000 chunk 328 optimal weight: 2.9990 chunk 398 optimal weight: 9.9990 chunk 174 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS C 218 GLN C 239 GLN C 422 ASN E 969 ASN ** E1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 3 GLN ** B 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 112 GLN ** G 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 148 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 = 0.3827 r_free = 0.3827 target = 0.101308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.073577 restraints weight = 96461.531| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 2.29 r_work: 0.3042 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2920 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.4947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 36039 Z= 0.153 Angle : 0.618 13.650 49163 Z= 0.309 Chirality : 0.045 0.383 5650 Planarity : 0.004 0.051 6287 Dihedral : 5.173 59.205 4841 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.04 % Favored : 91.96 % Rotamer: Outliers : 2.98 % Allowed : 16.52 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.24 (0.12), residues: 4428 helix: 1.63 (0.21), residues: 627 sheet: -1.39 (0.15), residues: 1073 loop : -2.42 (0.11), residues: 2728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG I 143 TYR 0.021 0.001 TYR B 50 PHE 0.030 0.002 PHE B 210 TRP 0.022 0.001 TRP G 36 HIS 0.010 0.001 HIS B 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.15 (35947) covalent geometry : angle 0.61001 / 0.31 (48941) SS BOND : bond 0.00484 / 0.35 ( 54) SS BOND : angle 1.71802 / 1.16 ( 108) hydrogen bonds : bond 0.03885 / 2.59 ( 978) hydrogen bonds : angle 5.43991 / 3.74 ( 2673) link_NAG-ASN : bond 0.00360 / 0.20 ( 38) link_NAG-ASN : angle 1.39719 / 0.92 ( 114) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8856 Ramachandran restraints generated. 4428 Oldfield, 0 Emsley, 4428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8856 Ramachandran restraints generated. 4428 Oldfield, 0 Emsley, 4428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 3885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 329 time to evaluate : 1.418 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 226 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8407 (mm) REVERT: A 774 GLN cc_start: 0.8509 (OUTLIER) cc_final: 0.8161 (mp-120) REVERT: A 858 LEU cc_start: 0.9154 (OUTLIER) cc_final: 0.8931 (mt) REVERT: A 994 ASP cc_start: 0.8264 (m-30) cc_final: 0.8026 (t70) REVERT: C 177 MET cc_start: 0.6034 (mtt) cc_final: 0.5754 (mtt) REVERT: C 375 SER cc_start: 0.8480 (m) cc_final: 0.8276 (t) REVERT: C 458 LYS cc_start: 0.8369 (OUTLIER) cc_final: 0.7697 (mttp) REVERT: C 778 THR cc_start: 0.9470 (OUTLIER) cc_final: 0.9113 (p) REVERT: C 995 ARG cc_start: 0.8639 (OUTLIER) cc_final: 0.8370 (mtm-85) REVERT: C 1091 ARG cc_start: 0.8731 (OUTLIER) cc_final: 0.7721 (mtm-85) REVERT: E 150 LYS cc_start: 0.7741 (OUTLIER) cc_final: 0.7057 (ttpt) REVERT: E 277 LEU cc_start: 0.9182 (OUTLIER) cc_final: 0.8881 (pp) REVERT: E 490 PHE cc_start: 0.7302 (m-80) cc_final: 0.6976 (m-80) REVERT: E 934 ILE cc_start: 0.8739 (mm) cc_final: 0.8491 (mm) REVERT: D 155 GLU cc_start: 0.6440 (pm20) cc_final: 0.6205 (pt0) REVERT: B 24 ARG cc_start: 0.7732 (mtp85) cc_final: 0.7355 (mmm160) REVERT: B 59 ILE cc_start: 0.7719 (mp) cc_final: 0.7194 (mm) REVERT: B 155 LEU cc_start: 0.6391 (OUTLIER) cc_final: 0.6020 (pp) REVERT: F 36 TRP cc_start: 0.7387 (m100) cc_final: 0.6785 (m100) REVERT: F 81 MET cc_start: 0.6472 (tmm) cc_final: 0.6151 (tmm) REVERT: F 112 GLN cc_start: 0.6965 (OUTLIER) cc_final: 0.6703 (pm20) REVERT: G 1 GLU cc_start: 0.6549 (mm-30) cc_final: 0.6121 (mm-30) REVERT: G 17 GLU cc_start: 0.7763 (mp0) cc_final: 0.7398 (mp0) REVERT: G 104 LYS cc_start: 0.7658 (pptt) cc_final: 0.7170 (ptmt) REVERT: H 171 HIS cc_start: 0.4637 (OUTLIER) cc_final: 0.3365 (t-90) REVERT: H 177 LEU cc_start: 0.8415 (mt) cc_final: 0.7742 (tt) REVERT: I 31 ASN cc_start: 0.6809 (p0) cc_final: 0.5883 (p0) REVERT: I 78 ARG cc_start: 0.7698 (tpp-160) cc_final: 0.7358 (ptm160) REVERT: I 88 TYR cc_start: 0.7392 (m-80) cc_final: 0.6722 (m-10) outliers start: 114 outliers final: 96 residues processed: 421 average time/residue: 0.2521 time to fit residues: 166.9659 Evaluate side-chains 424 residues out of total 3885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 316 time to evaluate : 1.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 765 ARG Chi-restraints excluded: chain A residue 774 GLN Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 218 GLN Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 453 TYR Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 995 ARG Chi-restraints excluded: chain C residue 1091 ARG Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 150 LYS Chi-restraints excluded: chain E residue 182 LYS Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 238 PHE Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 312 ILE Chi-restraints excluded: chain E residue 489 TYR Chi-restraints excluded: chain E residue 508 TYR Chi-restraints excluded: chain E residue 525 CYS Chi-restraints excluded: chain E residue 546 LEU Chi-restraints excluded: chain E residue 599 THR Chi-restraints excluded: chain E residue 656 VAL Chi-restraints excluded: chain E residue 705 VAL Chi-restraints excluded: chain E residue 712 ILE Chi-restraints excluded: chain E residue 719 THR Chi-restraints excluded: chain E residue 721 SER Chi-restraints excluded: chain E residue 735 SER Chi-restraints excluded: chain E residue 858 LEU Chi-restraints excluded: chain E residue 878 LEU Chi-restraints excluded: chain E residue 964 LYS Chi-restraints excluded: chain E residue 1072 GLU Chi-restraints excluded: chain E residue 1116 THR Chi-restraints excluded: chain E residue 1128 VAL Chi-restraints excluded: chain E residue 1129 VAL Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain F residue 54 ILE Chi-restraints excluded: chain F residue 112 GLN Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 167 THR Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 106 TRP Chi-restraints excluded: chain H residue 149 VAL Chi-restraints excluded: chain H residue 171 HIS Chi-restraints excluded: chain H residue 185 LEU Chi-restraints excluded: chain I residue 1 GLU Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 17 GLU Chi-restraints excluded: chain I residue 38 GLN Chi-restraints excluded: chain I residue 80 GLU Chi-restraints excluded: chain I residue 180 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 360 optimal weight: 30.0000 chunk 348 optimal weight: 8.9990 chunk 356 optimal weight: 0.9980 chunk 441 optimal weight: 0.9990 chunk 410 optimal weight: 20.0000 chunk 298 optimal weight: 1.9990 chunk 167 optimal weight: 0.6980 chunk 206 optimal weight: 0.7980 chunk 170 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 80 optimal weight: 3.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 992 GLN ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS C 218 GLN ** E 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 3 GLN ** B 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 148 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 = 0.3837 r_free = 0.3837 target = 0.101818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.074220 restraints weight = 96041.968| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 2.23 r_work: 0.3070 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.4954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 36039 Z= 0.130 Angle : 0.606 13.260 49163 Z= 0.301 Chirality : 0.045 0.371 5650 Planarity : 0.005 0.121 6287 Dihedral : 5.082 59.224 4841 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 2.90 % Allowed : 16.71 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.10 (0.12), residues: 4428 helix: 1.79 (0.21), residues: 627 sheet: -1.26 (0.15), residues: 1071 loop : -2.36 (0.11), residues: 2730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG I 143 TYR 0.021 0.001 TYR B 50 PHE 0.037 0.001 PHE A 79 TRP 0.023 0.001 TRP G 36 HIS 0.009 0.001 HIS B 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.13 (35947) covalent geometry : angle 0.59911 / 0.30 (48941) SS BOND : bond 0.00490 / 0.36 ( 54) SS BOND : angle 1.63240 / 1.11 ( 108) hydrogen bonds : bond 0.03656 / 2.44 ( 978) hydrogen bonds : angle 5.32652 / 3.66 ( 2673) link_NAG-ASN : bond 0.00338 / 0.19 ( 38) link_NAG-ASN : angle 1.33599 / 0.88 ( 114) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13448.40 seconds wall clock time: 229 minutes 54.42 seconds (13794.42 seconds total)