Starting phenix.real_space_refine on Mon Jul 6 14:27:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7yr3_34044/07_2026/7yr3_34044.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yr3_34044/07_2026/7yr3_34044.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.52 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7yr3_34044/07_2026/7yr3_34044.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yr3_34044/07_2026/7yr3_34044.map" model { file = "/net/cci-nas-00/data/ceres_data/7yr3_34044/07_2026/7yr3_34044.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yr3_34044/07_2026/7yr3_34044.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7yr3_34044/07_2026/7yr3_34044.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7yr3_34044/07_2026/7yr3_34044.cif" } resolution = 3.52 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= 0.026 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: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 S 167 5.16 5 Cl 2 4.86 5 C 22772 2.51 5 N 5862 2.21 5 O 7094 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 43 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: 35899 Number of models: 1 Model: "" Number of chains: 21 Chain: "B" Number of atoms: 8258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1058, 8258 Classifications: {'peptide': 1058} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 56, 'TRANS': 1001} Chain breaks: 3 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "C" Number of atoms: 8426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1080, 8426 Classifications: {'peptide': 1080} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 58, 'TRANS': 1021} Chain breaks: 2 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 38 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 26 Chain: "D" Number of atoms: 4870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4870 Classifications: {'peptide': 597} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 569} Chain: "F" Number of atoms: 8335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1068, 8335 Classifications: {'peptide': 1068} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 57, 'TRANS': 1010} Chain breaks: 3 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "G" Number of atoms: 4870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4870 Classifications: {'peptide': 597} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 569} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 210 Unusual residues: {'NAG': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen chiralities: 15 Chain: "C" Number of atoms: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 238 Unusual residues: {'NAG': 17} Classifications: {'undetermined': 17} Link IDs: {None: 16} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen chiralities: 17 Chain: "D" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 58 Unusual residues: {' CL': 1, ' ZN': 1, 'NAG': 4} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "F" 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: "G" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 58 Unusual residues: {' CL': 1, ' ZN': 1, 'NAG': 4} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "D" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 71 Classifications: {'water': 71} Link IDs: {None: 70} Chain: "G" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 71 Classifications: {'water': 71} Link IDs: {None: 70} Time building chain proxies: 7.09, per 1000 atoms: 0.20 Number of scatterers: 35899 At special positions: 0 Unit cell: (152.88, 163.28, 243.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 Cl 2 17.00 S 167 16.00 O 7094 8.00 N 5862 7.00 C 22772 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 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=2.05 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 D 133 " - pdb=" SG CYS D 141 " distance=2.03 Simple disulfide: pdb=" SG CYS D 344 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 530 " - pdb=" SG CYS D 542 " distance=2.03 Simple disulfide: pdb=" SG CYS F 131 " - pdb=" SG CYS F 166 " distance=2.03 Simple disulfide: pdb=" SG CYS F 291 " - pdb=" SG CYS F 301 " distance=2.03 Simple disulfide: pdb=" SG CYS F 336 " - pdb=" SG CYS F 361 " distance=2.02 Simple disulfide: pdb=" SG CYS F 379 " - pdb=" SG CYS F 432 " distance=2.04 Simple disulfide: pdb=" SG CYS F 391 " - pdb=" SG CYS F 525 " distance=2.03 Simple disulfide: pdb=" SG CYS F 480 " - pdb=" SG CYS F 488 " distance=2.03 Simple disulfide: pdb=" SG CYS F 617 " - pdb=" SG CYS F 649 " distance=2.03 Simple disulfide: pdb=" SG CYS F 662 " - pdb=" SG CYS F 671 " distance=2.03 Simple disulfide: pdb=" SG CYS F 738 " - pdb=" SG CYS F 760 " distance=2.03 Simple disulfide: pdb=" SG CYS F 743 " - pdb=" SG CYS F 749 " distance=2.03 Simple disulfide: pdb=" SG CYS F1032 " - pdb=" SG CYS F1043 " distance=2.03 Simple disulfide: pdb=" SG CYS F1082 " - pdb=" SG CYS F1126 " distance=2.03 Simple disulfide: pdb=" SG CYS G 133 " - pdb=" SG CYS G 141 " distance=2.03 Simple disulfide: pdb=" SG CYS G 344 " - pdb=" SG CYS G 361 " distance=2.03 Simple disulfide: pdb=" SG CYS G 530 " - pdb=" SG CYS G 542 " 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=5, symmetry=0 Links applied BETA1-4 " NAG A 1 " - " NAG A 2 " " NAG E 1 " - " NAG E 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " NAG-ASN " NAG B1310 " - " ASN B 603 " " NAG B1311 " - " ASN B 616 " " NAG B1312 " - " ASN B 657 " " NAG B1313 " - " ASN B 709 " " NAG C1310 " - " ASN C 603 " " NAG C1311 " - " ASN C 616 " " NAG C1312 " - " ASN C 657 " " NAG C1313 " - " ASN C 709 " " NAG C1315 " - " ASN C1134 " " NAG D 903 " - " ASN D 546 " " NAG D 904 " - " ASN D 90 " " NAG D 905 " - " ASN D 322 " " NAG D 906 " - " ASN D 53 " " NAG F1309 " - " ASN F 616 " " NAG F1311 " - " ASN F 709 " " NAG F1313 " - " ASN F1134 " " NAG G 903 " - " ASN G 546 " " NAG G 904 " - " ASN G 90 " " NAG G 905 " - " ASN G 322 " " NAG G 906 " - " ASN G 53 " " NAG H 1 " - " ASN B1074 " " NAG I 1 " - " ASN C 717 " " NAG K 1 " - " ASN C1074 " " NAG N 1 " - " ASN F1074 " Number of additional bonds: simple=5, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.43 Conformation dependent library (CDL) restraints added in 1.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D 901 " pdb="ZN ZN D 901 " - pdb=" ND1 HIS D 378 " pdb="ZN ZN D 901 " - pdb=" NE2 HIS D 374 " pdb=" ZN G 901 " pdb="ZN ZN G 901 " - pdb=" NE2 HIS G 374 " pdb="ZN ZN G 901 " - pdb=" NE2 HIS G 378 " 8748 Ramachandran restraints generated. 4374 Oldfield, 0 Emsley, 4374 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8262 Finding SS restraints... Secondary structure from input PDB file: 114 helices and 57 sheets defined 34.6% alpha, 14.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.25 Creating SS restraints... Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.630A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 372 removed outlier: 4.070A pdb=" N PHE B 371 " --> pdb=" O LEU B 368 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ALA B 372 " --> pdb=" O TYR B 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 368 through 372' Processing helix chain 'B' and resid 384 through 388 removed outlier: 3.644A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 384 through 388' Processing helix chain 'B' and resid 403 through 410 removed outlier: 4.341A pdb=" N SER B 408 " --> pdb=" O ASN B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 421 Processing helix chain 'B' and resid 737 through 742 Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.537A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 760 through 783 removed outlier: 3.567A pdb=" N ARG B 765 " --> pdb=" O THR B 761 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLN B 779 " --> pdb=" O ASP B 775 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 869 through 884 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 908 removed outlier: 3.861A pdb=" N ALA B 903 " --> pdb=" O PRO B 899 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 918 Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.798A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 976 through 982 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 3.792A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLN B1002 " --> pdb=" O THR B 998 " (cutoff:3.500A) Processing helix chain 'C' and resid 109 through 111 No H-bonds generated for 'chain 'C' and resid 109 through 111' Processing helix chain 'C' and resid 244 through 247 removed outlier: 3.621A pdb=" N SER C 247 " --> pdb=" O LEU C 244 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 244 through 247' Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 366 through 371 removed outlier: 3.878A pdb=" N TYR C 369 " --> pdb=" O SER C 366 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ASN C 370 " --> pdb=" O VAL C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 756 removed outlier: 3.701A pdb=" N SER C 750 " --> pdb=" O SER C 746 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N TYR C 756 " --> pdb=" O LEU C 752 " (cutoff:3.500A) Processing helix chain 'C' and resid 760 through 783 removed outlier: 3.837A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLN C 779 " --> pdb=" O ASP C 775 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 825 Processing helix chain 'C' and resid 866 through 884 removed outlier: 3.596A pdb=" N ALA C 871 " --> pdb=" O ASP C 867 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N GLN C 872 " --> pdb=" O GLU C 868 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.709A 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 913 through 918 removed outlier: 4.150A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLU C 918 " --> pdb=" O ASN C 914 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 913 through 918' Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.906A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR C 941 " --> pdb=" O SER C 937 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 976 through 983 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.668A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 53 removed outlier: 4.049A pdb=" N GLN D 24 " --> pdb=" O THR D 20 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ASP D 38 " --> pdb=" O HIS D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 82 removed outlier: 4.212A pdb=" N MET D 82 " --> pdb=" O THR D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 102 Processing helix chain 'D' and resid 109 through 129 Processing helix chain 'D' and resid 146 through 155 Processing helix chain 'D' and resid 157 through 172 removed outlier: 4.077A pdb=" N VAL D 172 " --> pdb=" O TRP D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 194 Proline residue: D 178 - end of helix Processing helix chain 'D' and resid 198 through 205 Processing helix chain 'D' and resid 218 through 252 removed outlier: 3.666A pdb=" N LEU D 222 " --> pdb=" O SER D 218 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ILE D 223 " --> pdb=" O ARG D 219 " (cutoff:3.500A) Proline residue: D 235 - end of helix Processing helix chain 'D' and resid 265 through 267 No H-bonds generated for 'chain 'D' and resid 265 through 267' Processing helix chain 'D' and resid 275 through 277 No H-bonds generated for 'chain 'D' and resid 275 through 277' Processing helix chain 'D' and resid 278 through 283 Processing helix chain 'D' and resid 293 through 300 Processing helix chain 'D' and resid 303 through 319 Processing helix chain 'D' and resid 324 through 331 removed outlier: 3.915A pdb=" N TRP D 328 " --> pdb=" O THR D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 385 removed outlier: 3.968A pdb=" N TYR D 385 " --> pdb=" O TYR D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 393 Processing helix chain 'D' and resid 400 through 414 Processing helix chain 'D' and resid 414 through 421 removed outlier: 3.801A pdb=" N ILE D 421 " --> pdb=" O HIS D 417 " (cutoff:3.500A) Processing helix chain 'D' and resid 425 through 429 removed outlier: 4.454A pdb=" N GLN D 429 " --> pdb=" O PRO D 426 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 446 Processing helix chain 'D' and resid 449 through 465 Processing helix chain 'D' and resid 469 through 471 No H-bonds generated for 'chain 'D' and resid 469 through 471' Processing helix chain 'D' and resid 472 through 481 removed outlier: 4.598A pdb=" N GLU D 479 " --> pdb=" O LYS D 475 " (cutoff:3.500A) Processing helix chain 'D' and resid 498 through 502 Processing helix chain 'D' and resid 503 through 508 removed outlier: 3.510A pdb=" N SER D 507 " --> pdb=" O LEU D 503 " (cutoff:3.500A) Processing helix chain 'D' and resid 513 through 533 Processing helix chain 'D' and resid 538 through 542 Processing helix chain 'D' and resid 547 through 561 removed outlier: 3.844A pdb=" N MET D 557 " --> pdb=" O LYS D 553 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU D 560 " --> pdb=" O ASN D 556 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLY D 561 " --> pdb=" O MET D 557 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 575 removed outlier: 3.636A pdb=" N VAL D 573 " --> pdb=" O ALA D 569 " (cutoff:3.500A) Processing helix chain 'D' and resid 581 through 599 Proline residue: D 590 - end of helix Processing helix chain 'D' and resid 600 through 602 No H-bonds generated for 'chain 'D' and resid 600 through 602' Processing helix chain 'F' and resid 294 through 303 Processing helix chain 'F' and resid 338 through 343 Processing helix chain 'F' and resid 367 through 372 removed outlier: 3.972A pdb=" N ASN F 370 " --> pdb=" O VAL F 367 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ALA F 372 " --> pdb=" O TYR F 369 " (cutoff:3.500A) Processing helix chain 'F' and resid 405 through 408 removed outlier: 3.705A pdb=" N SER F 408 " --> pdb=" O ASN F 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 405 through 408' Processing helix chain 'F' and resid 417 through 422 Processing helix chain 'F' and resid 737 through 743 removed outlier: 3.574A pdb=" N TYR F 741 " --> pdb=" O ASP F 737 " (cutoff:3.500A) Processing helix chain 'F' and resid 746 through 755 removed outlier: 3.639A pdb=" N GLN F 755 " --> pdb=" O ASN F 751 " (cutoff:3.500A) Processing helix chain 'F' and resid 760 through 783 Processing helix chain 'F' and resid 816 through 826 Processing helix chain 'F' and resid 869 through 884 Processing helix chain 'F' and resid 886 through 891 removed outlier: 4.085A pdb=" N ALA F 890 " --> pdb=" O TRP F 886 " (cutoff:3.500A) Processing helix chain 'F' and resid 897 through 908 removed outlier: 3.516A pdb=" N TYR F 904 " --> pdb=" O MET F 900 " (cutoff:3.500A) Processing helix chain 'F' and resid 913 through 918 removed outlier: 4.295A pdb=" N TYR F 917 " --> pdb=" O GLN F 913 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLU F 918 " --> pdb=" O ASN F 914 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 913 through 918' Processing helix chain 'F' and resid 919 through 941 removed outlier: 3.896A pdb=" N GLN F 935 " --> pdb=" O ILE F 931 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ASP F 936 " --> pdb=" O GLY F 932 " (cutoff:3.500A) Processing helix chain 'F' and resid 945 through 965 Processing helix chain 'F' and resid 976 through 984 Processing helix chain 'F' and resid 985 through 1033 removed outlier: 3.583A pdb=" N GLU F 990 " --> pdb=" O PRO F 986 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N VAL F 991 " --> pdb=" O PRO F 987 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLN F 992 " --> pdb=" O GLU F 988 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ARG F 995 " --> pdb=" O VAL F 991 " (cutoff:3.500A) Processing helix chain 'G' and resid 20 through 52 removed outlier: 3.550A pdb=" N GLN G 24 " --> pdb=" O THR G 20 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ASP G 38 " --> pdb=" O HIS G 34 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 83 Processing helix chain 'G' and resid 92 through 101 removed outlier: 3.585A pdb=" N GLN G 96 " --> pdb=" O THR G 92 " (cutoff:3.500A) Processing helix chain 'G' and resid 109 through 129 Processing helix chain 'G' and resid 146 through 155 Processing helix chain 'G' and resid 157 through 194 removed outlier: 3.613A pdb=" N VAL G 172 " --> pdb=" O TRP G 168 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N GLN G 175 " --> pdb=" O GLU G 171 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU G 176 " --> pdb=" O VAL G 172 " (cutoff:3.500A) Proline residue: G 178 - end of helix Processing helix chain 'G' and resid 198 through 206 Processing helix chain 'G' and resid 218 through 252 removed outlier: 3.504A pdb=" N ILE G 223 " --> pdb=" O ARG G 219 " (cutoff:3.500A) Proline residue: G 235 - end of helix Processing helix chain 'G' and resid 253 through 256 removed outlier: 4.155A pdb=" N ILE G 256 " --> pdb=" O PRO G 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 253 through 256' Processing helix chain 'G' and resid 275 through 277 No H-bonds generated for 'chain 'G' and resid 275 through 277' Processing helix chain 'G' and resid 278 through 283 Processing helix chain 'G' and resid 293 through 301 Processing helix chain 'G' and resid 303 through 317 Processing helix chain 'G' and resid 324 through 331 removed outlier: 4.069A pdb=" N TRP G 328 " --> pdb=" O THR G 324 " (cutoff:3.500A) Processing helix chain 'G' and resid 365 through 385 removed outlier: 3.546A pdb=" N TYR G 385 " --> pdb=" O TYR G 381 " (cutoff:3.500A) Processing helix chain 'G' and resid 389 through 393 Processing helix chain 'G' and resid 400 through 414 removed outlier: 3.585A pdb=" N THR G 414 " --> pdb=" O LEU G 410 " (cutoff:3.500A) Processing helix chain 'G' and resid 414 through 421 Processing helix chain 'G' and resid 425 through 429 removed outlier: 4.518A pdb=" N GLN G 429 " --> pdb=" O PRO G 426 " (cutoff:3.500A) Processing helix chain 'G' and resid 431 through 465 removed outlier: 3.695A pdb=" N GLU G 435 " --> pdb=" O ASP G 431 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N GLY G 448 " --> pdb=" O LEU G 444 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N THR G 449 " --> pdb=" O THR G 445 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU G 450 " --> pdb=" O ILE G 446 " (cutoff:3.500A) Proline residue: G 451 - end of helix Processing helix chain 'G' and resid 469 through 471 No H-bonds generated for 'chain 'G' and resid 469 through 471' Processing helix chain 'G' and resid 472 through 484 removed outlier: 3.529A pdb=" N LYS G 476 " --> pdb=" O GLN G 472 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N GLU G 479 " --> pdb=" O LYS G 475 " (cutoff:3.500A) Processing helix chain 'G' and resid 498 through 502 Processing helix chain 'G' and resid 503 through 508 Processing helix chain 'G' and resid 513 through 533 Processing helix chain 'G' and resid 538 through 542 removed outlier: 3.616A pdb=" N LYS G 541 " --> pdb=" O PRO G 538 " (cutoff:3.500A) Processing helix chain 'G' and resid 547 through 561 removed outlier: 3.609A pdb=" N MET G 557 " --> pdb=" O LYS G 553 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LEU G 560 " --> pdb=" O ASN G 556 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLY G 561 " --> pdb=" O MET G 557 " (cutoff:3.500A) Processing helix chain 'G' and resid 565 through 575 removed outlier: 4.005A pdb=" N VAL G 573 " --> pdb=" O ALA G 569 " (cutoff:3.500A) Processing helix chain 'G' and resid 581 through 600 Proline residue: G 590 - end of helix Processing sheet with id=AA1, first strand: chain 'B' and resid 27 through 30 Processing sheet with id=AA2, first strand: chain 'B' and resid 36 through 37 removed outlier: 7.257A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 42 through 43 Processing sheet with id=AA4, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.743A pdb=" N HIS B 49 " --> pdb=" O LEU B 277 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.615A pdb=" N LEU B 84 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLY B 107 " --> pdb=" O ARG B 237 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 204 through 208 removed outlier: 3.630A pdb=" N TYR B 204 " --> pdb=" O VAL B 193 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYS B 206 " --> pdb=" O GLU B 191 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA B 93 " --> pdb=" O TYR B 266 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 311 through 319 removed outlier: 3.793A pdb=" N GLY B 311 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N THR B 599 " --> pdb=" O GLY B 311 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N THR B 315 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLN B 613 " --> pdb=" O GLY B 594 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N SER B 596 " --> pdb=" O LEU B 611 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N TYR B 612 " --> pdb=" O CYS B 649 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.738A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ALA B 397 " --> pdb=" O LYS B 356 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ASP B 398 " --> pdb=" O VAL B 512 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 452 through 454 removed outlier: 4.086A pdb=" N TYR B 453 " --> pdb=" O GLN B 493 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 538 through 541 Processing sheet with id=AB2, first strand: chain 'B' and resid 654 through 660 removed outlier: 4.725A pdb=" N THR B 696 " --> pdb=" O VAL B 656 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ASN B 658 " --> pdb=" O THR B 696 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ILE B 664 " --> pdb=" O ALA B 672 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 701 through 704 Processing sheet with id=AB4, first strand: chain 'B' and resid 711 through 713 Processing sheet with id=AB5, first strand: chain 'B' and resid 717 through 722 Processing sheet with id=AB6, first strand: chain 'B' and resid 717 through 722 removed outlier: 3.700A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AB8, first strand: chain 'C' and resid 26 through 30 Processing sheet with id=AB9, first strand: chain 'C' and resid 36 through 37 removed outlier: 7.061A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'C' and resid 50 through 55 removed outlier: 3.946A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.595A pdb=" N LEU C 84 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N ARG C 237 " --> pdb=" O GLY C 107 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLY C 107 " --> pdb=" O ARG C 237 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 205 through 208 removed outlier: 3.547A pdb=" N LYS C 206 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU C 191 " --> pdb=" O LYS C 206 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 311 through 319 removed outlier: 3.731A pdb=" N THR C 599 " --> pdb=" O GLY C 311 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 324 through 326 removed outlier: 7.090A pdb=" N GLU C 324 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N ASN C 542 " --> pdb=" O GLU C 324 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N ILE C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 324 through 326 removed outlier: 7.090A pdb=" N GLU C 324 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N ASN C 542 " --> pdb=" O GLU C 324 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N ILE C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.262A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TYR C 396 " --> pdb=" O SER C 514 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.355A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 453 through 454 removed outlier: 4.311A pdb=" N TYR C 453 " --> pdb=" O GLN C 493 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLN C 493 " --> pdb=" O TYR C 453 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AD2, first strand: chain 'C' and resid 655 through 656 removed outlier: 4.356A pdb=" N THR C 696 " --> pdb=" O VAL C 656 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE C 664 " --> pdb=" O ALA C 672 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.545A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.545A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N GLN C1106 " --> pdb=" O GLU C1111 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N GLU C1111 " --> pdb=" O GLN C1106 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 735 through 736 Processing sheet with id=AD6, first strand: chain 'C' and resid 1081 through 1082 Processing sheet with id=AD7, first strand: chain 'C' and resid 1089 through 1090 Processing sheet with id=AD8, first strand: chain 'D' and resid 132 through 133 Processing sheet with id=AD9, first strand: chain 'D' and resid 262 through 263 removed outlier: 6.024A pdb=" N LEU D 262 " --> pdb=" O VAL D 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'D' and resid 347 through 352 removed outlier: 6.091A pdb=" N ASP D 355 " --> pdb=" O LEU D 351 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'F' and resid 26 through 30 Processing sheet with id=AE3, first strand: chain 'F' and resid 36 through 37 removed outlier: 6.808A pdb=" N VAL F 36 " --> pdb=" O LEU F 223 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'F' and resid 50 through 55 removed outlier: 3.622A pdb=" N ASP F 287 " --> pdb=" O LYS F 278 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'F' and resid 84 through 85 removed outlier: 3.826A pdb=" N PHE F 106 " --> pdb=" O LEU F 117 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'F' and resid 205 through 208 removed outlier: 3.514A pdb=" N LYS F 206 " --> pdb=" O GLU F 191 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU F 191 " --> pdb=" O LYS F 206 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA F 93 " --> pdb=" O TYR F 266 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'F' and resid 311 through 313 removed outlier: 4.311A pdb=" N TYR F 612 " --> pdb=" O CYS F 649 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'F' and resid 354 through 355 removed outlier: 3.597A pdb=" N ASN F 354 " --> pdb=" O SER F 399 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'F' and resid 452 through 454 removed outlier: 3.821A pdb=" N TYR F 453 " --> pdb=" O GLN F 493 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'F' and resid 473 through 474 Processing sheet with id=AF2, first strand: chain 'F' and resid 542 through 543 Processing sheet with id=AF3, first strand: chain 'F' and resid 551 through 554 Processing sheet with id=AF4, first strand: chain 'F' and resid 654 through 660 removed outlier: 5.336A pdb=" N GLU F 654 " --> pdb=" O ALA F 694 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N THR F 696 " --> pdb=" O GLU F 654 " (cutoff:3.500A) removed outlier: 8.491A pdb=" N VAL F 656 " --> pdb=" O THR F 696 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N SER F 691 " --> pdb=" O GLN F 675 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLN F 675 " --> pdb=" O SER F 691 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ILE F 670 " --> pdb=" O ILE F 666 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'F' and resid 711 through 715 Processing sheet with id=AF6, first strand: chain 'F' and resid 718 through 722 removed outlier: 7.008A pdb=" N VAL F1065 " --> pdb=" O LEU F1049 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'F' and resid 725 through 728 Processing sheet with id=AF8, first strand: chain 'F' and resid 733 through 735 removed outlier: 4.491A pdb=" N LYS F 733 " --> pdb=" O LEU F 861 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N SER F 735 " --> pdb=" O THR F 859 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'F' and resid 1081 through 1082 Processing sheet with id=AG1, first strand: chain 'G' and resid 132 through 133 Processing sheet with id=AG2, first strand: chain 'G' and resid 262 through 263 removed outlier: 5.932A pdb=" N LEU G 262 " --> pdb=" O VAL G 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG2 Processing sheet with id=AG3, first strand: chain 'G' and resid 347 through 352 removed outlier: 6.156A pdb=" N ASP G 355 " --> pdb=" O LEU G 351 " (cutoff:3.500A) 1343 hydrogen bonds defined for protein. 3765 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.92 Time building geometry restraints manager: 4.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 11390 1.35 - 1.47: 9320 1.47 - 1.59: 15682 1.59 - 1.72: 0 1.72 - 1.84: 236 Bond restraints: 36628 Sorted by residual: bond pdb=" C1 NAG N 1 " pdb=" O5 NAG N 1 " ideal model delta sigma weight residual 1.406 1.484 -0.078 2.00e-02 2.50e+03 1.52e+01 bond pdb=" C1 NAG K 1 " pdb=" O5 NAG K 1 " ideal model delta sigma weight residual 1.406 1.482 -0.076 2.00e-02 2.50e+03 1.44e+01 bond pdb=" N ILE F 332 " pdb=" CA ILE F 332 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.25e-02 6.40e+03 8.27e+00 bond pdb=" N ASN F 331 " pdb=" CA ASN F 331 " ideal model delta sigma weight residual 1.456 1.490 -0.034 1.25e-02 6.40e+03 7.58e+00 bond pdb=" N ASN F 334 " pdb=" CA ASN F 334 " ideal model delta sigma weight residual 1.457 1.493 -0.035 1.29e-02 6.01e+03 7.41e+00 ... (remaining 36623 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.79: 49434 2.79 - 5.58: 370 5.58 - 8.36: 30 8.36 - 11.15: 2 11.15 - 13.94: 1 Bond angle restraints: 49837 Sorted by residual: angle pdb=" C ASN B1135 " pdb=" CA ASN B1135 " pdb=" CB ASN B1135 " ideal model delta sigma weight residual 115.79 109.59 6.20 1.19e+00 7.06e-01 2.71e+01 angle pdb=" C TYR F1138 " pdb=" N ASP F1139 " pdb=" CA ASP F1139 " ideal model delta sigma weight residual 120.97 134.91 -13.94 2.84e+00 1.24e-01 2.41e+01 angle pdb=" CA LEU F 335 " pdb=" C LEU F 335 " pdb=" O LEU F 335 " ideal model delta sigma weight residual 122.27 116.63 5.64 1.16e+00 7.43e-01 2.36e+01 angle pdb=" N PHE C 759 " pdb=" CA PHE C 759 " pdb=" C PHE C 759 " ideal model delta sigma weight residual 113.20 107.50 5.70 1.21e+00 6.83e-01 2.22e+01 angle pdb=" N MET D 123 " pdb=" CA MET D 123 " pdb=" CB MET D 123 " ideal model delta sigma weight residual 110.28 116.50 -6.22 1.55e+00 4.16e-01 1.61e+01 ... (remaining 49832 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 19172 17.93 - 35.86: 1659 35.86 - 53.79: 284 53.79 - 71.72: 46 71.72 - 89.65: 42 Dihedral angle restraints: 21203 sinusoidal: 8353 harmonic: 12850 Sorted by residual: dihedral pdb=" CB CYS B 662 " pdb=" SG CYS B 662 " pdb=" SG CYS B 671 " pdb=" CB CYS B 671 " ideal model delta sinusoidal sigma weight residual -86.00 -8.45 -77.55 1 1.00e+01 1.00e-02 7.53e+01 dihedral pdb=" CB CYS B1082 " pdb=" SG CYS B1082 " pdb=" SG CYS B1126 " pdb=" CB CYS B1126 " ideal model delta sinusoidal sigma weight residual -86.00 -10.44 -75.56 1 1.00e+01 1.00e-02 7.21e+01 dihedral pdb=" CB CYS C 336 " pdb=" SG CYS C 336 " pdb=" SG CYS C 361 " pdb=" CB CYS C 361 " ideal model delta sinusoidal sigma weight residual 93.00 33.35 59.65 1 1.00e+01 1.00e-02 4.75e+01 ... (remaining 21200 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 5118 0.079 - 0.158: 542 0.158 - 0.236: 13 0.236 - 0.315: 2 0.315 - 0.394: 1 Chirality restraints: 5676 Sorted by residual: chirality pdb=" C1 NAG H 1 " pdb=" ND2 ASN B1074 " pdb=" C2 NAG H 1 " pdb=" O5 NAG H 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.01 -0.39 2.00e-01 2.50e+01 3.88e+00 chirality pdb=" CB ILE B 664 " pdb=" CA ILE B 664 " pdb=" CG1 ILE B 664 " pdb=" CG2 ILE B 664 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.29 2.00e-01 2.50e+01 2.12e+00 chirality pdb=" CB ILE B 197 " pdb=" CA ILE B 197 " pdb=" CG1 ILE B 197 " pdb=" CG2 ILE B 197 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.24 2.00e-01 2.50e+01 1.49e+00 ... (remaining 5673 not shown) Planarity restraints: 6396 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU C 754 " -0.016 2.00e-02 2.50e+03 3.25e-02 1.06e+01 pdb=" C LEU C 754 " 0.056 2.00e-02 2.50e+03 pdb=" O LEU C 754 " -0.021 2.00e-02 2.50e+03 pdb=" N GLN C 755 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS F 336 " -0.052 5.00e-02 4.00e+02 7.83e-02 9.80e+00 pdb=" N PRO F 337 " 0.135 5.00e-02 4.00e+02 pdb=" CA PRO F 337 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO F 337 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 349 " -0.010 2.00e-02 2.50e+03 1.52e-02 5.80e+00 pdb=" CG TRP D 349 " 0.039 2.00e-02 2.50e+03 pdb=" CD1 TRP D 349 " -0.025 2.00e-02 2.50e+03 pdb=" CD2 TRP D 349 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP D 349 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP D 349 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP D 349 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 349 " 0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 349 " -0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP D 349 " -0.000 2.00e-02 2.50e+03 ... (remaining 6393 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.52: 360 2.52 - 3.12: 27839 3.12 - 3.71: 55440 3.71 - 4.31: 75783 4.31 - 4.90: 125387 Nonbonded interactions: 284809 Sorted by model distance: nonbonded pdb=" CD2 HIS D 378 " pdb="ZN ZN D 901 " model vdw 1.930 1.960 nonbonded pdb=" OG SER C 605 " pdb=" OE1 GLN C 607 " model vdw 2.128 3.040 nonbonded pdb=" OG1 THR B 912 " pdb=" NE2 GLN B1106 " model vdw 2.153 3.120 nonbonded pdb=" OG SER D 607 " pdb=" OD1 ASP D 609 " model vdw 2.161 3.040 nonbonded pdb=" OE2 GLU G 398 " pdb=" O HOH G1001 " model vdw 2.161 3.040 ... (remaining 284804 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' } ncs_group { reference = (chain 'B' and (resid 25 through 825 or resid 856 through 1313)) selection = (chain 'C' and (resid 25 through 620 or resid 643 through 825 or resid 856 throu \ gh 1313)) selection = (chain 'F' and (resid 25 through 620 or resid 643 through 825 or resid 856 throu \ gh 1313)) } ncs_group { reference = chain 'D' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.470 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 38.680 Find NCS groups from input model: 1.530 Set up NCS constraints: 0.170 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:1.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7421 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 : 0.004 0.080 36712 Z= 0.187 Angle : 0.636 13.940 50020 Z= 0.325 Chirality : 0.045 0.394 5676 Planarity : 0.004 0.078 6372 Dihedral : 13.889 89.653 12815 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.82 % Favored : 92.02 % Rotamer: Outliers : 0.13 % Allowed : 0.36 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.88 (0.13), residues: 4374 helix: 1.25 (0.15), residues: 1336 sheet: -0.84 (0.20), residues: 652 loop : -1.65 (0.13), residues: 2386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 237 TYR 0.033 0.001 TYR B 160 PHE 0.037 0.001 PHE D 369 TRP 0.039 0.001 TRP D 349 HIS 0.013 0.001 HIS D 373 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.19 (36628) covalent geometry : angle 0.62824 / 0.32 (49837) SS BOND : bond 0.00433 / 0.26 ( 42) SS BOND : angle 1.25456 / 0.86 ( 84) hydrogen bonds : bond 0.18912 / 12.18 ( 1325) hydrogen bonds : angle 7.72092 / 5.31 ( 3765) metal coordination : bond 0.02443 / 1.23 ( 4) Misc. bond : bond 0.00134 / 0.06 ( 5) link_BETA1-4 : bond 0.00439 / 0.27 ( 9) link_BETA1-4 : angle 1.90299 / 1.30 ( 27) link_NAG-ASN : bond 0.00257 / 0.16 ( 24) link_NAG-ASN : angle 2.04492 / 1.53 ( 72) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8748 Ramachandran restraints generated. 4374 Oldfield, 0 Emsley, 4374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8748 Ramachandran restraints generated. 4374 Oldfield, 0 Emsley, 4374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 3860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 275 time to evaluate : 1.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 453 TYR cc_start: 0.7960 (p90) cc_final: 0.7318 (p90) REVERT: D 360 MET cc_start: 0.0575 (tpt) cc_final: 0.0306 (tpp) REVERT: D 378 HIS cc_start: 0.2844 (t-90) cc_final: 0.2175 (t-90) REVERT: F 200 TYR cc_start: 0.6108 (m-80) cc_final: 0.5758 (m-80) REVERT: G 123 MET cc_start: 0.2181 (tpt) cc_final: 0.1253 (ptm) outliers start: 5 outliers final: 1 residues processed: 279 average time/residue: 0.2014 time to fit residues: 97.7672 Evaluate side-chains 209 residues out of total 3860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 208 time to evaluate : 1.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 335 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: chunk 432 optimal weight: 4.9990 chunk 197 optimal weight: 0.8980 chunk 388 optimal weight: 3.9990 chunk 215 optimal weight: 20.0000 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 0.5980 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 10.0000 chunk 401 optimal weight: 0.7980 chunk 424 optimal weight: 10.0000 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 211 ASN B 334 ASN ** B 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN ** C 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 ASN C 394 ASN C 613 GLN ** D 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 544 ASN F 580 GLN F1106 GLN G 552 GLN G 556 ASN G 601 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4520 r_free = 0.4520 target = 0.190558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.128442 restraints weight = 77921.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.132126 restraints weight = 41065.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.129969 restraints weight = 29875.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.131257 restraints weight = 23475.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.132117 restraints weight = 17624.768| |-----------------------------------------------------------------------------| r_work (final): 0.3725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7383 moved from start: 0.0845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 36712 Z= 0.154 Angle : 0.610 9.429 50020 Z= 0.308 Chirality : 0.044 0.273 5676 Planarity : 0.004 0.092 6372 Dihedral : 4.411 29.718 4731 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.82 % Favored : 92.04 % Rotamer: Outliers : 0.57 % Allowed : 5.98 % Favored : 93.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.82 (0.13), residues: 4374 helix: 1.39 (0.14), residues: 1331 sheet: -0.64 (0.21), residues: 641 loop : -1.72 (0.13), residues: 2402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 357 TYR 0.027 0.001 TYR B 160 PHE 0.023 0.001 PHE D 369 TRP 0.020 0.001 TRP B 353 HIS 0.012 0.001 HIS D 373 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 (36628) covalent geometry : angle 0.60227 / 0.31 (49837) SS BOND : bond 0.00317 / 0.18 ( 42) SS BOND : angle 1.26875 / 0.88 ( 84) hydrogen bonds : bond 0.04721 / 3.13 ( 1325) hydrogen bonds : angle 5.89985 / 4.07 ( 3765) metal coordination : bond 0.01993 / 1.01 ( 4) Misc. bond : bond 0.00094 / 0.04 ( 5) link_BETA1-4 : bond 0.00385 / 0.20 ( 9) link_BETA1-4 : angle 2.10754 / 1.52 ( 27) link_NAG-ASN : bond 0.00284 / 0.17 ( 24) link_NAG-ASN : angle 2.00333 / 1.46 ( 72) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8748 Ramachandran restraints generated. 4374 Oldfield, 0 Emsley, 4374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8748 Ramachandran restraints generated. 4374 Oldfield, 0 Emsley, 4374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 3860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 235 time to evaluate : 1.318 Fit side-chains revert: symmetry clash REVERT: C 428 ASP cc_start: 0.8751 (m-30) cc_final: 0.8026 (m-30) REVERT: C 955 ASN cc_start: 0.8639 (m-40) cc_final: 0.8293 (t0) REVERT: D 67 ASP cc_start: 0.2136 (m-30) cc_final: 0.1872 (p0) REVERT: D 378 HIS cc_start: 0.2079 (t-90) cc_final: 0.1572 (t-90) REVERT: F 224 GLU cc_start: 0.7856 (pm20) cc_final: 0.7350 (pm20) REVERT: F 565 PHE cc_start: 0.7399 (m-10) cc_final: 0.7156 (m-80) REVERT: G 123 MET cc_start: 0.2095 (tpt) cc_final: 0.1247 (ptm) outliers start: 22 outliers final: 13 residues processed: 248 average time/residue: 0.1869 time to fit residues: 81.2369 Evaluate side-chains 214 residues out of total 3860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 201 time to evaluate : 1.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 1111 GLU Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 249 MET Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 531 THR Chi-restraints excluded: chain F residue 569 ILE Chi-restraints excluded: chain F residue 740 MET Chi-restraints excluded: chain F residue 762 GLN Chi-restraints excluded: chain G residue 297 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: chunk 108 optimal weight: 4.9990 chunk 383 optimal weight: 10.0000 chunk 426 optimal weight: 10.0000 chunk 67 optimal weight: 0.9980 chunk 163 optimal weight: 4.9990 chunk 396 optimal weight: 9.9990 chunk 239 optimal weight: 0.0980 chunk 157 optimal weight: 0.0980 chunk 151 optimal weight: 5.9990 chunk 89 optimal weight: 2.9990 chunk 379 optimal weight: 8.9990 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 ASN ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 804 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4519 r_free = 0.4519 target = 0.191510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.129874 restraints weight = 77384.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.133416 restraints weight = 42710.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.132759 restraints weight = 25036.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.133120 restraints weight = 19787.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.133396 restraints weight = 20267.575| |-----------------------------------------------------------------------------| r_work (final): 0.3713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7377 moved from start: 0.1110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 36712 Z= 0.154 Angle : 0.589 11.969 50020 Z= 0.296 Chirality : 0.043 0.272 5676 Planarity : 0.004 0.093 6372 Dihedral : 4.381 30.076 4729 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.96 % Favored : 91.91 % Rotamer: Outliers : 0.88 % Allowed : 8.61 % Favored : 90.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.13), residues: 4374 helix: 1.51 (0.14), residues: 1311 sheet: -0.69 (0.20), residues: 644 loop : -1.73 (0.13), residues: 2419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 204 TYR 0.024 0.001 TYR B 160 PHE 0.018 0.001 PHE B 201 TRP 0.019 0.001 TRP B 353 HIS 0.010 0.001 HIS G 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.15 (36628) covalent geometry : angle 0.58238 / 0.29 (49837) SS BOND : bond 0.00345 / 0.21 ( 42) SS BOND : angle 1.18647 / 0.82 ( 84) hydrogen bonds : bond 0.04165 / 2.76 ( 1325) hydrogen bonds : angle 5.54549 / 3.82 ( 3765) metal coordination : bond 0.01725 / 0.87 ( 4) Misc. bond : bond 0.00091 / 0.04 ( 5) link_BETA1-4 : bond 0.00512 / 0.32 ( 9) link_BETA1-4 : angle 1.87055 / 1.37 ( 27) link_NAG-ASN : bond 0.00250 / 0.15 ( 24) link_NAG-ASN : angle 1.90763 / 1.41 ( 72) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8748 Ramachandran restraints generated. 4374 Oldfield, 0 Emsley, 4374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8748 Ramachandran restraints generated. 4374 Oldfield, 0 Emsley, 4374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 3860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 231 time to evaluate : 1.268 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 646 ARG cc_start: 0.6800 (tpm170) cc_final: 0.6572 (tpm170) REVERT: B 1002 GLN cc_start: 0.8477 (tm-30) cc_final: 0.8038 (tm-30) REVERT: C 424 LYS cc_start: 0.7703 (pttp) cc_final: 0.7439 (pttp) REVERT: C 780 GLU cc_start: 0.7811 (OUTLIER) cc_final: 0.7414 (mp0) REVERT: C 955 ASN cc_start: 0.8658 (m-40) cc_final: 0.8254 (t0) REVERT: D 67 ASP cc_start: 0.2267 (m-30) cc_final: 0.1981 (p0) REVERT: D 358 ILE cc_start: 0.3850 (mt) cc_final: 0.3469 (tp) REVERT: D 376 MET cc_start: -0.0570 (tmm) cc_final: -0.0922 (tmm) REVERT: D 378 HIS cc_start: 0.1782 (t-90) cc_final: 0.1214 (t-170) REVERT: G 123 MET cc_start: 0.2041 (tpt) cc_final: 0.1140 (ptm) outliers start: 34 outliers final: 16 residues processed: 251 average time/residue: 0.1922 time to fit residues: 84.1415 Evaluate side-chains 225 residues out of total 3860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 208 time to evaluate : 1.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 1111 GLU Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 249 MET Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 512 VAL Chi-restraints excluded: chain F residue 531 THR Chi-restraints excluded: chain F residue 569 ILE Chi-restraints excluded: chain F residue 740 MET Chi-restraints excluded: chain F residue 979 ASP Chi-restraints excluded: chain G residue 297 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: chunk 376 optimal weight: 5.9990 chunk 369 optimal weight: 0.0770 chunk 45 optimal weight: 0.7980 chunk 215 optimal weight: 20.0000 chunk 371 optimal weight: 2.9990 chunk 277 optimal weight: 7.9990 chunk 239 optimal weight: 7.9990 chunk 108 optimal weight: 2.9990 chunk 146 optimal weight: 20.0000 chunk 12 optimal weight: 8.9990 chunk 48 optimal weight: 10.0000 overall best weight: 2.5744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 121 ASN B 282 ASN ** B1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 87 ASN C 360 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 801 ASN ** D 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 277 ASN ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 914 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4500 r_free = 0.4500 target = 0.191218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.128604 restraints weight = 75926.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.131319 restraints weight = 41200.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.130725 restraints weight = 27853.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.132096 restraints weight = 22627.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.132094 restraints weight = 18271.690| |-----------------------------------------------------------------------------| r_work (final): 0.3685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7428 moved from start: 0.1375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.100 36712 Z= 0.188 Angle : 0.611 9.991 50020 Z= 0.306 Chirality : 0.044 0.280 5676 Planarity : 0.004 0.095 6372 Dihedral : 4.459 30.808 4729 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.80 % Favored : 91.08 % Rotamer: Outliers : 1.59 % Allowed : 10.46 % Favored : 87.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.86 (0.13), residues: 4374 helix: 1.46 (0.14), residues: 1310 sheet: -0.74 (0.20), residues: 644 loop : -1.76 (0.12), residues: 2420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 214 TYR 0.023 0.002 TYR B 160 PHE 0.015 0.001 PHE F 92 TRP 0.020 0.001 TRP B 353 HIS 0.010 0.001 HIS G 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00437 / 0.19 (36628) covalent geometry : angle 0.60400 / 0.30 (49837) SS BOND : bond 0.00316 / 0.19 ( 42) SS BOND : angle 1.22234 / 0.84 ( 84) hydrogen bonds : bond 0.04030 / 2.66 ( 1325) hydrogen bonds : angle 5.41509 / 3.73 ( 3765) metal coordination : bond 0.01583 / 0.80 ( 4) Misc. bond : bond 0.00091 / 0.04 ( 5) link_BETA1-4 : bond 0.00474 / 0.29 ( 9) link_BETA1-4 : angle 1.90975 / 1.39 ( 27) link_NAG-ASN : bond 0.00258 / 0.16 ( 24) link_NAG-ASN : angle 1.92070 / 1.43 ( 72) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8748 Ramachandran restraints generated. 4374 Oldfield, 0 Emsley, 4374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8748 Ramachandran restraints generated. 4374 Oldfield, 0 Emsley, 4374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 3860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 216 time to evaluate : 1.321 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 646 ARG cc_start: 0.6991 (tpm170) cc_final: 0.6616 (tpm170) REVERT: B 759 PHE cc_start: 0.8314 (OUTLIER) cc_final: 0.7966 (t80) REVERT: B 878 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.8336 (mp) REVERT: B 983 ARG cc_start: 0.8353 (ttm110) cc_final: 0.8091 (ttm110) REVERT: B 1002 GLN cc_start: 0.8512 (tm-30) cc_final: 0.8073 (tm-30) REVERT: C 453 TYR cc_start: 0.7877 (p90) cc_final: 0.7260 (p90) REVERT: C 568 ASP cc_start: 0.8104 (p0) cc_final: 0.7845 (p0) REVERT: C 780 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.7424 (mp0) REVERT: C 955 ASN cc_start: 0.8750 (m-40) cc_final: 0.8323 (t0) REVERT: D 67 ASP cc_start: 0.2258 (m-30) cc_final: 0.1992 (p0) REVERT: D 358 ILE cc_start: 0.4197 (mt) cc_final: 0.3660 (tp) REVERT: G 123 MET cc_start: 0.1660 (tpt) cc_final: 0.0637 (ptm) REVERT: G 376 MET cc_start: -0.1993 (ptm) cc_final: -0.2287 (ttp) outliers start: 61 outliers final: 30 residues processed: 264 average time/residue: 0.2005 time to fit residues: 92.6067 Evaluate side-chains 234 residues out of total 3860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 201 time to evaluate : 1.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1111 GLU Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 379 ILE Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 396 TYR Chi-restraints excluded: chain F residue 512 VAL Chi-restraints excluded: chain F residue 531 THR Chi-restraints excluded: chain F residue 533 LEU Chi-restraints excluded: chain F residue 569 ILE Chi-restraints excluded: chain F residue 740 MET Chi-restraints excluded: chain F residue 869 MET Chi-restraints excluded: chain F residue 979 ASP Chi-restraints excluded: chain F residue 1104 VAL Chi-restraints excluded: chain G residue 38 ASP Chi-restraints excluded: chain G residue 297 MET Chi-restraints excluded: chain G residue 364 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: chunk 151 optimal weight: 10.0000 chunk 382 optimal weight: 5.9990 chunk 207 optimal weight: 2.9990 chunk 288 optimal weight: 10.0000 chunk 198 optimal weight: 3.9990 chunk 164 optimal weight: 0.9990 chunk 161 optimal weight: 9.9990 chunk 94 optimal weight: 2.9990 chunk 313 optimal weight: 20.0000 chunk 23 optimal weight: 20.0000 chunk 133 optimal weight: 0.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 87 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F1005 GLN G 578 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4496 r_free = 0.4496 target = 0.188779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.127856 restraints weight = 77879.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.130638 restraints weight = 40818.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.130337 restraints weight = 24289.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.131120 restraints weight = 19971.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.131219 restraints weight = 17335.514| |-----------------------------------------------------------------------------| r_work (final): 0.3698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 moved from start: 0.1574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.103 36712 Z= 0.178 Angle : 0.609 11.592 50020 Z= 0.304 Chirality : 0.044 0.355 5676 Planarity : 0.004 0.096 6372 Dihedral : 4.480 30.305 4729 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.41 % Favored : 91.47 % Rotamer: Outliers : 1.51 % Allowed : 12.38 % Favored : 86.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.88 (0.13), residues: 4374 helix: 1.52 (0.14), residues: 1300 sheet: -0.87 (0.20), residues: 660 loop : -1.77 (0.13), residues: 2414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 204 TYR 0.022 0.001 TYR B 160 PHE 0.021 0.001 PHE G 314 TRP 0.020 0.001 TRP B 353 HIS 0.009 0.001 HIS G 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.18 (36628) covalent geometry : angle 0.60197 / 0.30 (49837) SS BOND : bond 0.00447 / 0.26 ( 42) SS BOND : angle 1.26123 / 0.86 ( 84) hydrogen bonds : bond 0.03904 / 2.58 ( 1325) hydrogen bonds : angle 5.31847 / 3.67 ( 3765) metal coordination : bond 0.02026 / 1.01 ( 4) Misc. bond : bond 0.00088 / 0.04 ( 5) link_BETA1-4 : bond 0.00467 / 0.27 ( 9) link_BETA1-4 : angle 1.89847 / 1.39 ( 27) link_NAG-ASN : bond 0.00255 / 0.16 ( 24) link_NAG-ASN : angle 1.98371 / 1.48 ( 72) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8748 Ramachandran restraints generated. 4374 Oldfield, 0 Emsley, 4374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8748 Ramachandran restraints generated. 4374 Oldfield, 0 Emsley, 4374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 3860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 227 time to evaluate : 1.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 646 ARG cc_start: 0.7000 (tpm170) cc_final: 0.6593 (tpm170) REVERT: B 759 PHE cc_start: 0.8350 (OUTLIER) cc_final: 0.7997 (t80) REVERT: B 878 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.8354 (mp) REVERT: B 983 ARG cc_start: 0.8357 (ttm110) cc_final: 0.8124 (ttm110) REVERT: B 1002 GLN cc_start: 0.8509 (tm-30) cc_final: 0.8075 (tm-30) REVERT: C 396 TYR cc_start: 0.7105 (m-80) cc_final: 0.6309 (m-10) REVERT: C 453 TYR cc_start: 0.7846 (p90) cc_final: 0.7250 (p90) REVERT: C 568 ASP cc_start: 0.8012 (p0) cc_final: 0.7784 (p0) REVERT: C 780 GLU cc_start: 0.7811 (OUTLIER) cc_final: 0.7416 (mp0) REVERT: C 955 ASN cc_start: 0.8805 (m-40) cc_final: 0.8378 (t0) REVERT: C 1095 PHE cc_start: 0.8381 (OUTLIER) cc_final: 0.7765 (t80) REVERT: C 1123 SER cc_start: 0.8307 (t) cc_final: 0.8053 (p) REVERT: D 67 ASP cc_start: 0.2278 (m-30) cc_final: 0.1977 (p0) REVERT: D 152 MET cc_start: -0.0573 (mmp) cc_final: -0.2033 (ttp) REVERT: D 333 LEU cc_start: -0.0695 (OUTLIER) cc_final: -0.0977 (pp) REVERT: D 356 PHE cc_start: 0.1527 (m-80) cc_final: 0.1037 (m-80) REVERT: D 379 ILE cc_start: -0.3931 (OUTLIER) cc_final: -0.4202 (mt) REVERT: F 177 MET cc_start: 0.7061 (ttt) cc_final: 0.6709 (mmp) REVERT: G 123 MET cc_start: 0.1675 (tpt) cc_final: 0.0590 (ptm) REVERT: G 175 GLN cc_start: 0.4460 (mp10) cc_final: 0.4218 (pp30) outliers start: 58 outliers final: 41 residues processed: 268 average time/residue: 0.2007 time to fit residues: 93.5026 Evaluate side-chains 253 residues out of total 3860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 206 time to evaluate : 1.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 1095 PHE Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1111 GLU Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 249 MET Chi-restraints excluded: chain D residue 333 LEU Chi-restraints excluded: chain D residue 379 ILE Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain F residue 396 TYR Chi-restraints excluded: chain F residue 512 VAL Chi-restraints excluded: chain F residue 531 THR Chi-restraints excluded: chain F residue 569 ILE Chi-restraints excluded: chain F residue 598 ILE Chi-restraints excluded: chain F residue 740 MET Chi-restraints excluded: chain F residue 869 MET Chi-restraints excluded: chain F residue 911 VAL Chi-restraints excluded: chain F residue 979 ASP Chi-restraints excluded: chain F residue 1097 SER Chi-restraints excluded: chain F residue 1104 VAL Chi-restraints excluded: chain F residue 1122 VAL Chi-restraints excluded: chain G residue 38 ASP Chi-restraints excluded: chain G residue 297 MET Chi-restraints excluded: chain G residue 360 MET Chi-restraints excluded: chain G residue 364 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: chunk 166 optimal weight: 5.9990 chunk 258 optimal weight: 9.9990 chunk 136 optimal weight: 8.9990 chunk 29 optimal weight: 0.9980 chunk 284 optimal weight: 20.0000 chunk 96 optimal weight: 0.9990 chunk 13 optimal weight: 4.9990 chunk 122 optimal weight: 0.0870 chunk 30 optimal weight: 8.9990 chunk 157 optimal weight: 8.9990 chunk 256 optimal weight: 20.0000 overall best weight: 2.6164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 378 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4502 r_free = 0.4502 target = 0.196091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.136502 restraints weight = 75097.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.137939 restraints weight = 45546.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.139449 restraints weight = 30542.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.139095 restraints weight = 24424.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.138712 restraints weight = 20807.717| |-----------------------------------------------------------------------------| r_work (final): 0.3682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 moved from start: 0.1778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 1.142 36712 Z= 0.275 Angle : 0.622 10.442 50020 Z= 0.310 Chirality : 0.044 0.300 5676 Planarity : 0.004 0.098 6372 Dihedral : 4.538 30.522 4729 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.98 % Favored : 90.90 % Rotamer: Outliers : 1.87 % Allowed : 13.06 % Favored : 85.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.13), residues: 4374 helix: 1.50 (0.15), residues: 1305 sheet: -0.91 (0.20), residues: 660 loop : -1.81 (0.12), residues: 2409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 357 TYR 0.021 0.001 TYR B 160 PHE 0.021 0.001 PHE C 86 TRP 0.022 0.001 TRP B 353 HIS 0.008 0.001 HIS G 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00446 / 0.19 (36628) covalent geometry : angle 0.61404 / 0.31 (49837) SS BOND : bond 0.00409 / 0.29 ( 42) SS BOND : angle 1.35919 / 0.93 ( 84) hydrogen bonds : bond 0.03890 / 2.57 ( 1325) hydrogen bonds : angle 5.26517 / 3.63 ( 3765) metal coordination : bond 0.57094 / 27.19 ( 4) Misc. bond : bond 0.00088 / 0.04 ( 5) link_BETA1-4 : bond 0.00478 / 0.28 ( 9) link_BETA1-4 : angle 1.93401 / 1.41 ( 27) link_NAG-ASN : bond 0.00261 / 0.17 ( 24) link_NAG-ASN : angle 1.98706 / 1.49 ( 72) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8748 Ramachandran restraints generated. 4374 Oldfield, 0 Emsley, 4374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8748 Ramachandran restraints generated. 4374 Oldfield, 0 Emsley, 4374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 3860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 225 time to evaluate : 1.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 646 ARG cc_start: 0.6996 (tpm170) cc_final: 0.6722 (tpm170) REVERT: B 759 PHE cc_start: 0.8348 (OUTLIER) cc_final: 0.7975 (t80) REVERT: B 878 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8342 (mp) REVERT: B 983 ARG cc_start: 0.8346 (ttm110) cc_final: 0.8096 (ttm110) REVERT: B 1002 GLN cc_start: 0.8508 (tm-30) cc_final: 0.8046 (tm-30) REVERT: C 453 TYR cc_start: 0.7848 (p90) cc_final: 0.7248 (p90) REVERT: C 568 ASP cc_start: 0.8075 (p0) cc_final: 0.7819 (p0) REVERT: C 619 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7963 (pp20) REVERT: C 780 GLU cc_start: 0.7851 (OUTLIER) cc_final: 0.7447 (mp0) REVERT: C 955 ASN cc_start: 0.8831 (m-40) cc_final: 0.8377 (t0) REVERT: C 1095 PHE cc_start: 0.8452 (OUTLIER) cc_final: 0.7884 (t80) REVERT: C 1123 SER cc_start: 0.8368 (t) cc_final: 0.8131 (p) REVERT: D 67 ASP cc_start: 0.2253 (m-30) cc_final: 0.1975 (p0) REVERT: D 152 MET cc_start: -0.0593 (mmp) cc_final: -0.2079 (ttp) REVERT: D 333 LEU cc_start: -0.0836 (OUTLIER) cc_final: -0.1114 (pp) REVERT: F 177 MET cc_start: 0.7327 (ttt) cc_final: 0.6842 (mmp) REVERT: F 224 GLU cc_start: 0.8017 (pm20) cc_final: 0.7558 (pm20) REVERT: G 123 MET cc_start: 0.1750 (tpt) cc_final: 0.0688 (ptm) outliers start: 72 outliers final: 41 residues processed: 280 average time/residue: 0.2109 time to fit residues: 101.9165 Evaluate side-chains 253 residues out of total 3860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 206 time to evaluate : 1.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 619 GLU Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 1095 PHE Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1111 GLU Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 249 MET Chi-restraints excluded: chain D residue 333 LEU Chi-restraints excluded: chain D residue 573 VAL Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain F residue 512 VAL Chi-restraints excluded: chain F residue 531 THR Chi-restraints excluded: chain F residue 569 ILE Chi-restraints excluded: chain F residue 598 ILE Chi-restraints excluded: chain F residue 740 MET Chi-restraints excluded: chain F residue 869 MET Chi-restraints excluded: chain F residue 911 VAL Chi-restraints excluded: chain F residue 979 ASP Chi-restraints excluded: chain F residue 1097 SER Chi-restraints excluded: chain F residue 1104 VAL Chi-restraints excluded: chain F residue 1122 VAL Chi-restraints excluded: chain G residue 38 ASP Chi-restraints excluded: chain G residue 297 MET Chi-restraints excluded: chain G residue 360 MET Chi-restraints excluded: chain G residue 364 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: chunk 175 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 163 optimal weight: 3.9990 chunk 369 optimal weight: 0.6980 chunk 117 optimal weight: 7.9990 chunk 102 optimal weight: 0.9990 chunk 32 optimal weight: 40.0000 chunk 263 optimal weight: 20.0000 chunk 38 optimal weight: 4.9990 chunk 371 optimal weight: 1.9990 chunk 423 optimal weight: 4.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 505 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4518 r_free = 0.4518 target = 0.199650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.142158 restraints weight = 74782.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.140792 restraints weight = 45597.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.141533 restraints weight = 36242.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.141556 restraints weight = 27302.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.141452 restraints weight = 25850.018| |-----------------------------------------------------------------------------| r_work (final): 0.3699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7377 moved from start: 0.1901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 36712 Z= 0.146 Angle : 0.595 10.680 50020 Z= 0.296 Chirality : 0.044 0.277 5676 Planarity : 0.004 0.099 6372 Dihedral : 4.450 29.626 4729 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.18 % Favored : 91.70 % Rotamer: Outliers : 1.85 % Allowed : 13.89 % Favored : 84.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.86 (0.13), residues: 4374 helix: 1.59 (0.15), residues: 1303 sheet: -0.93 (0.20), residues: 667 loop : -1.77 (0.13), residues: 2404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 204 TYR 0.026 0.001 TYR D 196 PHE 0.023 0.001 PHE G 464 TRP 0.020 0.001 TRP D 48 HIS 0.008 0.001 HIS G 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 (36628) covalent geometry : angle 0.58834 / 0.29 (49837) SS BOND : bond 0.00298 / 0.19 ( 42) SS BOND : angle 1.20826 / 0.83 ( 84) hydrogen bonds : bond 0.03730 / 2.47 ( 1325) hydrogen bonds : angle 5.18173 / 3.58 ( 3765) metal coordination : bond 0.01496 / 0.73 ( 4) Misc. bond : bond 0.00081 / 0.04 ( 5) link_BETA1-4 : bond 0.00477 / 0.29 ( 9) link_BETA1-4 : angle 1.85154 / 1.36 ( 27) link_NAG-ASN : bond 0.00247 / 0.16 ( 24) link_NAG-ASN : angle 1.92539 / 1.45 ( 72) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8748 Ramachandran restraints generated. 4374 Oldfield, 0 Emsley, 4374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8748 Ramachandran restraints generated. 4374 Oldfield, 0 Emsley, 4374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 3860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 229 time to evaluate : 1.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 646 ARG cc_start: 0.6963 (tpm170) cc_final: 0.6665 (tpm170) REVERT: B 759 PHE cc_start: 0.8373 (OUTLIER) cc_final: 0.7997 (t80) REVERT: B 878 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8340 (mp) REVERT: B 983 ARG cc_start: 0.8361 (ttm110) cc_final: 0.8107 (ttm110) REVERT: B 1002 GLN cc_start: 0.8477 (tm-30) cc_final: 0.8033 (tm-30) REVERT: C 389 ASP cc_start: 0.7995 (t0) cc_final: 0.7752 (t0) REVERT: C 453 TYR cc_start: 0.7926 (p90) cc_final: 0.7314 (p90) REVERT: C 619 GLU cc_start: 0.8389 (OUTLIER) cc_final: 0.8100 (pp20) REVERT: C 780 GLU cc_start: 0.7851 (OUTLIER) cc_final: 0.7435 (mp0) REVERT: C 955 ASN cc_start: 0.8816 (m-40) cc_final: 0.8342 (t0) REVERT: C 1095 PHE cc_start: 0.8421 (OUTLIER) cc_final: 0.7768 (t80) REVERT: C 1123 SER cc_start: 0.8378 (t) cc_final: 0.8147 (p) REVERT: D 67 ASP cc_start: 0.2257 (m-30) cc_final: 0.1996 (p0) REVERT: D 152 MET cc_start: -0.0696 (mmp) cc_final: -0.2095 (ttp) REVERT: D 333 LEU cc_start: -0.0711 (OUTLIER) cc_final: -0.1011 (pp) REVERT: F 177 MET cc_start: 0.7431 (ttt) cc_final: 0.6834 (mmp) REVERT: F 224 GLU cc_start: 0.7958 (pm20) cc_final: 0.7486 (pm20) REVERT: G 123 MET cc_start: 0.1717 (tpt) cc_final: 0.1055 (tpt) outliers start: 71 outliers final: 48 residues processed: 280 average time/residue: 0.2087 time to fit residues: 100.7865 Evaluate side-chains 265 residues out of total 3860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 211 time to evaluate : 1.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 619 GLU Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 1095 PHE Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 249 MET Chi-restraints excluded: chain D residue 333 LEU Chi-restraints excluded: chain D residue 573 VAL Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 62 VAL Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain F residue 512 VAL Chi-restraints excluded: chain F residue 518 LEU Chi-restraints excluded: chain F residue 531 THR Chi-restraints excluded: chain F residue 569 ILE Chi-restraints excluded: chain F residue 598 ILE Chi-restraints excluded: chain F residue 740 MET Chi-restraints excluded: chain F residue 761 THR Chi-restraints excluded: chain F residue 869 MET Chi-restraints excluded: chain F residue 911 VAL Chi-restraints excluded: chain F residue 979 ASP Chi-restraints excluded: chain F residue 1104 VAL Chi-restraints excluded: chain F residue 1122 VAL Chi-restraints excluded: chain G residue 38 ASP Chi-restraints excluded: chain G residue 297 MET Chi-restraints excluded: chain G residue 360 MET Chi-restraints excluded: chain G residue 364 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: chunk 211 optimal weight: 1.9990 chunk 262 optimal weight: 10.0000 chunk 357 optimal weight: 3.9990 chunk 8 optimal weight: 9.9990 chunk 120 optimal weight: 2.9990 chunk 105 optimal weight: 10.0000 chunk 76 optimal weight: 0.9990 chunk 310 optimal weight: 0.9980 chunk 366 optimal weight: 0.6980 chunk 152 optimal weight: 8.9990 chunk 202 optimal weight: 3.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4505 r_free = 0.4505 target = 0.191958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.130493 restraints weight = 75785.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.134939 restraints weight = 40549.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.133409 restraints weight = 22570.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.134477 restraints weight = 21973.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.134375 restraints weight = 19255.607| |-----------------------------------------------------------------------------| r_work (final): 0.3707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 36712 Z= 0.138 Angle : 0.595 13.016 50020 Z= 0.296 Chirality : 0.044 0.270 5676 Planarity : 0.004 0.099 6372 Dihedral : 4.405 29.227 4729 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.41 % Favored : 91.47 % Rotamer: Outliers : 1.80 % Allowed : 14.18 % Favored : 84.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.82 (0.13), residues: 4374 helix: 1.60 (0.15), residues: 1305 sheet: -0.90 (0.20), residues: 671 loop : -1.74 (0.13), residues: 2398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 204 TYR 0.020 0.001 TYR B 160 PHE 0.017 0.001 PHE C 238 TRP 0.023 0.001 TRP D 48 HIS 0.007 0.001 HIS G 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 (36628) covalent geometry : angle 0.58836 / 0.29 (49837) SS BOND : bond 0.00297 / 0.19 ( 42) SS BOND : angle 1.20449 / 0.84 ( 84) hydrogen bonds : bond 0.03674 / 2.43 ( 1325) hydrogen bonds : angle 5.14678 / 3.55 ( 3765) metal coordination : bond 0.02210 / 1.10 ( 4) Misc. bond : bond 0.00078 / 0.03 ( 5) link_BETA1-4 : bond 0.00471 / 0.28 ( 9) link_BETA1-4 : angle 1.76947 / 1.30 ( 27) link_NAG-ASN : bond 0.00245 / 0.15 ( 24) link_NAG-ASN : angle 1.88829 / 1.43 ( 72) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8748 Ramachandran restraints generated. 4374 Oldfield, 0 Emsley, 4374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8748 Ramachandran restraints generated. 4374 Oldfield, 0 Emsley, 4374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 3860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 224 time to evaluate : 1.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 646 ARG cc_start: 0.6981 (tpm170) cc_final: 0.6668 (tpm170) REVERT: B 759 PHE cc_start: 0.8425 (OUTLIER) cc_final: 0.8151 (t80) REVERT: B 878 LEU cc_start: 0.8670 (OUTLIER) cc_final: 0.8325 (mp) REVERT: B 983 ARG cc_start: 0.8319 (ttm110) cc_final: 0.8033 (ttm110) REVERT: B 1002 GLN cc_start: 0.8475 (tm-30) cc_final: 0.8042 (tm-30) REVERT: C 389 ASP cc_start: 0.7808 (t0) cc_final: 0.7590 (t0) REVERT: C 453 TYR cc_start: 0.7801 (p90) cc_final: 0.7281 (p90) REVERT: C 619 GLU cc_start: 0.8043 (OUTLIER) cc_final: 0.7780 (pp20) REVERT: C 780 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.7422 (mp0) REVERT: C 955 ASN cc_start: 0.8800 (m-40) cc_final: 0.8313 (t0) REVERT: C 1095 PHE cc_start: 0.8388 (OUTLIER) cc_final: 0.7739 (t80) REVERT: C 1123 SER cc_start: 0.8367 (t) cc_final: 0.8151 (p) REVERT: D 67 ASP cc_start: 0.2281 (m-30) cc_final: 0.1984 (p0) REVERT: D 333 LEU cc_start: -0.0903 (OUTLIER) cc_final: -0.1161 (pp) REVERT: F 177 MET cc_start: 0.7296 (ttt) cc_final: 0.6816 (mmp) REVERT: F 220 PHE cc_start: 0.7375 (t80) cc_final: 0.7105 (t80) REVERT: F 224 GLU cc_start: 0.7960 (pm20) cc_final: 0.7521 (pm20) REVERT: F 806 LEU cc_start: 0.8916 (OUTLIER) cc_final: 0.8648 (mm) REVERT: G 514 ARG cc_start: 0.1210 (OUTLIER) cc_final: 0.0934 (mtm180) outliers start: 69 outliers final: 53 residues processed: 275 average time/residue: 0.2122 time to fit residues: 100.7375 Evaluate side-chains 276 residues out of total 3860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 215 time to evaluate : 1.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 201 PHE Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 619 GLU Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1095 PHE Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1111 GLU Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 333 LEU Chi-restraints excluded: chain D residue 573 VAL Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 62 VAL Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 312 ILE Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain F residue 510 VAL Chi-restraints excluded: chain F residue 512 VAL Chi-restraints excluded: chain F residue 531 THR Chi-restraints excluded: chain F residue 569 ILE Chi-restraints excluded: chain F residue 598 ILE Chi-restraints excluded: chain F residue 740 MET Chi-restraints excluded: chain F residue 761 THR Chi-restraints excluded: chain F residue 806 LEU Chi-restraints excluded: chain F residue 869 MET Chi-restraints excluded: chain F residue 911 VAL Chi-restraints excluded: chain F residue 979 ASP Chi-restraints excluded: chain F residue 1097 SER Chi-restraints excluded: chain F residue 1104 VAL Chi-restraints excluded: chain F residue 1122 VAL Chi-restraints excluded: chain G residue 38 ASP Chi-restraints excluded: chain G residue 156 LEU Chi-restraints excluded: chain G residue 297 MET Chi-restraints excluded: chain G residue 360 MET Chi-restraints excluded: chain G residue 364 VAL Chi-restraints excluded: chain G residue 514 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: chunk 259 optimal weight: 5.9990 chunk 132 optimal weight: 0.9990 chunk 164 optimal weight: 3.9990 chunk 353 optimal weight: 0.7980 chunk 234 optimal weight: 3.9990 chunk 229 optimal weight: 9.9990 chunk 135 optimal weight: 0.8980 chunk 83 optimal weight: 2.9990 chunk 185 optimal weight: 4.9990 chunk 376 optimal weight: 2.9990 chunk 278 optimal weight: 0.3980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4483 r_free = 0.4483 target = 0.187440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.122375 restraints weight = 79554.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.122774 restraints weight = 37950.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 68)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.123602 restraints weight = 23026.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.124643 restraints weight = 17185.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.125316 restraints weight = 13853.614| |-----------------------------------------------------------------------------| r_work (final): 0.3714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 36712 Z= 0.125 Angle : 0.587 13.028 50020 Z= 0.291 Chirality : 0.043 0.269 5676 Planarity : 0.004 0.100 6372 Dihedral : 4.327 28.659 4729 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.70 % Favored : 92.18 % Rotamer: Outliers : 1.72 % Allowed : 14.85 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.76 (0.13), residues: 4374 helix: 1.61 (0.15), residues: 1313 sheet: -0.87 (0.20), residues: 669 loop : -1.69 (0.13), residues: 2392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 204 TYR 0.029 0.001 TYR D 196 PHE 0.016 0.001 PHE C1095 TRP 0.026 0.001 TRP D 48 HIS 0.007 0.001 HIS G 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.12 (36628) covalent geometry : angle 0.58068 / 0.29 (49837) SS BOND : bond 0.00260 / 0.16 ( 42) SS BOND : angle 1.13949 / 0.79 ( 84) hydrogen bonds : bond 0.03584 / 2.38 ( 1325) hydrogen bonds : angle 5.08295 / 3.51 ( 3765) metal coordination : bond 0.02002 / 1.01 ( 4) Misc. bond : bond 0.00076 / 0.03 ( 5) link_BETA1-4 : bond 0.00474 / 0.30 ( 9) link_BETA1-4 : angle 1.67785 / 1.24 ( 27) link_NAG-ASN : bond 0.00252 / 0.15 ( 24) link_NAG-ASN : angle 1.83128 / 1.40 ( 72) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8748 Ramachandran restraints generated. 4374 Oldfield, 0 Emsley, 4374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8748 Ramachandran restraints generated. 4374 Oldfield, 0 Emsley, 4374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 3860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 222 time to evaluate : 1.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 646 ARG cc_start: 0.6981 (tpm170) cc_final: 0.6662 (tpm170) REVERT: B 759 PHE cc_start: 0.8432 (OUTLIER) cc_final: 0.8157 (t80) REVERT: B 878 LEU cc_start: 0.8693 (OUTLIER) cc_final: 0.8295 (mp) REVERT: B 983 ARG cc_start: 0.8227 (ttm110) cc_final: 0.8020 (ttm110) REVERT: B 1002 GLN cc_start: 0.8517 (tm-30) cc_final: 0.8087 (tm-30) REVERT: C 389 ASP cc_start: 0.7686 (t0) cc_final: 0.7472 (t0) REVERT: C 453 TYR cc_start: 0.7957 (p90) cc_final: 0.7357 (p90) REVERT: C 568 ASP cc_start: 0.7999 (p0) cc_final: 0.7677 (p0) REVERT: C 619 GLU cc_start: 0.7967 (OUTLIER) cc_final: 0.7693 (pp20) REVERT: C 780 GLU cc_start: 0.7828 (OUTLIER) cc_final: 0.7396 (mp0) REVERT: C 955 ASN cc_start: 0.8790 (m-40) cc_final: 0.8339 (t0) REVERT: C 1095 PHE cc_start: 0.8385 (OUTLIER) cc_final: 0.7696 (t80) REVERT: C 1123 SER cc_start: 0.8383 (t) cc_final: 0.8152 (p) REVERT: F 177 MET cc_start: 0.7066 (ttt) cc_final: 0.6726 (mmp) REVERT: F 220 PHE cc_start: 0.7402 (t80) cc_final: 0.7134 (t80) REVERT: F 224 GLU cc_start: 0.7822 (pm20) cc_final: 0.7340 (pm20) REVERT: F 806 LEU cc_start: 0.8885 (OUTLIER) cc_final: 0.8621 (mm) REVERT: G 514 ARG cc_start: 0.1841 (tmm-80) cc_final: 0.1434 (mtm180) outliers start: 66 outliers final: 52 residues processed: 269 average time/residue: 0.2129 time to fit residues: 98.7016 Evaluate side-chains 270 residues out of total 3860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 212 time to evaluate : 1.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 201 PHE Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 619 GLU Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1095 PHE Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1111 GLU Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 573 VAL Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 62 VAL Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 312 ILE Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain F residue 510 VAL Chi-restraints excluded: chain F residue 512 VAL Chi-restraints excluded: chain F residue 531 THR Chi-restraints excluded: chain F residue 569 ILE Chi-restraints excluded: chain F residue 598 ILE Chi-restraints excluded: chain F residue 740 MET Chi-restraints excluded: chain F residue 806 LEU Chi-restraints excluded: chain F residue 869 MET Chi-restraints excluded: chain F residue 911 VAL Chi-restraints excluded: chain F residue 979 ASP Chi-restraints excluded: chain F residue 1097 SER Chi-restraints excluded: chain F residue 1122 VAL Chi-restraints excluded: chain G residue 156 LEU Chi-restraints excluded: chain G residue 297 MET Chi-restraints excluded: chain G residue 360 MET Chi-restraints excluded: chain G residue 364 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: chunk 302 optimal weight: 5.9990 chunk 369 optimal weight: 0.8980 chunk 150 optimal weight: 5.9990 chunk 48 optimal weight: 1.9990 chunk 409 optimal weight: 20.0000 chunk 317 optimal weight: 0.4980 chunk 396 optimal weight: 9.9990 chunk 216 optimal weight: 9.9990 chunk 23 optimal weight: 7.9990 chunk 308 optimal weight: 5.9990 chunk 311 optimal weight: 2.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 87 ASN C 148 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 194 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4467 r_free = 0.4467 target = 0.187041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.123239 restraints weight = 79197.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.127166 restraints weight = 41049.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.125360 restraints weight = 25972.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.126987 restraints weight = 20537.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.126686 restraints weight = 17679.495| |-----------------------------------------------------------------------------| r_work (final): 0.3668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.2212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.112 36712 Z= 0.184 Angle : 0.627 13.105 50020 Z= 0.311 Chirality : 0.044 0.279 5676 Planarity : 0.004 0.100 6372 Dihedral : 4.470 29.628 4729 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.71 % Favored : 91.18 % Rotamer: Outliers : 1.87 % Allowed : 14.62 % Favored : 83.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.13), residues: 4374 helix: 1.51 (0.15), residues: 1305 sheet: -0.91 (0.20), residues: 676 loop : -1.76 (0.13), residues: 2393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 357 TYR 0.027 0.001 TYR D 196 PHE 0.018 0.001 PHE C1095 TRP 0.027 0.001 TRP D 48 HIS 0.008 0.001 HIS D 373 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.18 (36628) covalent geometry : angle 0.62006 / 0.31 (49837) SS BOND : bond 0.00287 / 0.18 ( 42) SS BOND : angle 1.29883 / 0.87 ( 84) hydrogen bonds : bond 0.03780 / 2.51 ( 1325) hydrogen bonds : angle 5.17838 / 3.57 ( 3765) metal coordination : bond 0.02382 / 1.19 ( 4) Misc. bond : bond 0.00082 / 0.04 ( 5) link_BETA1-4 : bond 0.00559 / 0.33 ( 9) link_BETA1-4 : angle 1.83926 / 1.33 ( 27) link_NAG-ASN : bond 0.00241 / 0.16 ( 24) link_NAG-ASN : angle 1.90099 / 1.45 ( 72) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8748 Ramachandran restraints generated. 4374 Oldfield, 0 Emsley, 4374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8748 Ramachandran restraints generated. 4374 Oldfield, 0 Emsley, 4374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 3860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 212 time to evaluate : 1.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 646 ARG cc_start: 0.7059 (tpm170) cc_final: 0.6626 (tpm170) REVERT: B 759 PHE cc_start: 0.8475 (OUTLIER) cc_final: 0.8158 (t80) REVERT: B 878 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8360 (mp) REVERT: B 1002 GLN cc_start: 0.8580 (tm-30) cc_final: 0.8114 (tm-30) REVERT: C 342 PHE cc_start: 0.7519 (m-80) cc_final: 0.7292 (m-80) REVERT: C 389 ASP cc_start: 0.7809 (t0) cc_final: 0.7598 (t0) REVERT: C 568 ASP cc_start: 0.7973 (p0) cc_final: 0.7661 (p0) REVERT: C 619 GLU cc_start: 0.8201 (OUTLIER) cc_final: 0.7909 (pp20) REVERT: C 780 GLU cc_start: 0.7875 (OUTLIER) cc_final: 0.7428 (mp0) REVERT: C 955 ASN cc_start: 0.8830 (m-40) cc_final: 0.8333 (t0) REVERT: C 1095 PHE cc_start: 0.8498 (OUTLIER) cc_final: 0.7867 (t80) REVERT: C 1123 SER cc_start: 0.8435 (t) cc_final: 0.8190 (p) REVERT: D 152 MET cc_start: -0.1041 (mmp) cc_final: -0.1370 (mtm) REVERT: F 177 MET cc_start: 0.7200 (ttt) cc_final: 0.6804 (mmp) REVERT: F 224 GLU cc_start: 0.8000 (pm20) cc_final: 0.7515 (pm20) REVERT: F 368 LEU cc_start: 0.4943 (OUTLIER) cc_final: 0.4366 (pp) REVERT: F 806 LEU cc_start: 0.8899 (OUTLIER) cc_final: 0.8635 (mm) REVERT: G 514 ARG cc_start: 0.1626 (tmm-80) cc_final: 0.1335 (mtm180) outliers start: 72 outliers final: 55 residues processed: 266 average time/residue: 0.2097 time to fit residues: 96.2048 Evaluate side-chains 268 residues out of total 3860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 206 time to evaluate : 1.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 201 PHE Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 619 GLU Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 1095 PHE Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1111 GLU Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 573 VAL Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 62 VAL Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 312 ILE Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain F residue 368 LEU Chi-restraints excluded: chain F residue 510 VAL Chi-restraints excluded: chain F residue 512 VAL Chi-restraints excluded: chain F residue 518 LEU Chi-restraints excluded: chain F residue 531 THR Chi-restraints excluded: chain F residue 569 ILE Chi-restraints excluded: chain F residue 598 ILE Chi-restraints excluded: chain F residue 740 MET Chi-restraints excluded: chain F residue 806 LEU Chi-restraints excluded: chain F residue 869 MET Chi-restraints excluded: chain F residue 911 VAL Chi-restraints excluded: chain F residue 979 ASP Chi-restraints excluded: chain F residue 1097 SER Chi-restraints excluded: chain F residue 1104 VAL Chi-restraints excluded: chain F residue 1122 VAL Chi-restraints excluded: chain G residue 38 ASP Chi-restraints excluded: chain G residue 156 LEU Chi-restraints excluded: chain G residue 297 MET Chi-restraints excluded: chain G residue 360 MET Chi-restraints excluded: chain G residue 364 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: chunk 47 optimal weight: 9.9990 chunk 177 optimal weight: 3.9990 chunk 302 optimal weight: 4.9990 chunk 185 optimal weight: 0.0060 chunk 81 optimal weight: 0.5980 chunk 413 optimal weight: 5.9990 chunk 126 optimal weight: 8.9990 chunk 225 optimal weight: 1.9990 chunk 327 optimal weight: 0.9980 chunk 181 optimal weight: 3.9990 chunk 354 optimal weight: 0.0030 overall best weight: 0.7208 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN B 239 GLN ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4503 r_free = 0.4503 target = 0.191352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.128232 restraints weight = 77950.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.132815 restraints weight = 39205.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.131023 restraints weight = 23305.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.132648 restraints weight = 20951.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.132680 restraints weight = 16811.290| |-----------------------------------------------------------------------------| r_work (final): 0.3732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7368 moved from start: 0.2293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.077 36712 Z= 0.110 Angle : 0.581 12.647 50020 Z= 0.288 Chirality : 0.043 0.264 5676 Planarity : 0.004 0.100 6372 Dihedral : 4.290 28.191 4729 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.13 % Favored : 92.75 % Rotamer: Outliers : 1.59 % Allowed : 14.91 % Favored : 83.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.13), residues: 4374 helix: 1.60 (0.15), residues: 1317 sheet: -0.76 (0.20), residues: 671 loop : -1.69 (0.13), residues: 2386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 457 TYR 0.043 0.001 TYR C 473 PHE 0.024 0.001 PHE D 315 TRP 0.031 0.001 TRP D 48 HIS 0.007 0.001 HIS G 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 (36628) covalent geometry : angle 0.57487 / 0.29 (49837) SS BOND : bond 0.00249 / 0.15 ( 42) SS BOND : angle 1.02874 / 0.69 ( 84) hydrogen bonds : bond 0.03502 / 2.34 ( 1325) hydrogen bonds : angle 5.02184 / 3.46 ( 3765) metal coordination : bond 0.01990 / 1.00 ( 4) Misc. bond : bond 0.00076 / 0.03 ( 5) link_BETA1-4 : bond 0.00502 / 0.31 ( 9) link_BETA1-4 : angle 1.63166 / 1.22 ( 27) link_NAG-ASN : bond 0.00274 / 0.17 ( 24) link_NAG-ASN : angle 1.80907 / 1.39 ( 72) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7752.37 seconds wall clock time: 134 minutes 33.53 seconds (8073.53 seconds total)