Starting phenix.real_space_refine on Tue Aug 26 11:04:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yr3_34044/08_2025/7yr3_34044.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yr3_34044/08_2025/7yr3_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_34044/08_2025/7yr3_34044.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yr3_34044/08_2025/7yr3_34044.map" model { file = "/net/cci-nas-00/data/ceres_data/7yr3_34044/08_2025/7yr3_34044.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yr3_34044/08_2025/7yr3_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-2.0-5787/lib/python3.9/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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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 dihedrals: 45 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 dihedrals: 51 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 dihedrals: 12 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 dihedrals: 39 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 dihedrals: 12 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: 8.84, per 1000 atoms: 0.25 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: 3.42 Conformation dependent library (CDL) restraints added in 1.6 seconds Enol-peptide restraints added in 1.2 microseconds 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: 1.64 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: 8.90 Time building geometry restraints manager: 4.16 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 - 25.58: 21464 25.58 - 51.17: 1057 51.17 - 76.75: 133 76.75 - 102.33: 33 102.33 - 127.92: 7 Dihedral angle restraints: 22694 sinusoidal: 9844 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 22691 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: 2.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.600 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 40.370 Find NCS groups from input model: 1.000 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7280 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 : 14.552 127.918 14306 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 aren 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 covalent geometry : bond 0.00389 (36628) covalent geometry : angle 0.62824 (49837) SS BOND : bond 0.00433 ( 42) SS BOND : angle 1.25456 ( 84) hydrogen bonds : bond 0.18912 ( 1325) hydrogen bonds : angle 7.72092 ( 3765) metal coordination : bond 0.02443 ( 4) Misc. bond : bond 0.00134 ( 5) link_BETA1-4 : bond 0.00439 ( 9) link_BETA1-4 : angle 1.90299 ( 27) link_NAG-ASN : bond 0.00257 ( 24) link_NAG-ASN : angle 2.04492 ( 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 : 1.332 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: 0.0576 (tpt) cc_final: 0.0307 (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: 0.2180 (tpt) cc_final: 0.1253 (ptm) outliers start: 5 outliers final: 1 residues processed: 279 average time/residue: 0.2037 time to fit residues: 99.0063 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 : 1.337 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** B 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 211 ASN B 282 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: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4521 r_free = 0.4521 target = 0.190657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.128527 restraints weight = 77868.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.132246 restraints weight = 41083.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.130487 restraints weight = 27296.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.132059 restraints weight = 20790.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.131987 restraints weight = 16672.232| |-----------------------------------------------------------------------------| r_work (final): 0.3718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7256 moved from start: 0.0870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 36712 Z= 0.153 Angle : 0.615 9.409 50020 Z= 0.309 Chirality : 0.044 0.253 5676 Planarity : 0.004 0.091 6372 Dihedral : 8.669 103.614 6222 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.82 % Favored : 92.04 % Rotamer: Outliers : 0.60 % Allowed : 6.04 % Favored : 93.37 % 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 aren not related in a simple way. whole: -0.82 (0.13), residues: 4374 helix: 1.39 (0.14), residues: 1331 sheet: -0.59 (0.21), residues: 635 loop : -1.73 (0.13), residues: 2408 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 0.024 0.001 PHE D 369 TRP 0.021 0.001 TRP C 64 HIS 0.012 0.001 HIS D 373 Details of bonding type rmsd covalent geometry : bond 0.00343 (36628) covalent geometry : angle 0.60707 (49837) SS BOND : bond 0.00311 ( 42) SS BOND : angle 1.25740 ( 84) hydrogen bonds : bond 0.04642 ( 1325) hydrogen bonds : angle 5.88882 ( 3765) metal coordination : bond 0.02041 ( 4) Misc. bond : bond 0.00112 ( 5) link_BETA1-4 : bond 0.00528 ( 9) link_BETA1-4 : angle 2.15609 ( 27) link_NAG-ASN : bond 0.00279 ( 24) link_NAG-ASN : angle 2.07159 ( 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 261 residues out of total 3860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 238 time to evaluate : 1.380 Fit side-chains REVERT: C 428 ASP cc_start: 0.8766 (m-30) cc_final: 0.8037 (m-30) REVERT: C 523 THR cc_start: 0.8635 (m) cc_final: 0.8433 (p) REVERT: C 955 ASN cc_start: 0.8633 (m-40) cc_final: 0.8266 (t0) REVERT: D 67 ASP cc_start: 0.2135 (m-30) cc_final: 0.1867 (p0) REVERT: F 224 GLU cc_start: 0.7851 (pm20) cc_final: 0.7348 (pm20) REVERT: F 565 PHE cc_start: 0.7384 (m-10) cc_final: 0.7144 (m-80) REVERT: F 580 GLN cc_start: 0.7885 (OUTLIER) cc_final: 0.7682 (pp30) REVERT: G 123 MET cc_start: 0.2091 (tpt) cc_final: 0.1246 (ptm) outliers start: 23 outliers final: 14 residues processed: 252 average time/residue: 0.2020 time to fit residues: 89.0213 Evaluate side-chains 220 residues out of total 3860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 205 time to evaluate : 1.395 ------------------------------------------------------------------------------- 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 580 GLN Chi-restraints excluded: chain F residue 740 MET Chi-restraints excluded: chain F residue 747 THR 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: 0.5980 chunk 383 optimal weight: 8.9990 chunk 426 optimal weight: 8.9990 chunk 67 optimal weight: 0.5980 chunk 163 optimal weight: 0.9990 chunk 396 optimal weight: 8.9990 chunk 239 optimal weight: 0.0030 chunk 157 optimal weight: 5.9990 chunk 151 optimal weight: 10.0000 chunk 89 optimal weight: 1.9990 chunk 379 optimal weight: 10.0000 overall best weight: 0.8394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 26 GLN ** 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 644 GLN ** D 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 804 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4528 r_free = 0.4528 target = 0.190294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.128082 restraints weight = 78951.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 73)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.127236 restraints weight = 38594.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.128094 restraints weight = 24174.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.129025 restraints weight = 17161.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.129739 restraints weight = 13950.905| |-----------------------------------------------------------------------------| r_work (final): 0.3751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7383 moved from start: 0.1136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 36712 Z= 0.116 Angle : 0.567 10.429 50020 Z= 0.285 Chirality : 0.043 0.257 5676 Planarity : 0.004 0.092 6372 Dihedral : 7.708 103.007 6220 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.09 % Favored : 92.78 % Rotamer: Outliers : 0.83 % Allowed : 8.74 % Favored : 90.43 % 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 aren not related in a simple way. whole: -0.73 (0.13), residues: 4374 helix: 1.58 (0.15), residues: 1309 sheet: -0.63 (0.20), residues: 641 loop : -1.70 (0.12), residues: 2424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 214 TYR 0.024 0.001 TYR B 160 PHE 0.016 0.001 PHE B 201 TRP 0.016 0.001 TRP B 353 HIS 0.011 0.001 HIS D 373 Details of bonding type rmsd covalent geometry : bond 0.00256 (36628) covalent geometry : angle 0.56034 (49837) SS BOND : bond 0.00300 ( 42) SS BOND : angle 1.05941 ( 84) hydrogen bonds : bond 0.04018 ( 1325) hydrogen bonds : angle 5.48290 ( 3765) metal coordination : bond 0.01870 ( 4) Misc. bond : bond 0.00093 ( 5) link_BETA1-4 : bond 0.00494 ( 9) link_BETA1-4 : angle 1.82015 ( 27) link_NAG-ASN : bond 0.00268 ( 24) link_NAG-ASN : angle 1.94141 ( 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 285 residues out of total 3860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 253 time to evaluate : 1.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 646 ARG cc_start: 0.6824 (tpm170) cc_final: 0.6557 (tpm170) REVERT: B 878 LEU cc_start: 0.8653 (tt) cc_final: 0.8296 (mp) REVERT: B 1002 GLN cc_start: 0.8416 (tm-30) cc_final: 0.8081 (tm-30) REVERT: C 424 LYS cc_start: 0.7788 (pttp) cc_final: 0.7578 (pttp) REVERT: C 780 GLU cc_start: 0.7745 (OUTLIER) cc_final: 0.7372 (mp0) REVERT: C 955 ASN cc_start: 0.8700 (m-40) cc_final: 0.8214 (t0) REVERT: D 152 MET cc_start: -0.0778 (mmp) cc_final: -0.2103 (tmm) REVERT: G 123 MET cc_start: 0.2292 (tpt) cc_final: 0.1238 (ptm) outliers start: 32 outliers final: 14 residues processed: 273 average time/residue: 0.2037 time to fit residues: 97.0160 Evaluate side-chains 226 residues out of total 3860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 211 time to evaluate : 1.554 ------------------------------------------------------------------------------- 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 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 979 ASP Chi-restraints excluded: chain G residue 297 MET Chi-restraints excluded: chain G residue 364 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: chunk 376 optimal weight: 0.0870 chunk 369 optimal weight: 4.9990 chunk 45 optimal weight: 0.0570 chunk 215 optimal weight: 20.0000 chunk 371 optimal weight: 3.9990 chunk 277 optimal weight: 7.9990 chunk 239 optimal weight: 0.8980 chunk 108 optimal weight: 5.9990 chunk 146 optimal weight: 20.0000 chunk 12 optimal weight: 8.9990 chunk 48 optimal weight: 30.0000 overall best weight: 2.0080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 121 ASN ** B 196 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 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 378 HIS F 762 GLN F 914 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4535 r_free = 0.4535 target = 0.201600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.144739 restraints weight = 73986.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.143110 restraints weight = 54170.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.143704 restraints weight = 37283.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.143704 restraints weight = 32936.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.143588 restraints weight = 26936.536| |-----------------------------------------------------------------------------| r_work (final): 0.3748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7111 moved from start: 0.1339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 1.048 36712 Z= 0.242 Angle : 0.586 9.722 50020 Z= 0.293 Chirality : 0.043 0.338 5676 Planarity : 0.004 0.094 6372 Dihedral : 7.440 102.602 6220 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.12 % Favored : 91.77 % Rotamer: Outliers : 1.53 % Allowed : 10.04 % Favored : 88.42 % 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 aren not related in a simple way. whole: -0.76 (0.13), residues: 4374 helix: 1.55 (0.14), residues: 1313 sheet: -0.65 (0.20), residues: 641 loop : -1.72 (0.13), residues: 2420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 204 TYR 0.023 0.001 TYR B 160 PHE 0.015 0.001 PHE D 369 TRP 0.018 0.001 TRP B 353 HIS 0.011 0.001 HIS D 373 Details of bonding type rmsd covalent geometry : bond 0.00367 (36628) covalent geometry : angle 0.57855 (49837) SS BOND : bond 0.00280 ( 42) SS BOND : angle 1.15155 ( 84) hydrogen bonds : bond 0.03900 ( 1325) hydrogen bonds : angle 5.33476 ( 3765) metal coordination : bond 0.52392 ( 4) Misc. bond : bond 0.00091 ( 5) link_BETA1-4 : bond 0.00492 ( 9) link_BETA1-4 : angle 1.81439 ( 27) link_NAG-ASN : bond 0.00263 ( 24) link_NAG-ASN : angle 1.97290 ( 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 275 residues out of total 3860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 216 time to evaluate : 1.361 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 646 ARG cc_start: 0.6961 (tpm170) cc_final: 0.6579 (tpm170) REVERT: B 878 LEU cc_start: 0.8743 (tt) cc_final: 0.8304 (mp) REVERT: B 1002 GLN cc_start: 0.8497 (tm-30) cc_final: 0.8097 (tm-30) REVERT: C 453 TYR cc_start: 0.7983 (p90) cc_final: 0.7442 (p90) REVERT: C 780 GLU cc_start: 0.7829 (OUTLIER) cc_final: 0.7480 (mp0) REVERT: C 955 ASN cc_start: 0.8664 (m-40) cc_final: 0.8284 (t0) REVERT: D 67 ASP cc_start: 0.2202 (m-30) cc_final: 0.1902 (p0) REVERT: G 123 MET cc_start: 0.2316 (tpt) cc_final: 0.1172 (ptm) REVERT: G 175 GLN cc_start: 0.4340 (mp10) cc_final: 0.3993 (pp30) REVERT: G 376 MET cc_start: -0.1586 (ptm) cc_final: -0.1848 (ttp) outliers start: 59 outliers final: 31 residues processed: 259 average time/residue: 0.2004 time to fit residues: 91.4151 Evaluate side-chains 238 residues out of total 3860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 206 time to evaluate : 1.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 C residue 51 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 179 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 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 249 MET Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 84 LEU 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 598 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 1050 MET Chi-restraints excluded: chain F residue 1104 VAL 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: 9.9990 chunk 382 optimal weight: 5.9990 chunk 207 optimal weight: 3.9990 chunk 288 optimal weight: 10.0000 chunk 198 optimal weight: 4.9990 chunk 164 optimal weight: 0.8980 chunk 161 optimal weight: 10.0000 chunk 94 optimal weight: 0.8980 chunk 313 optimal weight: 40.0000 chunk 23 optimal weight: 20.0000 chunk 133 optimal weight: 6.9990 overall best weight: 3.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** C 801 ASN ** D 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 277 ASN ** D 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 578 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4485 r_free = 0.4485 target = 0.189092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.127235 restraints weight = 76576.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.130276 restraints weight = 42281.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.129251 restraints weight = 27046.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.130569 restraints weight = 21118.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.130590 restraints weight = 16845.757| |-----------------------------------------------------------------------------| r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7289 moved from start: 0.1626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.130 36712 Z= 0.232 Angle : 0.647 11.082 50020 Z= 0.323 Chirality : 0.045 0.286 5676 Planarity : 0.004 0.096 6372 Dihedral : 7.599 103.177 6220 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.85 % Favored : 91.04 % Rotamer: Outliers : 1.56 % Allowed : 11.81 % Favored : 86.63 % 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 aren not related in a simple way. whole: -0.92 (0.13), residues: 4374 helix: 1.48 (0.14), residues: 1298 sheet: -0.84 (0.20), residues: 661 loop : -1.80 (0.12), residues: 2415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 357 TYR 0.025 0.002 TYR D 196 PHE 0.021 0.002 PHE C 400 TRP 0.024 0.001 TRP B 353 HIS 0.018 0.002 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00542 (36628) covalent geometry : angle 0.63793 (49837) SS BOND : bond 0.00471 ( 42) SS BOND : angle 1.48377 ( 84) hydrogen bonds : bond 0.04090 ( 1325) hydrogen bonds : angle 5.38613 ( 3765) metal coordination : bond 0.06247 ( 4) Misc. bond : bond 0.00097 ( 5) link_BETA1-4 : bond 0.00467 ( 9) link_BETA1-4 : angle 2.06030 ( 27) link_NAG-ASN : bond 0.00327 ( 24) link_NAG-ASN : angle 2.21714 ( 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 277 residues out of total 3860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 217 time to evaluate : 1.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 611 LEU cc_start: 0.9417 (tp) cc_final: 0.9202 (tt) REVERT: B 646 ARG cc_start: 0.7025 (tpm170) cc_final: 0.6620 (tpm170) REVERT: B 697 MET cc_start: 0.7898 (mtp) cc_final: 0.7697 (mtt) REVERT: B 759 PHE cc_start: 0.8387 (OUTLIER) cc_final: 0.8031 (t80) REVERT: B 878 LEU cc_start: 0.8754 (OUTLIER) cc_final: 0.8323 (tt) REVERT: B 983 ARG cc_start: 0.8353 (ttm110) cc_final: 0.8121 (ttm110) REVERT: B 1002 GLN cc_start: 0.8525 (tm-30) cc_final: 0.8056 (tm-30) REVERT: C 453 TYR cc_start: 0.7893 (p90) cc_final: 0.7295 (p90) REVERT: C 619 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.7785 (pp20) REVERT: C 780 GLU cc_start: 0.7846 (OUTLIER) cc_final: 0.7449 (mp0) REVERT: C 955 ASN cc_start: 0.8817 (m-40) cc_final: 0.8383 (t0) REVERT: C 1095 PHE cc_start: 0.8378 (OUTLIER) cc_final: 0.7889 (t80) REVERT: D 67 ASP cc_start: 0.2272 (m-30) cc_final: 0.1981 (p0) REVERT: D 152 MET cc_start: -0.0594 (mmp) cc_final: -0.2040 (ttp) REVERT: D 333 LEU cc_start: -0.0554 (OUTLIER) cc_final: -0.0844 (pp) REVERT: F 177 MET cc_start: 0.7088 (ttt) cc_final: 0.6765 (mmp) REVERT: G 123 MET cc_start: 0.1741 (tpt) cc_final: 0.0675 (ptm) REVERT: G 175 GLN cc_start: 0.4444 (mp10) cc_final: 0.4187 (pp30) outliers start: 60 outliers final: 44 residues processed: 259 average time/residue: 0.1878 time to fit residues: 83.6135 Evaluate side-chains 255 residues out of total 3860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 205 time to evaluate : 1.336 ------------------------------------------------------------------------------- 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 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 87 ASN Chi-restraints excluded: chain C residue 90 VAL 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 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 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 533 LEU 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 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: 3.9990 chunk 258 optimal weight: 7.9990 chunk 136 optimal weight: 9.9990 chunk 29 optimal weight: 1.9990 chunk 284 optimal weight: 20.0000 chunk 96 optimal weight: 0.9990 chunk 13 optimal weight: 5.9990 chunk 122 optimal weight: 4.9990 chunk 30 optimal weight: 0.0470 chunk 157 optimal weight: 7.9990 chunk 256 optimal weight: 20.0000 overall best weight: 2.4086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4507 r_free = 0.4507 target = 0.195583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.135141 restraints weight = 74352.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.136717 restraints weight = 45570.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.137799 restraints weight = 28694.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.137907 restraints weight = 20787.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.138180 restraints weight = 20341.885| |-----------------------------------------------------------------------------| r_work (final): 0.3696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7229 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 : 0.004 0.108 36712 Z= 0.180 Angle : 0.611 10.505 50020 Z= 0.306 Chirality : 0.044 0.273 5676 Planarity : 0.004 0.097 6372 Dihedral : 7.437 102.680 6220 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.44 % Favored : 91.45 % Rotamer: Outliers : 1.69 % Allowed : 13.03 % Favored : 85.28 % 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 aren not related in a simple way. whole: -0.93 (0.13), residues: 4374 helix: 1.49 (0.15), residues: 1305 sheet: -0.93 (0.20), residues: 670 loop : -1.81 (0.12), residues: 2399 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 0.019 0.001 PHE B 565 TRP 0.020 0.001 TRP B 353 HIS 0.011 0.001 HIS D 373 Details of bonding type rmsd covalent geometry : bond 0.00417 (36628) covalent geometry : angle 0.60220 (49837) SS BOND : bond 0.00355 ( 42) SS BOND : angle 1.34121 ( 84) hydrogen bonds : bond 0.03899 ( 1325) hydrogen bonds : angle 5.29463 ( 3765) metal coordination : bond 0.02378 ( 4) Misc. bond : bond 0.00092 ( 5) link_BETA1-4 : bond 0.00482 ( 9) link_BETA1-4 : angle 2.05132 ( 27) link_NAG-ASN : bond 0.00280 ( 24) link_NAG-ASN : angle 2.11597 ( 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 289 residues out of total 3860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 224 time to evaluate : 1.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 611 LEU cc_start: 0.9384 (tp) cc_final: 0.9172 (tt) REVERT: B 646 ARG cc_start: 0.6993 (tpm170) cc_final: 0.6684 (tpm170) REVERT: B 759 PHE cc_start: 0.8346 (OUTLIER) cc_final: 0.8025 (t80) REVERT: B 878 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.8259 (tt) REVERT: B 983 ARG cc_start: 0.8356 (ttm110) cc_final: 0.8110 (ttm110) REVERT: B 1002 GLN cc_start: 0.8477 (tm-30) cc_final: 0.8036 (tm-30) REVERT: C 453 TYR cc_start: 0.7832 (p90) cc_final: 0.7257 (p90) REVERT: C 780 GLU cc_start: 0.7838 (OUTLIER) cc_final: 0.7426 (mp0) REVERT: C 955 ASN cc_start: 0.8824 (m-40) cc_final: 0.8367 (t0) REVERT: C 1095 PHE cc_start: 0.8415 (OUTLIER) cc_final: 0.7895 (t80) REVERT: C 1123 SER cc_start: 0.8319 (t) cc_final: 0.8086 (p) REVERT: D 67 ASP cc_start: 0.2249 (m-30) cc_final: 0.1956 (p0) REVERT: D 152 MET cc_start: -0.0600 (mmp) cc_final: -0.2091 (ttp) REVERT: D 196 TYR cc_start: 0.2057 (m-80) cc_final: 0.1850 (m-80) REVERT: D 333 LEU cc_start: -0.0834 (OUTLIER) cc_final: -0.1116 (pp) REVERT: D 356 PHE cc_start: 0.1763 (m-80) cc_final: 0.1129 (m-80) REVERT: F 177 MET cc_start: 0.7361 (ttt) cc_final: 0.6821 (mmp) REVERT: F 224 GLU cc_start: 0.8013 (pm20) cc_final: 0.7537 (pm20) REVERT: G 175 GLN cc_start: 0.4409 (mp10) cc_final: 0.4196 (pp30) outliers start: 65 outliers final: 41 residues processed: 273 average time/residue: 0.2022 time to fit residues: 95.9688 Evaluate side-chains 254 residues out of total 3860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 208 time to evaluate : 1.396 ------------------------------------------------------------------------------- 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 B residue 1129 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 312 ILE 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 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 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 118 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 979 ASP Chi-restraints excluded: chain F residue 1097 SER 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: 0.9990 chunk 73 optimal weight: 0.4980 chunk 163 optimal weight: 4.9990 chunk 369 optimal weight: 2.9990 chunk 117 optimal weight: 0.1980 chunk 102 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 263 optimal weight: 10.0000 chunk 38 optimal weight: 0.7980 chunk 371 optimal weight: 1.9990 chunk 423 optimal weight: 10.0000 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 61 ASN ** 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** ** D 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 544 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4507 r_free = 0.4507 target = 0.195576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.131667 restraints weight = 75963.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.134952 restraints weight = 35157.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.136943 restraints weight = 21668.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.138240 restraints weight = 16016.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.138978 restraints weight = 13282.313| |-----------------------------------------------------------------------------| r_work (final): 0.3749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.076 36712 Z= 0.109 Angle : 0.565 10.655 50020 Z= 0.283 Chirality : 0.043 0.261 5676 Planarity : 0.004 0.097 6372 Dihedral : 6.973 101.170 6220 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.68 % Favored : 92.20 % Rotamer: Outliers : 1.51 % Allowed : 13.63 % Favored : 84.86 % 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 aren not related in a simple way. whole: -0.73 (0.13), residues: 4374 helix: 1.66 (0.14), residues: 1310 sheet: -0.77 (0.20), residues: 654 loop : -1.71 (0.13), residues: 2410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 204 TYR 0.021 0.001 TYR C1067 PHE 0.015 0.001 PHE B 565 TRP 0.023 0.001 TRP D 48 HIS 0.009 0.001 HIS D 373 Details of bonding type rmsd covalent geometry : bond 0.00242 (36628) covalent geometry : angle 0.55759 (49837) SS BOND : bond 0.00276 ( 42) SS BOND : angle 1.06704 ( 84) hydrogen bonds : bond 0.03546 ( 1325) hydrogen bonds : angle 5.06875 ( 3765) metal coordination : bond 0.02078 ( 4) Misc. bond : bond 0.00081 ( 5) link_BETA1-4 : bond 0.00502 ( 9) link_BETA1-4 : angle 1.76323 ( 27) link_NAG-ASN : bond 0.00289 ( 24) link_NAG-ASN : angle 1.98450 ( 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 299 residues out of total 3860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 241 time to evaluate : 1.149 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 646 ARG cc_start: 0.6996 (tpm170) cc_final: 0.6705 (tpm170) REVERT: B 759 PHE cc_start: 0.8344 (OUTLIER) cc_final: 0.8000 (t80) REVERT: B 878 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8262 (mp) REVERT: B 983 ARG cc_start: 0.8276 (ttm110) cc_final: 0.8058 (ttm110) REVERT: B 1002 GLN cc_start: 0.8457 (tm-30) cc_final: 0.7971 (tm-30) REVERT: C 389 ASP cc_start: 0.7631 (t0) cc_final: 0.7429 (t0) REVERT: C 453 TYR cc_start: 0.7930 (p90) cc_final: 0.7375 (p90) REVERT: C 780 GLU cc_start: 0.7798 (OUTLIER) cc_final: 0.7419 (mp0) REVERT: C 955 ASN cc_start: 0.8757 (m-40) cc_final: 0.8328 (t0) REVERT: C 1095 PHE cc_start: 0.8400 (OUTLIER) cc_final: 0.7609 (t80) REVERT: C 1123 SER cc_start: 0.8350 (t) cc_final: 0.8103 (p) REVERT: D 152 MET cc_start: -0.1145 (mmp) cc_final: -0.2277 (ttp) REVERT: D 297 MET cc_start: 0.0240 (mpp) cc_final: -0.0715 (mtt) REVERT: G 123 MET cc_start: 0.1836 (tpt) cc_final: 0.1310 (tpt) REVERT: G 175 GLN cc_start: 0.4462 (mp10) cc_final: 0.4239 (pp30) outliers start: 58 outliers final: 37 residues processed: 284 average time/residue: 0.2060 time to fit residues: 100.9931 Evaluate side-chains 255 residues out of total 3860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 214 time to evaluate : 1.317 ------------------------------------------------------------------------------- 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 294 ASP 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 C residue 350 VAL 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 D residue 108 LEU Chi-restraints excluded: chain D residue 142 LEU 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 118 LEU 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 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 1104 VAL Chi-restraints excluded: chain F residue 1122 VAL 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: 0.7980 chunk 262 optimal weight: 10.0000 chunk 357 optimal weight: 0.9980 chunk 8 optimal weight: 10.0000 chunk 120 optimal weight: 2.9990 chunk 105 optimal weight: 10.0000 chunk 76 optimal weight: 3.9990 chunk 310 optimal weight: 2.9990 chunk 366 optimal weight: 5.9990 chunk 152 optimal weight: 6.9990 chunk 202 optimal weight: 0.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 87 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 139 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 = 0.4501 r_free = 0.4501 target = 0.188045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.127692 restraints weight = 78585.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.131005 restraints weight = 41614.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.129602 restraints weight = 27075.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.131095 restraints weight = 20974.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.131155 restraints weight = 17294.082| |-----------------------------------------------------------------------------| r_work (final): 0.3708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7275 moved from start: 0.1964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.091 36712 Z= 0.148 Angle : 0.598 15.602 50020 Z= 0.296 Chirality : 0.044 0.266 5676 Planarity : 0.004 0.098 6372 Dihedral : 6.976 101.833 6220 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.05 % Favored : 91.84 % Rotamer: Outliers : 1.64 % Allowed : 14.36 % Favored : 84.00 % 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 aren not related in a simple way. whole: -0.74 (0.13), residues: 4374 helix: 1.64 (0.15), residues: 1306 sheet: -0.81 (0.20), residues: 663 loop : -1.69 (0.13), residues: 2405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C1107 TYR 0.025 0.001 TYR D 196 PHE 0.016 0.001 PHE C1095 TRP 0.025 0.001 TRP D 48 HIS 0.009 0.001 HIS D 373 Details of bonding type rmsd covalent geometry : bond 0.00343 (36628) covalent geometry : angle 0.59036 (49837) SS BOND : bond 0.00269 ( 42) SS BOND : angle 1.12480 ( 84) hydrogen bonds : bond 0.03650 ( 1325) hydrogen bonds : angle 5.09163 ( 3765) metal coordination : bond 0.01709 ( 4) Misc. bond : bond 0.00082 ( 5) link_BETA1-4 : bond 0.00437 ( 9) link_BETA1-4 : angle 1.96706 ( 27) link_NAG-ASN : bond 0.00259 ( 24) link_NAG-ASN : angle 2.00189 ( 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 283 residues out of total 3860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 220 time to evaluate : 1.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 646 ARG cc_start: 0.7015 (tpm170) cc_final: 0.6587 (tpm170) REVERT: B 759 PHE cc_start: 0.8405 (OUTLIER) cc_final: 0.8135 (t80) REVERT: B 878 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.8290 (mp) REVERT: B 1002 GLN cc_start: 0.8483 (tm-30) cc_final: 0.8047 (tm-30) REVERT: C 389 ASP cc_start: 0.7685 (t0) cc_final: 0.7466 (t0) REVERT: C 453 TYR cc_start: 0.7927 (p90) cc_final: 0.7313 (p90) REVERT: C 619 GLU cc_start: 0.8039 (OUTLIER) cc_final: 0.7736 (pp20) REVERT: C 780 GLU cc_start: 0.7843 (OUTLIER) cc_final: 0.7439 (mp0) REVERT: C 955 ASN cc_start: 0.8797 (m-40) cc_final: 0.8323 (t0) REVERT: C 1095 PHE cc_start: 0.8438 (OUTLIER) cc_final: 0.7656 (t80) REVERT: C 1123 SER cc_start: 0.8381 (t) cc_final: 0.8154 (p) REVERT: D 358 ILE cc_start: 0.4127 (OUTLIER) cc_final: 0.3824 (mt) REVERT: F 224 GLU cc_start: 0.7877 (pm20) cc_final: 0.7406 (pm20) REVERT: G 123 MET cc_start: 0.1615 (tpt) cc_final: 0.1020 (tpt) REVERT: G 175 GLN cc_start: 0.4598 (mp10) cc_final: 0.4216 (pp30) outliers start: 63 outliers final: 43 residues processed: 264 average time/residue: 0.2032 time to fit residues: 93.1582 Evaluate side-chains 259 residues out of total 3860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 210 time to evaluate : 1.405 ------------------------------------------------------------------------------- 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 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 87 ASN Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 350 VAL 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 D residue 108 LEU Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 358 ILE 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 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 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 360 MET Chi-restraints excluded: chain G residue 364 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: chunk 259 optimal weight: 0.0470 chunk 132 optimal weight: 0.6980 chunk 164 optimal weight: 3.9990 chunk 353 optimal weight: 0.7980 chunk 234 optimal weight: 3.9990 chunk 229 optimal weight: 10.0000 chunk 135 optimal weight: 0.0170 chunk 83 optimal weight: 0.9980 chunk 185 optimal weight: 2.9990 chunk 376 optimal weight: 2.9990 chunk 278 optimal weight: 1.9990 overall best weight: 0.5116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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** ** D 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4509 r_free = 0.4509 target = 0.189505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.123573 restraints weight = 80004.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.124169 restraints weight = 37618.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.125693 restraints weight = 22754.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.126711 restraints weight = 16548.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.127333 restraints weight = 13475.257| |-----------------------------------------------------------------------------| r_work (final): 0.3745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.2115 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= 0.104 Angle : 0.576 13.286 50020 Z= 0.286 Chirality : 0.043 0.253 5676 Planarity : 0.004 0.099 6372 Dihedral : 6.716 100.661 6220 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.09 % Favored : 92.80 % Rotamer: Outliers : 1.48 % Allowed : 14.65 % Favored : 83.87 % 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 aren not related in a simple way. whole: -0.65 (0.13), residues: 4374 helix: 1.65 (0.15), residues: 1321 sheet: -0.61 (0.20), residues: 650 loop : -1.65 (0.13), residues: 2403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C1107 TYR 0.021 0.001 TYR C1067 PHE 0.036 0.001 PHE G 464 TRP 0.031 0.001 TRP D 48 HIS 0.008 0.001 HIS D 373 Details of bonding type rmsd covalent geometry : bond 0.00226 (36628) covalent geometry : angle 0.56922 (49837) SS BOND : bond 0.00219 ( 42) SS BOND : angle 0.94945 ( 84) hydrogen bonds : bond 0.03439 ( 1325) hydrogen bonds : angle 4.96703 ( 3765) metal coordination : bond 0.01828 ( 4) Misc. bond : bond 0.00077 ( 5) link_BETA1-4 : bond 0.00497 ( 9) link_BETA1-4 : angle 1.86512 ( 27) link_NAG-ASN : bond 0.00295 ( 24) link_NAG-ASN : angle 1.91477 ( 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 282 residues out of total 3860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 225 time to evaluate : 1.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 646 ARG cc_start: 0.6998 (tpm170) cc_final: 0.6549 (tpm170) REVERT: B 759 PHE cc_start: 0.8362 (OUTLIER) cc_final: 0.8068 (t80) REVERT: B 878 LEU cc_start: 0.8650 (OUTLIER) cc_final: 0.8293 (mp) REVERT: B 1002 GLN cc_start: 0.8463 (tm-30) cc_final: 0.7991 (tm-30) REVERT: B 1029 MET cc_start: 0.8752 (tpp) cc_final: 0.8221 (ttm) REVERT: C 389 ASP cc_start: 0.7653 (t0) cc_final: 0.7441 (t0) REVERT: C 453 TYR cc_start: 0.7954 (p90) cc_final: 0.7415 (p90) REVERT: C 568 ASP cc_start: 0.7961 (p0) cc_final: 0.7660 (p0) REVERT: C 955 ASN cc_start: 0.8817 (m-40) cc_final: 0.8350 (t0) REVERT: C 1095 PHE cc_start: 0.8242 (OUTLIER) cc_final: 0.7373 (t80) REVERT: C 1123 SER cc_start: 0.8361 (t) cc_final: 0.8114 (p) REVERT: G 514 ARG cc_start: 0.2081 (OUTLIER) cc_final: 0.1734 (mtm180) outliers start: 57 outliers final: 38 residues processed: 266 average time/residue: 0.1802 time to fit residues: 83.5315 Evaluate side-chains 255 residues out of total 3860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 213 time to evaluate : 1.180 ------------------------------------------------------------------------------- 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 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 759 PHE 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 277 LEU Chi-restraints excluded: chain C residue 350 VAL 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 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 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 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 1104 VAL Chi-restraints excluded: chain F residue 1122 VAL Chi-restraints excluded: chain G residue 360 MET Chi-restraints excluded: chain G residue 514 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: chunk 302 optimal weight: 4.9990 chunk 369 optimal weight: 4.9990 chunk 150 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 409 optimal weight: 20.0000 chunk 317 optimal weight: 0.9990 chunk 396 optimal weight: 0.9990 chunk 216 optimal weight: 0.9990 chunk 23 optimal weight: 5.9990 chunk 308 optimal weight: 4.9990 chunk 311 optimal weight: 5.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4508 r_free = 0.4508 target = 0.188411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.128010 restraints weight = 79636.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.131881 restraints weight = 41294.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.131213 restraints weight = 24327.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.132423 restraints weight = 18905.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.132386 restraints weight = 17025.588| |-----------------------------------------------------------------------------| r_work (final): 0.3729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7237 moved from start: 0.2152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 36712 Z= 0.139 Angle : 0.591 13.451 50020 Z= 0.293 Chirality : 0.044 0.338 5676 Planarity : 0.004 0.099 6372 Dihedral : 6.731 101.033 6220 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.70 % Favored : 92.18 % Rotamer: Outliers : 1.43 % Allowed : 14.98 % Favored : 83.58 % 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 aren not related in a simple way. whole: -0.67 (0.13), residues: 4374 helix: 1.67 (0.15), residues: 1309 sheet: -0.71 (0.20), residues: 669 loop : -1.65 (0.13), residues: 2396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C1107 TYR 0.020 0.001 TYR B 160 PHE 0.021 0.001 PHE G 464 TRP 0.029 0.001 TRP D 48 HIS 0.008 0.001 HIS D 373 Details of bonding type rmsd covalent geometry : bond 0.00323 (36628) covalent geometry : angle 0.58340 (49837) SS BOND : bond 0.00248 ( 42) SS BOND : angle 1.37935 ( 84) hydrogen bonds : bond 0.03543 ( 1325) hydrogen bonds : angle 5.00241 ( 3765) metal coordination : bond 0.01906 ( 4) Misc. bond : bond 0.00078 ( 5) link_BETA1-4 : bond 0.00487 ( 9) link_BETA1-4 : angle 1.90911 ( 27) link_NAG-ASN : bond 0.00243 ( 24) link_NAG-ASN : angle 1.91933 ( 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 268 residues out of total 3860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 213 time to evaluate : 1.198 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 646 ARG cc_start: 0.6885 (tpm170) cc_final: 0.6469 (tpm170) REVERT: B 759 PHE cc_start: 0.8373 (OUTLIER) cc_final: 0.8122 (t80) REVERT: B 878 LEU cc_start: 0.8647 (OUTLIER) cc_final: 0.8277 (mp) REVERT: B 1002 GLN cc_start: 0.8516 (tm-30) cc_final: 0.8099 (tm-30) REVERT: B 1029 MET cc_start: 0.8797 (tpp) cc_final: 0.8347 (ttm) REVERT: C 389 ASP cc_start: 0.7709 (t0) cc_final: 0.7496 (t0) REVERT: C 453 TYR cc_start: 0.7886 (p90) cc_final: 0.7283 (p90) REVERT: C 568 ASP cc_start: 0.7984 (p0) cc_final: 0.7685 (p0) REVERT: C 780 GLU cc_start: 0.7811 (OUTLIER) cc_final: 0.7417 (mp0) REVERT: C 955 ASN cc_start: 0.8787 (m-40) cc_final: 0.8414 (t0) REVERT: C 1095 PHE cc_start: 0.8322 (OUTLIER) cc_final: 0.7518 (t80) REVERT: C 1123 SER cc_start: 0.8397 (t) cc_final: 0.8148 (p) REVERT: D 462 MET cc_start: -0.1405 (mmm) cc_final: -0.1613 (mmm) REVERT: F 224 GLU cc_start: 0.7862 (pm20) cc_final: 0.7414 (pm20) REVERT: G 514 ARG cc_start: 0.1624 (tmm-80) cc_final: 0.1189 (mtm180) outliers start: 55 outliers final: 44 residues processed: 252 average time/residue: 0.1802 time to fit residues: 79.2152 Evaluate side-chains 259 residues out of total 3860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 211 time to evaluate : 1.289 ------------------------------------------------------------------------------- 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 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 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 277 LEU Chi-restraints excluded: chain C residue 350 VAL 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 620 VAL Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 738 CYS 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 118 LEU 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 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 360 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: chunk 47 optimal weight: 20.0000 chunk 177 optimal weight: 5.9990 chunk 302 optimal weight: 4.9990 chunk 185 optimal weight: 4.9990 chunk 81 optimal weight: 0.6980 chunk 413 optimal weight: 5.9990 chunk 126 optimal weight: 9.9990 chunk 225 optimal weight: 0.6980 chunk 327 optimal weight: 0.2980 chunk 181 optimal weight: 2.9990 chunk 354 optimal weight: 0.6980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 148 ASN ** 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 = 0.4516 r_free = 0.4516 target = 0.189110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.128557 restraints weight = 78943.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.132275 restraints weight = 40802.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.131346 restraints weight = 24362.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.132476 restraints weight = 19904.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.132488 restraints weight = 17346.944| |-----------------------------------------------------------------------------| r_work (final): 0.3734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7243 moved from start: 0.2244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 36712 Z= 0.118 Angle : 0.584 13.014 50020 Z= 0.289 Chirality : 0.043 0.269 5676 Planarity : 0.004 0.099 6372 Dihedral : 6.653 100.945 6220 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.27 % Favored : 92.62 % Rotamer: Outliers : 1.30 % Allowed : 15.27 % 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 aren not related in a simple way. whole: -0.64 (0.13), residues: 4374 helix: 1.67 (0.15), residues: 1317 sheet: -0.72 (0.20), residues: 676 loop : -1.63 (0.13), residues: 2381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C1107 TYR 0.020 0.001 TYR C1067 PHE 0.023 0.001 PHE G 464 TRP 0.032 0.001 TRP D 48 HIS 0.008 0.001 HIS D 373 Details of bonding type rmsd covalent geometry : bond 0.00269 (36628) covalent geometry : angle 0.57657 (49837) SS BOND : bond 0.00234 ( 42) SS BOND : angle 1.19044 ( 84) hydrogen bonds : bond 0.03476 ( 1325) hydrogen bonds : angle 4.98107 ( 3765) metal coordination : bond 0.01785 ( 4) Misc. bond : bond 0.00078 ( 5) link_BETA1-4 : bond 0.00473 ( 9) link_BETA1-4 : angle 1.86433 ( 27) link_NAG-ASN : bond 0.00260 ( 24) link_NAG-ASN : angle 1.88574 ( 72) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8684.03 seconds wall clock time: 150 minutes 5.75 seconds (9005.75 seconds total)