Starting phenix.real_space_refine on Fri Mar 6 00:14:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7k8v_22732/03_2026/7k8v_22732_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7k8v_22732/03_2026/7k8v_22732.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7k8v_22732/03_2026/7k8v_22732.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7k8v_22732/03_2026/7k8v_22732.map" model { file = "/net/cci-nas-00/data/ceres_data/7k8v_22732/03_2026/7k8v_22732_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7k8v_22732/03_2026/7k8v_22732_neut.cif" } resolution = 3.8 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= 0.002 sd= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 114 5.16 5 C 16767 2.51 5 N 4319 2.21 5 O 5048 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 164 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 26248 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 7451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 978, 7451 Classifications: {'peptide': 978} Incomplete info: {'truncation_to_alanine': 56} Link IDs: {'PTRANS': 47, 'TRANS': 930} Chain breaks: 12 Unresolved non-hydrogen bonds: 215 Unresolved non-hydrogen angles: 271 Unresolved non-hydrogen dihedrals: 176 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ASN:plan1': 6, 'ASP:plan': 12, 'PHE:plan': 3, 'GLU:plan': 12, 'TYR:plan': 3, 'GLN:plan1': 1, 'HIS:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 155 Chain: "B" Number of atoms: 7416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 973, 7416 Classifications: {'peptide': 973} Incomplete info: {'truncation_to_alanine': 58} Link IDs: {'PTRANS': 47, 'TRANS': 925} Chain breaks: 13 Unresolved non-hydrogen bonds: 215 Unresolved non-hydrogen angles: 271 Unresolved non-hydrogen dihedrals: 172 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ASP:plan': 9, 'ASN:plan1': 6, 'GLU:plan': 14, 'GLN:plan1': 5, 'TYR:plan': 3, 'PHE:plan': 1, 'HIS:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 158 Chain: "C" Number of atoms: 7433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 977, 7433 Classifications: {'peptide': 977} Incomplete info: {'truncation_to_alanine': 64} Link IDs: {'PTRANS': 47, 'TRANS': 929} Chain breaks: 11 Unresolved non-hydrogen bonds: 224 Unresolved non-hydrogen angles: 282 Unresolved non-hydrogen dihedrals: 179 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ASN:plan1': 6, 'ASP:plan': 13, 'GLN:plan1': 3, 'GLU:plan': 15, 'TYR:plan': 3, 'PHE:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 161 Chain: "H" Number of atoms: 891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 891 Classifications: {'peptide': 126} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 6, 'TRANS': 119} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 87 Unresolved non-hydrogen angles: 104 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 4, 'PHE:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 49 Chain: "L" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 796 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 98} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 20 Chain: "M" Number of atoms: 891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 891 Classifications: {'peptide': 126} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 6, 'TRANS': 119} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 87 Unresolved non-hydrogen angles: 104 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 4, 'PHE:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 49 Chain: "N" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 796 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 98} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 20 Chain: "D" 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: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 6.65, per 1000 atoms: 0.25 Number of scatterers: 26248 At special positions: 0 Unit cell: (127.908, 139.612, 200.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 114 16.00 O 5048 8.00 N 4319 7.00 C 16767 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=40, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS 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=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 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=2.02 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 538 " - pdb=" SG CYS C 590 " distance=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.02 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 H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 92 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 343 " " NAG A1304 " - " ASN A 616 " " NAG A1305 " - " ASN A 657 " " NAG A1306 " - " ASN A 709 " " NAG A1307 " - " ASN A 801 " " NAG A1308 " - " ASN A1074 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 234 " " NAG B1304 " - " ASN B 343 " " NAG B1305 " - " ASN B 616 " " NAG B1306 " - " ASN B 657 " " NAG B1307 " - " ASN B 709 " " NAG B1308 " - " ASN B 717 " " NAG B1309 " - " ASN B1074 " " NAG B1310 " - " ASN B1098 " " NAG C1301 " - " ASN C 234 " " NAG C1302 " - " ASN C 709 " " NAG C1303 " - " ASN C1074 " " NAG D 1 " - " ASN A 234 " " NAG E 1 " - " ASN A 717 " " NAG F 1 " - " ASN A1098 " " NAG G 1 " - " ASN A1134 " " NAG I 1 " - " ASN B 801 " " NAG J 1 " - " ASN B1134 " " NAG K 1 " - " ASN C 717 " " NAG O 1 " - " ASN C 801 " " NAG P 1 " - " ASN C1098 " " NAG Q 1 " - " ASN C 343 " Time building additional restraints: 1.99 Conformation dependent library (CDL) restraints added in 925.4 milliseconds 6608 Ramachandran restraints generated. 3304 Oldfield, 0 Emsley, 3304 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6350 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 62 sheets defined 22.7% alpha, 24.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.18 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 364 through 371 removed outlier: 4.243A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 737 through 744 removed outlier: 3.629A pdb=" N GLY A 744 " --> pdb=" O MET A 740 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 755 removed outlier: 3.537A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.166A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 968 removed outlier: 3.831A pdb=" N LEU A 966 " --> pdb=" O LEU A 962 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N SER A 967 " --> pdb=" O VAL A 963 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.907A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 3.757A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 337 through 341 Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 383 through 387 removed outlier: 3.840A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 407 removed outlier: 3.743A pdb=" N GLU B 406 " --> pdb=" O ARG B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 755 Processing helix chain 'B' and resid 758 through 783 Processing helix chain 'B' and resid 816 through 825 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.058A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 968 removed outlier: 3.829A pdb=" N LEU B 966 " --> pdb=" O LEU B 962 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 982 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.914A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 365 through 371 Processing helix chain 'C' and resid 406 through 410 Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 737 through 744 removed outlier: 3.594A pdb=" N GLY C 744 " --> pdb=" O MET C 740 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 782 Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 912 through 941 removed outlier: 3.975A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N LYS C 921 " --> pdb=" O TYR C 917 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N LEU C 922 " --> pdb=" O GLU C 918 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 967 removed outlier: 3.725A pdb=" N LEU C 966 " --> pdb=" O LEU C 962 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER C 967 " --> pdb=" O VAL C 963 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.693A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1147 Processing helix chain 'H' and resid 60 through 64 removed outlier: 3.794A pdb=" N GLN H 64 " --> pdb=" O PRO H 61 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.620A pdb=" N THR H 87 " --> pdb=" O ALA H 84 " (cutoff:3.500A) Processing helix chain 'M' and resid 60 through 64 removed outlier: 3.695A pdb=" N GLN M 64 " --> pdb=" O PRO M 61 " (cutoff:3.500A) Processing helix chain 'M' and resid 83 through 87 removed outlier: 3.728A pdb=" N THR M 87 " --> pdb=" O ALA M 84 " (cutoff:3.500A) Processing helix chain 'N' and resid 50 through 52 No H-bonds generated for 'chain 'N' and resid 50 through 52' Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.721A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.733A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N THR C 553 " --> pdb=" O ASP C 586 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N THR C 588 " --> pdb=" O VAL C 551 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLY C 548 " --> pdb=" O PHE C 541 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLY C 550 " --> pdb=" O VAL C 539 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL C 539 " --> pdb=" O GLY C 550 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 50 through 55 removed outlier: 3.529A pdb=" N LYS A 278 " --> pdb=" O ASP A 287 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.895A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 224 through 230 removed outlier: 7.178A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE A 203 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU A 229 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LYS A 202 " --> pdb=" O LYS A 195 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N LYS A 195 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N TYR A 204 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N PHE A 194 " --> pdb=" O VAL A 90 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N VAL A 90 " --> pdb=" O PHE A 194 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N TYR A 91 " --> pdb=" O GLY A 268 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N GLY A 268 " --> pdb=" O TYR A 91 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 95 through 96 removed outlier: 3.964A pdb=" N GLU A 96 " --> pdb=" O ASN A 188 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ASN A 188 " --> pdb=" O GLU A 96 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 118 through 121 Processing sheet with id=AA8, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.360A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 324 through 328 removed outlier: 6.926A pdb=" N GLU A 324 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 8.485A pdb=" N ASN A 542 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N ILE A 326 " --> pdb=" O ASN A 542 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.644A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA A 397 " --> pdb=" O LYS A 356 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N PHE A 400 " --> pdb=" O VAL A 510 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL A 510 " --> pdb=" O PHE A 400 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILE A 402 " --> pdb=" O TYR A 508 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N ARG A 509 " --> pdb=" O TRP A 436 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N TRP A 436 " --> pdb=" O ARG A 509 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS A 378 " --> pdb=" O VAL A 433 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ALA A 435 " --> pdb=" O THR A 376 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.392A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB4, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.849A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.168A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 712 through 724 removed outlier: 3.916A pdb=" N ILE A 712 " --> pdb=" O PHE A1075 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS A1073 " --> pdb=" O ILE A 714 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 727 through 728 removed outlier: 3.525A pdb=" N VAL A1060 " --> pdb=" O LEU A 727 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL A1061 " --> pdb=" O GLN A1054 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1123 removed outlier: 3.547A pdb=" N ILE A1081 " --> pdb=" O HIS A1088 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AC1, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.893A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 36 through 37 removed outlier: 7.450A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 10.156A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU B 226 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N LYS B 202 " --> pdb=" O LYS B 195 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N LYS B 195 " --> pdb=" O LYS B 202 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N THR B 208 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N PHE B 194 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N VAL B 90 " --> pdb=" O PHE B 194 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 36 through 37 removed outlier: 7.450A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 10.156A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU B 226 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N LYS B 202 " --> pdb=" O LYS B 195 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N LYS B 195 " --> pdb=" O LYS B 202 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N THR B 208 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N SER B 94 " --> pdb=" O ARG B 190 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.505A pdb=" N PHE B 55 " --> pdb=" O GLN B 271 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 83 through 85 removed outlier: 3.868A pdb=" N ARG B 237 " --> pdb=" O GLY B 107 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N GLY B 107 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLN B 239 " --> pdb=" O ILE B 105 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ILE B 105 " --> pdb=" O GLN B 239 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 118 through 121 removed outlier: 3.547A pdb=" N LEU B 118 " --> pdb=" O LYS B 129 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LYS B 129 " --> pdb=" O LEU B 118 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.325A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N SER B 596 " --> pdb=" O LEU B 611 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N TYR B 612 " --> pdb=" O CYS B 649 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N CYS B 649 " --> pdb=" O TYR B 612 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 325 through 327 Processing sheet with id=AC9, first strand: chain 'B' and resid 355 through 356 removed outlier: 3.537A pdb=" N ASP B 398 " --> pdb=" O VAL B 512 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N VAL B 512 " --> pdb=" O ASP B 398 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 361 through 362 removed outlier: 5.479A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'B' and resid 565 through 566 removed outlier: 6.954A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'B' and resid 575 through 577 Processing sheet with id=AD4, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.493A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N SER B 673 " --> pdb=" O ILE B 693 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 717 through 728 removed outlier: 6.702A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER B 721 " --> pdb=" O THR B1066 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N TYR B1047 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 717 through 728 removed outlier: 6.702A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER B 721 " --> pdb=" O THR B1066 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD8, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 3.721A pdb=" N PHE B1089 " --> pdb=" O PHE B1121 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AE1, first strand: chain 'C' and resid 36 through 37 removed outlier: 6.970A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 10.480A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 9.951A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ILE C 203 " --> pdb=" O VAL C 227 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.687A pdb=" N ARG C 273 " --> pdb=" O ASP C 53 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.586A pdb=" N GLN C 239 " --> pdb=" O ILE C 105 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE C 105 " --> pdb=" O GLN C 239 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 118 through 121 removed outlier: 3.766A pdb=" N TYR C 170 " --> pdb=" O ILE C 128 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.773A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N GLN C 613 " --> pdb=" O GLY C 594 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.780A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N PHE C 400 " --> pdb=" O VAL C 510 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL C 510 " --> pdb=" O PHE C 400 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ILE C 402 " --> pdb=" O TYR C 508 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TYR C 508 " --> pdb=" O ILE C 402 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ARG C 509 " --> pdb=" O TRP C 436 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N CYS C 432 " --> pdb=" O LEU C 513 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LYS C 378 " --> pdb=" O VAL C 433 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA C 435 " --> pdb=" O THR C 376 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.712A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE9, first strand: chain 'C' and resid 654 through 660 removed outlier: 3.677A pdb=" N GLU C 654 " --> pdb=" O ILE C 692 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N THR C 696 " --> pdb=" O VAL C 656 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ASN C 658 " --> pdb=" O THR C 696 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA C 672 " --> pdb=" O ILE C 664 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ILE C 664 " --> pdb=" O ALA C 672 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 711 through 719 removed outlier: 3.613A pdb=" N ILE C 714 " --> pdb=" O LYS C1073 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYS C1073 " --> pdb=" O ILE C 714 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA C1056 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 722 through 728 removed outlier: 3.749A pdb=" N THR C 723 " --> pdb=" O HIS C1064 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N HIS C1064 " --> pdb=" O THR C 723 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLU C 725 " --> pdb=" O PHE C1062 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AF4, first strand: chain 'C' and resid 1120 through 1123 removed outlier: 3.554A pdb=" N PHE C1089 " --> pdb=" O PHE C1121 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE C1081 " --> pdb=" O HIS C1088 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AF6, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AF7, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.267A pdb=" N GLU H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF7 Processing sheet with id=AF8, first strand: chain 'H' and resid 45 through 46 removed outlier: 3.922A pdb=" N VAL H 37 " --> pdb=" O TYR H 91 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N TYR H 91 " --> pdb=" O VAL H 37 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'H' and resid 50 through 52 removed outlier: 3.604A pdb=" N ILE H 50 " --> pdb=" O ARG H 58 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'L' and resid 5 through 7 removed outlier: 3.918A pdb=" N THR L 5 " --> pdb=" O ARG L 24 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG L 24 " --> pdb=" O THR L 5 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL L 19 " --> pdb=" O ILE L 75 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N SER L 63 " --> pdb=" O THR L 74 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'L' and resid 53 through 54 removed outlier: 6.416A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLN L 38 " --> pdb=" O THR L 85 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N THR L 85 " --> pdb=" O GLN L 38 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'M' and resid 3 through 6 removed outlier: 3.523A pdb=" N GLN M 3 " --> pdb=" O SER M 25 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'M' and resid 10 through 11 removed outlier: 6.006A pdb=" N GLU M 10 " --> pdb=" O THR M 110 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLN M 39 " --> pdb=" O MET M 89 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N TYR M 91 " --> pdb=" O VAL M 37 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N VAL M 37 " --> pdb=" O TYR M 91 " (cutoff:3.500A) removed outlier: 7.990A pdb=" N TRP M 36 " --> pdb=" O MET M 48 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N MET M 48 " --> pdb=" O TRP M 36 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ILE M 50 " --> pdb=" O ARG M 58 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'M' and resid 71 through 72 Processing sheet with id=AG6, first strand: chain 'N' and resid 6 through 7 removed outlier: 3.832A pdb=" N THR N 22 " --> pdb=" O SER N 7 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'N' and resid 45 through 46 removed outlier: 3.670A pdb=" N ALA N 34 " --> pdb=" O GLN N 89 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLN N 89 " --> pdb=" O ALA N 34 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'N' and resid 48 through 49 928 hydrogen bonds defined for protein. 2556 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: 6.57 Time building geometry restraints manager: 2.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 8320 1.35 - 1.47: 6842 1.47 - 1.59: 11508 1.59 - 1.71: 0 1.71 - 1.83: 148 Bond restraints: 26818 Sorted by residual: bond pdb=" C1 NAG B1303 " pdb=" O5 NAG B1303 " ideal model delta sigma weight residual 1.406 1.487 -0.081 2.00e-02 2.50e+03 1.62e+01 bond pdb=" N THR C 29 " pdb=" CA THR C 29 " ideal model delta sigma weight residual 1.456 1.490 -0.035 1.23e-02 6.61e+03 7.88e+00 bond pdb=" N VAL C 62 " pdb=" CA VAL C 62 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.25e-02 6.40e+03 7.73e+00 bond pdb=" N TYR C 28 " pdb=" CA TYR C 28 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.34e-02 5.57e+03 6.48e+00 bond pdb=" N ASN C 30 " pdb=" CA ASN C 30 " ideal model delta sigma weight residual 1.454 1.487 -0.033 1.31e-02 5.83e+03 6.37e+00 ... (remaining 26813 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.07: 35948 2.07 - 4.13: 566 4.13 - 6.20: 28 6.20 - 8.26: 7 8.26 - 10.33: 1 Bond angle restraints: 36550 Sorted by residual: angle pdb=" N PRO H 100G" pdb=" CA PRO H 100G" pdb=" CB PRO H 100G" ideal model delta sigma weight residual 103.25 111.28 -8.03 1.05e+00 9.07e-01 5.85e+01 angle pdb=" N PRO M 100G" pdb=" CA PRO M 100G" pdb=" CB PRO M 100G" ideal model delta sigma weight residual 103.25 111.25 -8.00 1.05e+00 9.07e-01 5.80e+01 angle pdb=" N PRO M 100 " pdb=" CA PRO M 100 " pdb=" CB PRO M 100 " ideal model delta sigma weight residual 103.25 111.08 -7.83 1.05e+00 9.07e-01 5.56e+01 angle pdb=" N PRO H 100 " pdb=" CA PRO H 100 " pdb=" CB PRO H 100 " ideal model delta sigma weight residual 103.25 111.02 -7.77 1.05e+00 9.07e-01 5.48e+01 angle pdb=" N GLU A 169 " pdb=" CA GLU A 169 " pdb=" C GLU A 169 " ideal model delta sigma weight residual 112.97 108.93 4.04 1.06e+00 8.90e-01 1.45e+01 ... (remaining 36545 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.40: 15460 22.40 - 44.81: 773 44.81 - 67.21: 100 67.21 - 89.61: 48 89.61 - 112.01: 11 Dihedral angle restraints: 16392 sinusoidal: 6545 harmonic: 9847 Sorted by residual: dihedral pdb=" CB CYS C 291 " pdb=" SG CYS C 291 " pdb=" SG CYS C 301 " pdb=" CB CYS C 301 " ideal model delta sinusoidal sigma weight residual 93.00 5.63 87.37 1 1.00e+01 1.00e-02 9.16e+01 dihedral pdb=" CB CYS C1032 " pdb=" SG CYS C1032 " pdb=" SG CYS C1043 " pdb=" CB CYS C1043 " ideal model delta sinusoidal sigma weight residual 93.00 -179.85 -87.15 1 1.00e+01 1.00e-02 9.12e+01 dihedral pdb=" CB CYS A 738 " pdb=" SG CYS A 738 " pdb=" SG CYS A 760 " pdb=" CB CYS A 760 " ideal model delta sinusoidal sigma weight residual -86.00 -1.49 -84.51 1 1.00e+01 1.00e-02 8.68e+01 ... (remaining 16389 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.338: 4340 0.338 - 0.677: 4 0.677 - 1.015: 2 1.015 - 1.354: 2 1.354 - 1.692: 3 Chirality restraints: 4351 Sorted by residual: chirality pdb=" C1 NAG I 2 " pdb=" O4 NAG I 1 " pdb=" C2 NAG I 2 " pdb=" O5 NAG I 2 " both_signs ideal model delta sigma weight residual False -2.40 -0.71 -1.69 2.00e-02 2.50e+03 7.16e+03 chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -0.73 -1.67 2.00e-02 2.50e+03 6.95e+03 chirality pdb=" C1 NAG G 2 " pdb=" O4 NAG G 1 " pdb=" C2 NAG G 2 " pdb=" O5 NAG G 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.02 -1.38 2.00e-02 2.50e+03 4.77e+03 ... (remaining 4348 not shown) Planarity restraints: 4669 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN C1142 " 0.044 5.00e-02 4.00e+02 6.64e-02 7.06e+00 pdb=" N PRO C1143 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO C1143 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO C1143 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU C 916 " -0.008 2.00e-02 2.50e+03 1.53e-02 2.34e+00 pdb=" C LEU C 916 " 0.026 2.00e-02 2.50e+03 pdb=" O LEU C 916 " -0.010 2.00e-02 2.50e+03 pdb=" N TYR C 917 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS M 13 " -0.025 5.00e-02 4.00e+02 3.81e-02 2.33e+00 pdb=" N PRO M 14 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO M 14 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO M 14 " -0.021 5.00e-02 4.00e+02 ... (remaining 4666 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.58: 312 2.58 - 3.16: 22012 3.16 - 3.74: 40640 3.74 - 4.32: 55245 4.32 - 4.90: 89374 Nonbonded interactions: 207583 Sorted by model distance: nonbonded pdb=" CG1 VAL C 62 " pdb=" O VAL C 267 " model vdw 2.005 3.460 nonbonded pdb=" O LEU A 966 " pdb=" OG SER A 975 " model vdw 2.146 3.040 nonbonded pdb=" O LEU B 966 " pdb=" OG SER B 975 " model vdw 2.169 3.040 nonbonded pdb=" O LEU C 966 " pdb=" OG SER C 975 " model vdw 2.176 3.040 nonbonded pdb=" NE2 GLN B 644 " pdb=" O THR B 645 " model vdw 2.192 3.120 ... (remaining 207578 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 45 or (resid 46 and (name N or name CA or name \ C or name O or name CB )) or resid 47 through 52 or (resid 53 and (name N or nam \ e CA or name C or name O or name CB )) or resid 54 through 66 or resid 82 throug \ h 87 or (resid 88 and (name N or name CA or name C or name O or name CB )) or re \ sid 89 through 95 or (resid 96 through 97 and (name N or name CA or name C or na \ me O or name CB )) or resid 98 through 109 or (resid 110 through 113 and (name N \ or name CA or name C or name O or name CB )) or resid 116 through 124 or (resid \ 125 and (name N or name CA or name C or name O or name CB )) or resid 126 throu \ gh 131 or (resid 132 and (name N or name CA or name C or name O or name CB )) or \ resid 133 or (resid 134 through 138 and (name N or name CA or name C or name O \ or name CB )) or resid 139 through 140 or resid 166 through 168 or (resid 169 an \ d (name N or name CA or name C or name O or name CB )) or resid 170 through 171 \ or (resid 172 and (name N or name CA or name C or name O or name CB )) or resid \ 186 through 190 or (resid 191 and (name N or name CA or name C or name O or name \ CB )) or resid 192 through 196 or resid 200 through 210 or (resid 211 and (name \ N or name CA or name C or name O or name CB )) or (resid 215 and (name N or nam \ e CA or name C or name O or name CB )) or resid 216 through 217 or (resid 218 an \ d (name N or name CA or name C or name O or name CB )) or resid 219 through 223 \ or (resid 224 and (name N or name CA or name C or name O or name CB )) or resid \ 225 through 238 or (resid 239 and (name N or name CA or name C or name O or name \ CB )) or resid 240 through 263 or resid 265 through 308 or (resid 309 and (name \ N or name CA or name C or name O or name CB )) or resid 310 through 323 or (res \ id 324 and (name N or name CA or name C or name O or name CB )) or resid 325 thr \ ough 332 or (resid 333 and (name N or name CA or name C or name O or name CB )) \ or resid 334 through 528 or (resid 529 and (name N or name CA or name C or name \ O or name CB )) or resid 530 through 553 or (resid 554 and (name N or name CA or \ name C or name O or name CB )) or resid 555 through 793 or (resid 794 and (name \ N or name CA or name C or name O or name CB )) or resid 795 or (resid 796 and ( \ name N or name CA or name C or name O or name CB )) or resid 797 through 810 or \ (resid 811 and (name N or name CA or name C or name O or name CB )) or resid 813 \ through 827 or resid 856 through 866 or (resid 867 through 868 and (name N or n \ ame CA or name C or name O or name CB )) or resid 869 through 939 or (resid 940 \ and (name N or name CA or name C or name O or name CB )) or resid 941 through 98 \ 4 or (resid 985 and (name N or name CA or name C or name O or name CB )) or resi \ d 986 through 987 or (resid 988 through 989 and (name N or name CA or name C or \ name O or name CB )) or resid 990 through 1141 or (resid 1142 and (name N or nam \ e CA or name C or name O or name CB )) or resid 1143 through 1144 or (resid 1145 \ through 1146 and (name N or name CA or name C or name O or name CB )) or resid \ 1147 through 1303)) selection = (chain 'B' and (resid 27 through 45 or (resid 46 and (name N or name CA or name \ C or name O or name CB )) or resid 47 through 66 or resid 82 through 87 or (resi \ d 88 and (name N or name CA or name C or name O or name CB )) or resid 89 throug \ h 96 or (resid 97 and (name N or name CA or name C or name O or name CB )) or re \ sid 98 or (resid 99 and (name N or name CA or name C or name O or name CB )) or \ resid 100 through 109 or (resid 110 through 113 and (name N or name CA or name C \ or name O or name CB )) or resid 116 through 128 or (resid 129 and (name N or n \ ame CA or name C or name O or name CB )) or resid 130 through 134 or (resid 135 \ through 138 and (name N or name CA or name C or name O or name CB )) or resid 13 \ 9 through 140 or resid 166 through 168 or (resid 169 and (name N or name CA or n \ ame C or name O or name CB )) or resid 170 through 187 or (resid 188 and (name N \ or name CA or name C or name O or name CB )) or resid 189 through 190 or (resid \ 191 and (name N or name CA or name C or name O or name CB )) or resid 192 throu \ gh 195 or (resid 196 and (name N or name CA or name C or name O or name CB )) or \ resid 200 through 210 or (resid 211 through 215 and (name N or name CA or name \ C or name O or name CB )) or resid 216 through 241 or (resid 242 through 263 and \ (name N or name CA or name C or name O or name CB )) or resid 265 through 280 o \ r (resid 281 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 82 through 323 or (resid 324 and (name N or name CA or name C or name O or name \ CB )) or resid 325 through 567 or (resid 568 and (name N or name CA or name C or \ name O or name CB )) or resid 569 through 570 or (resid 571 and (name N or name \ CA or name C or name O or name CB )) or resid 572 through 581 or (resid 582 thr \ ough 583 and (name N or name CA or name C or name O or name CB )) or resid 584 t \ hrough 585 or (resid 586 and (name N or name CA or name C or name O or name CB ) \ ) or resid 587 through 613 or (resid 614 and (name N or name CA or name C or nam \ e O or name CB )) or resid 615 through 618 or (resid 619 and (name N or name CA \ or name C or name O or name CB )) or resid 620 through 676 or resid 690 through \ 744 or (resid 745 and (name N or name CA or name C or name O or name CB )) or re \ sid 746 through 810 or (resid 811 and (name N or name CA or name C or name O or \ name CB )) or resid 813 through 827 or resid 856 through 866 or (resid 867 throu \ gh 868 and (name N or name CA or name C or name O or name CB )) or resid 869 thr \ ough 920 or (resid 921 and (name N or name CA or name C or name O or name CB )) \ or resid 922 through 939 or (resid 940 and (name N or name CA or name C or name \ O or name CB )) or resid 941 through 984 or (resid 985 and (name N or name CA or \ name C or name O or name CB )) or resid 986 through 987 or (resid 988 through 9 \ 89 and (name N or name CA or name C or name O or name CB )) or resid 990 through \ 1072 or (resid 1073 and (name N or name CA or name C or name O or name CB )) or \ resid 1074 through 1117 or (resid 1118 and (name N or name CA or name C or name \ O or name CB )) or resid 1119 through 1143 or (resid 1144 through 1146 and (nam \ e N or name CA or name C or name O or name CB )) or resid 1147 through 1303)) selection = (chain 'C' and (resid 27 through 52 or (resid 53 and (name N or name CA or name \ C or name O or name CB )) or resid 54 through 66 or resid 82 through 95 or (resi \ d 96 through 97 and (name N or name CA or name C or name O or name CB )) or resi \ d 98 or (resid 99 and (name N or name CA or name C or name O or name CB )) or re \ sid 100 through 110 or (resid 111 through 113 and (name N or name CA or name C o \ r name O or name CB )) or resid 116 through 134 or (resid 135 through 138 and (n \ ame N or name CA or name C or name O or name CB )) or resid 139 through 140 or r \ esid 166 through 187 or (resid 188 and (name N or name CA or name C or name O or \ name CB )) or resid 189 through 195 or (resid 196 and (name N or name CA or nam \ e C or name O or name CB )) or resid 200 through 211 or resid 215 through 217 or \ (resid 218 and (name N or name CA or name C or name O or name CB )) or resid 21 \ 9 through 223 or (resid 224 and (name N or name CA or name C or name O or name C \ B )) or resid 225 through 238 or (resid 239 and (name N or name CA or name C or \ name O or name CB )) or resid 240 through 308 or (resid 309 and (name N or name \ CA or name C or name O or name CB )) or resid 310 through 332 or (resid 333 and \ (name N or name CA or name C or name O or name CB )) or resid 334 through 528 or \ (resid 529 and (name N or name CA or name C or name O or name CB )) or resid 53 \ 0 through 553 or (resid 554 and (name N or name CA or name C or name O or name C \ B )) or resid 555 through 567 or (resid 568 and (name N or name CA or name C or \ name O or name CB )) or resid 569 through 570 or (resid 571 and (name N or name \ CA or name C or name O or name CB )) or resid 572 through 581 or (resid 582 thro \ ugh 583 and (name N or name CA or name C or name O or name CB )) or resid 584 th \ rough 585 or (resid 586 and (name N or name CA or name C or name O or name CB )) \ or resid 587 through 618 or (resid 619 and (name N or name CA or name C or name \ O or name CB )) or resid 620 through 645 or (resid 646 through 647 and (name N \ or name CA or name C or name O or name CB )) or resid 648 through 793 or (resid \ 794 and (name N or name CA or name C or name O or name CB )) or resid 795 or (re \ sid 796 and (name N or name CA or name C or name O or name CB )) or resid 797 th \ rough 920 or (resid 921 and (name N or name CA or name C or name O or name CB )) \ or resid 922 through 1072 or (resid 1073 and (name N or name CA or name C or na \ me O or name CB )) or resid 1074 through 1117 or (resid 1118 and (name N or name \ CA or name C or name O or name CB )) or resid 1119 through 1141 or (resid 1142 \ and (name N or name CA or name C or name O or name CB )) or resid 1143 or (resid \ 1144 through 1146 and (name N or name CA or name C or name O or name CB )) or r \ esid 1147 through 1303)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'O' selection = chain 'P' selection = chain 'Q' } ncs_group { reference = chain 'H' selection = chain 'M' } ncs_group { reference = chain 'L' selection = chain 'N' } 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: 4.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.480 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 26.160 Find NCS groups from input model: 0.790 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 26899 Z= 0.189 Angle : 0.907 60.447 36753 Z= 0.426 Chirality : 0.069 1.692 4351 Planarity : 0.003 0.066 4638 Dihedral : 13.789 112.013 9922 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.75 % Favored : 95.10 % Rotamer: Outliers : 0.15 % Allowed : 4.00 % Favored : 95.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.90 (0.13), residues: 3304 helix: -1.11 (0.18), residues: 650 sheet: -1.52 (0.19), residues: 616 loop : -2.45 (0.12), residues: 2038 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 765 TYR 0.014 0.001 TYR L 91 PHE 0.017 0.001 PHE B 497 TRP 0.008 0.001 TRP M 36 HIS 0.005 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00327 (26818) covalent geometry : angle 0.62401 (36550) SS BOND : bond 0.00389 ( 40) SS BOND : angle 1.77635 ( 80) hydrogen bonds : bond 0.20973 ( 905) hydrogen bonds : angle 9.45044 ( 2556) link_BETA1-4 : bond 0.06439 ( 10) link_BETA1-4 : angle 22.28048 ( 30) link_NAG-ASN : bond 0.00502 ( 31) link_NAG-ASN : angle 3.01330 ( 93) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6608 Ramachandran restraints generated. 3304 Oldfield, 0 Emsley, 3304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6608 Ramachandran restraints generated. 3304 Oldfield, 0 Emsley, 3304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 291 time to evaluate : 0.749 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 PHE cc_start: 0.8763 (m-80) cc_final: 0.8265 (m-80) REVERT: A 360 ASN cc_start: 0.9503 (m-40) cc_final: 0.8653 (t0) REVERT: A 392 PHE cc_start: 0.7725 (m-80) cc_final: 0.7468 (m-10) REVERT: A 421 TYR cc_start: 0.9165 (m-10) cc_final: 0.8831 (m-10) REVERT: A 776 LYS cc_start: 0.9522 (tttt) cc_final: 0.9193 (tptt) REVERT: A 869 MET cc_start: 0.8996 (mtm) cc_final: 0.8372 (mtp) REVERT: A 872 GLN cc_start: 0.9205 (mt0) cc_final: 0.8989 (tp-100) REVERT: A 887 THR cc_start: 0.5163 (p) cc_final: 0.4962 (p) REVERT: A 1119 ASN cc_start: 0.9113 (t0) cc_final: 0.8672 (p0) REVERT: B 720 ILE cc_start: 0.8064 (mm) cc_final: 0.7653 (mm) REVERT: B 759 PHE cc_start: 0.8350 (m-80) cc_final: 0.7959 (m-80) REVERT: B 776 LYS cc_start: 0.9413 (tttt) cc_final: 0.8935 (tptt) REVERT: B 950 ASP cc_start: 0.9203 (t0) cc_final: 0.8911 (t0) REVERT: B 1017 GLU cc_start: 0.9269 (tt0) cc_final: 0.8619 (tp30) REVERT: B 1031 GLU cc_start: 0.8030 (tt0) cc_final: 0.7331 (tt0) REVERT: B 1107 ARG cc_start: 0.7759 (ptp-170) cc_final: 0.7367 (mtp180) REVERT: C 49 HIS cc_start: 0.7650 (t70) cc_final: 0.7404 (t-170) REVERT: C 699 LEU cc_start: 0.8393 (mm) cc_final: 0.8055 (mm) REVERT: C 780 GLU cc_start: 0.9015 (mt-10) cc_final: 0.8694 (mt-10) REVERT: C 913 GLN cc_start: 0.6339 (pt0) cc_final: 0.5793 (mt0) REVERT: C 1107 ARG cc_start: 0.7271 (mtt-85) cc_final: 0.6714 (mtt90) REVERT: C 1138 TYR cc_start: 0.9009 (t80) cc_final: 0.8752 (t80) REVERT: H 4 LEU cc_start: 0.8691 (tt) cc_final: 0.8060 (mm) REVERT: H 56 ASP cc_start: 0.8488 (t0) cc_final: 0.8184 (m-30) REVERT: L 4 MET cc_start: 0.7266 (mtp) cc_final: 0.5560 (tpp) REVERT: L 39 LYS cc_start: 0.8019 (mttt) cc_final: 0.7758 (mmtt) REVERT: M 89 MET cc_start: 0.8955 (ttm) cc_final: 0.8529 (tpp) outliers start: 4 outliers final: 2 residues processed: 295 average time/residue: 0.1823 time to fit residues: 82.8717 Evaluate side-chains 172 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 170 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 30 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 197 optimal weight: 10.0000 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 0.4980 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 5.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 658 ASN ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN A 953 ASN A1011 GLN A1036 GLN ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 331 ASN ** B 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 437 ASN B 439 ASN B 448 ASN ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 580 GLN B 675 GLN B 762 GLN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 949 GLN B 957 GLN C 207 HIS C 804 GLN C 901 GLN C 965 GLN H 3 GLN L 92 ASN ** M 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 37 GLN N 92 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.071810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.050209 restraints weight = 148944.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.052053 restraints weight = 76924.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.053293 restraints weight = 48684.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.054132 restraints weight = 34790.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.054631 restraints weight = 27476.626| |-----------------------------------------------------------------------------| r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.1474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 26899 Z= 0.146 Angle : 0.637 11.507 36753 Z= 0.322 Chirality : 0.046 0.362 4351 Planarity : 0.004 0.073 4638 Dihedral : 8.385 96.863 4462 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.12 % Favored : 94.76 % Rotamer: Outliers : 1.17 % Allowed : 8.69 % Favored : 90.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.13 (0.13), residues: 3304 helix: -0.17 (0.19), residues: 664 sheet: -1.31 (0.18), residues: 673 loop : -1.95 (0.13), residues: 1967 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG M 38 TYR 0.019 0.001 TYR N 49 PHE 0.025 0.001 PHE A 515 TRP 0.017 0.001 TRP H 82 HIS 0.013 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00309 (26818) covalent geometry : angle 0.61615 (36550) SS BOND : bond 0.00368 ( 40) SS BOND : angle 1.64024 ( 80) hydrogen bonds : bond 0.05062 ( 905) hydrogen bonds : angle 7.16177 ( 2556) link_BETA1-4 : bond 0.00653 ( 10) link_BETA1-4 : angle 1.90898 ( 30) link_NAG-ASN : bond 0.00585 ( 31) link_NAG-ASN : angle 2.76099 ( 93) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6608 Ramachandran restraints generated. 3304 Oldfield, 0 Emsley, 3304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6608 Ramachandran restraints generated. 3304 Oldfield, 0 Emsley, 3304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 184 time to evaluate : 0.857 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 PHE cc_start: 0.8773 (m-80) cc_final: 0.8255 (m-80) REVERT: A 201 PHE cc_start: 0.9381 (t80) cc_final: 0.9134 (m-80) REVERT: A 776 LYS cc_start: 0.9451 (tttt) cc_final: 0.9132 (tptt) REVERT: A 869 MET cc_start: 0.8880 (mtm) cc_final: 0.8273 (mtp) REVERT: A 1107 ARG cc_start: 0.7552 (mtt-85) cc_final: 0.7144 (mtt-85) REVERT: A 1119 ASN cc_start: 0.9069 (t0) cc_final: 0.8504 (p0) REVERT: B 166 CYS cc_start: 0.6362 (OUTLIER) cc_final: 0.6015 (t) REVERT: B 731 MET cc_start: 0.9128 (ptm) cc_final: 0.8747 (ptm) REVERT: B 759 PHE cc_start: 0.8149 (m-80) cc_final: 0.7857 (m-80) REVERT: B 776 LYS cc_start: 0.9412 (tttt) cc_final: 0.8975 (tptt) REVERT: B 950 ASP cc_start: 0.8944 (t0) cc_final: 0.8655 (t0) REVERT: B 1017 GLU cc_start: 0.9063 (tt0) cc_final: 0.8475 (tp30) REVERT: B 1031 GLU cc_start: 0.7854 (tt0) cc_final: 0.7497 (tt0) REVERT: B 1107 ARG cc_start: 0.7600 (ptp-170) cc_final: 0.7196 (mtp-110) REVERT: C 902 MET cc_start: 0.8438 (mmt) cc_final: 0.7937 (tpp) REVERT: C 1029 MET cc_start: 0.9118 (tpp) cc_final: 0.8882 (tpp) REVERT: C 1107 ARG cc_start: 0.7566 (mtt-85) cc_final: 0.7090 (mtt-85) REVERT: C 1138 TYR cc_start: 0.8776 (t80) cc_final: 0.8527 (t80) REVERT: H 4 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.8459 (mm) REVERT: H 56 ASP cc_start: 0.8775 (t0) cc_final: 0.8474 (m-30) REVERT: H 89 MET cc_start: 0.6110 (tpt) cc_final: 0.5474 (tpt) REVERT: L 4 MET cc_start: 0.7038 (mtp) cc_final: 0.5389 (tpp) REVERT: M 34 ILE cc_start: 0.8265 (tt) cc_final: 0.8037 (tp) REVERT: M 36 TRP cc_start: 0.5734 (m100) cc_final: 0.4902 (m100) REVERT: M 45 LEU cc_start: 0.5179 (mp) cc_final: 0.4891 (mt) REVERT: M 89 MET cc_start: 0.9050 (ttm) cc_final: 0.8801 (tpp) outliers start: 32 outliers final: 16 residues processed: 205 average time/residue: 0.1632 time to fit residues: 53.3697 Evaluate side-chains 164 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 146 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain M residue 38 ARG Chi-restraints excluded: chain M residue 108 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 248 optimal weight: 9.9990 chunk 115 optimal weight: 20.0000 chunk 139 optimal weight: 2.9990 chunk 203 optimal weight: 0.5980 chunk 325 optimal weight: 20.0000 chunk 56 optimal weight: 0.6980 chunk 288 optimal weight: 10.0000 chunk 187 optimal weight: 3.9990 chunk 268 optimal weight: 4.9990 chunk 201 optimal weight: 7.9990 chunk 191 optimal weight: 10.0000 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 804 GLN A 920 GLN ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 784 GLN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1058 HIS L 37 GLN ** M 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.069849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.048188 restraints weight = 149038.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.049964 restraints weight = 76474.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.051157 restraints weight = 48322.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.051949 restraints weight = 34746.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.052439 restraints weight = 27580.061| |-----------------------------------------------------------------------------| r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.2224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 26899 Z= 0.154 Angle : 0.601 10.299 36753 Z= 0.305 Chirality : 0.045 0.444 4351 Planarity : 0.004 0.071 4638 Dihedral : 6.743 91.540 4462 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.99 % Favored : 94.88 % Rotamer: Outliers : 1.61 % Allowed : 11.48 % Favored : 86.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.73 (0.14), residues: 3304 helix: 0.26 (0.20), residues: 652 sheet: -1.13 (0.18), residues: 644 loop : -1.70 (0.13), residues: 2008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 214 TYR 0.018 0.001 TYR H 79 PHE 0.021 0.001 PHE A 515 TRP 0.023 0.002 TRP M 36 HIS 0.009 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00327 (26818) covalent geometry : angle 0.57714 (36550) SS BOND : bond 0.00407 ( 40) SS BOND : angle 1.84043 ( 80) hydrogen bonds : bond 0.04541 ( 905) hydrogen bonds : angle 6.43131 ( 2556) link_BETA1-4 : bond 0.00563 ( 10) link_BETA1-4 : angle 1.89311 ( 30) link_NAG-ASN : bond 0.00556 ( 31) link_NAG-ASN : angle 2.75173 ( 93) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6608 Ramachandran restraints generated. 3304 Oldfield, 0 Emsley, 3304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6608 Ramachandran restraints generated. 3304 Oldfield, 0 Emsley, 3304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 165 time to evaluate : 0.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 PHE cc_start: 0.8833 (m-80) cc_final: 0.8287 (m-80) REVERT: A 776 LYS cc_start: 0.9492 (tttt) cc_final: 0.9197 (tptt) REVERT: A 869 MET cc_start: 0.8966 (mtm) cc_final: 0.8348 (mtp) REVERT: A 1107 ARG cc_start: 0.7669 (mtt-85) cc_final: 0.7206 (mtt-85) REVERT: B 166 CYS cc_start: 0.6331 (OUTLIER) cc_final: 0.5882 (t) REVERT: B 731 MET cc_start: 0.9185 (ptm) cc_final: 0.8815 (ptm) REVERT: B 740 MET cc_start: 0.9157 (tpp) cc_final: 0.8932 (tpp) REVERT: B 759 PHE cc_start: 0.8379 (m-80) cc_final: 0.8052 (m-80) REVERT: B 776 LYS cc_start: 0.9453 (tttt) cc_final: 0.9075 (tptt) REVERT: B 950 ASP cc_start: 0.9023 (t0) cc_final: 0.8731 (t0) REVERT: B 1031 GLU cc_start: 0.7942 (tt0) cc_final: 0.7599 (tt0) REVERT: C 436 TRP cc_start: 0.7784 (OUTLIER) cc_final: 0.7509 (m-10) REVERT: C 1107 ARG cc_start: 0.7741 (mtt-85) cc_final: 0.7093 (mtt-85) REVERT: C 1138 TYR cc_start: 0.8854 (t80) cc_final: 0.8636 (t80) REVERT: H 56 ASP cc_start: 0.8822 (t0) cc_final: 0.8527 (m-30) REVERT: L 4 MET cc_start: 0.7008 (mtp) cc_final: 0.5349 (tpp) REVERT: L 22 THR cc_start: 0.9187 (OUTLIER) cc_final: 0.8733 (p) REVERT: M 45 LEU cc_start: 0.5370 (mp) cc_final: 0.4995 (mt) REVERT: M 89 MET cc_start: 0.9040 (ttm) cc_final: 0.8792 (tpp) outliers start: 44 outliers final: 21 residues processed: 198 average time/residue: 0.1572 time to fit residues: 50.5152 Evaluate side-chains 154 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 130 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 436 TRP Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain H residue 32 TYR Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain M residue 108 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 160 optimal weight: 10.0000 chunk 129 optimal weight: 0.0370 chunk 204 optimal weight: 20.0000 chunk 283 optimal weight: 2.9990 chunk 249 optimal weight: 7.9990 chunk 37 optimal weight: 40.0000 chunk 153 optimal weight: 4.9990 chunk 266 optimal weight: 6.9990 chunk 163 optimal weight: 9.9990 chunk 214 optimal weight: 7.9990 chunk 184 optimal weight: 10.0000 overall best weight: 4.6066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 HIS ** B 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 641 ASN H 3 GLN L 27 GLN N 92 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.070174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.046371 restraints weight = 154508.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.047913 restraints weight = 80098.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.048865 restraints weight = 51449.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.049475 restraints weight = 38530.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 59)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.049947 restraints weight = 32049.801| |-----------------------------------------------------------------------------| r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.3117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 26899 Z= 0.215 Angle : 0.657 10.415 36753 Z= 0.335 Chirality : 0.045 0.403 4351 Planarity : 0.004 0.068 4638 Dihedral : 6.352 84.685 4462 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.14 % Favored : 93.73 % Rotamer: Outliers : 2.27 % Allowed : 14.12 % Favored : 83.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.62 (0.14), residues: 3304 helix: 0.36 (0.20), residues: 647 sheet: -1.07 (0.18), residues: 661 loop : -1.61 (0.14), residues: 1996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 237 TYR 0.031 0.002 TYR H 91 PHE 0.022 0.002 PHE B1089 TRP 0.029 0.002 TRP M 47 HIS 0.008 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00454 (26818) covalent geometry : angle 0.63230 (36550) SS BOND : bond 0.00633 ( 40) SS BOND : angle 2.25918 ( 80) hydrogen bonds : bond 0.04654 ( 905) hydrogen bonds : angle 6.36665 ( 2556) link_BETA1-4 : bond 0.00552 ( 10) link_BETA1-4 : angle 1.83721 ( 30) link_NAG-ASN : bond 0.00614 ( 31) link_NAG-ASN : angle 2.86685 ( 93) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6608 Ramachandran restraints generated. 3304 Oldfield, 0 Emsley, 3304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6608 Ramachandran restraints generated. 3304 Oldfield, 0 Emsley, 3304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 140 time to evaluate : 0.978 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 PHE cc_start: 0.8957 (m-80) cc_final: 0.8437 (m-80) REVERT: A 201 PHE cc_start: 0.9517 (t80) cc_final: 0.9215 (m-80) REVERT: A 776 LYS cc_start: 0.9502 (tttt) cc_final: 0.9179 (tptt) REVERT: A 869 MET cc_start: 0.8953 (mtm) cc_final: 0.8501 (mtp) REVERT: A 1107 ARG cc_start: 0.7799 (mtt-85) cc_final: 0.7479 (mtt-85) REVERT: A 1129 VAL cc_start: 0.8367 (t) cc_final: 0.8063 (p) REVERT: B 166 CYS cc_start: 0.6985 (OUTLIER) cc_final: 0.6615 (t) REVERT: B 731 MET cc_start: 0.9147 (ptm) cc_final: 0.8897 (ptm) REVERT: B 740 MET cc_start: 0.9150 (tpp) cc_final: 0.8891 (tpp) REVERT: B 776 LYS cc_start: 0.9457 (tttt) cc_final: 0.9147 (tptt) REVERT: B 950 ASP cc_start: 0.8986 (t0) cc_final: 0.8689 (t0) REVERT: B 1031 GLU cc_start: 0.7981 (tt0) cc_final: 0.7719 (tt0) REVERT: B 1107 ARG cc_start: 0.7338 (ptp-170) cc_final: 0.6970 (ptp-170) REVERT: C 1107 ARG cc_start: 0.7828 (mtt-85) cc_final: 0.7281 (mtt-85) REVERT: C 1138 TYR cc_start: 0.8986 (t80) cc_final: 0.8748 (t80) REVERT: L 4 MET cc_start: 0.7440 (mtp) cc_final: 0.6514 (tpp) REVERT: M 45 LEU cc_start: 0.4547 (mp) cc_final: 0.4150 (mt) REVERT: N 46 LEU cc_start: 0.4579 (OUTLIER) cc_final: 0.3280 (tt) outliers start: 62 outliers final: 36 residues processed: 191 average time/residue: 0.1557 time to fit residues: 48.4666 Evaluate side-chains 162 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 124 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 1061 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 966 LEU Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 749 CYS Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain H residue 32 TYR Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain N residue 46 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 302 optimal weight: 50.0000 chunk 242 optimal weight: 9.9990 chunk 223 optimal weight: 20.0000 chunk 2 optimal weight: 9.9990 chunk 91 optimal weight: 10.0000 chunk 248 optimal weight: 3.9990 chunk 145 optimal weight: 7.9990 chunk 312 optimal weight: 20.0000 chunk 142 optimal weight: 9.9990 chunk 115 optimal weight: 0.9980 chunk 52 optimal weight: 9.9990 overall best weight: 6.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 710 ASN ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1119 ASN ** B 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 935 GLN B1011 GLN C 188 ASN C 953 ASN C1101 HIS ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 90 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.067200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.043784 restraints weight = 156825.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.044998 restraints weight = 82035.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.045866 restraints weight = 53703.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 61)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.046508 restraints weight = 40652.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.046882 restraints weight = 33921.449| |-----------------------------------------------------------------------------| r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.4402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.122 26899 Z= 0.301 Angle : 0.758 13.218 36753 Z= 0.387 Chirality : 0.048 0.411 4351 Planarity : 0.006 0.156 4638 Dihedral : 6.505 76.659 4462 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 16.87 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.17 % Favored : 92.71 % Rotamer: Outliers : 3.19 % Allowed : 16.10 % Favored : 80.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.87 (0.14), residues: 3304 helix: -0.02 (0.19), residues: 665 sheet: -1.30 (0.18), residues: 704 loop : -1.70 (0.14), residues: 1935 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 995 TYR 0.026 0.002 TYR C1067 PHE 0.034 0.003 PHE A1042 TRP 0.022 0.002 TRP M 36 HIS 0.010 0.002 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00632 (26818) covalent geometry : angle 0.73146 (36550) SS BOND : bond 0.00708 ( 40) SS BOND : angle 2.57455 ( 80) hydrogen bonds : bond 0.05269 ( 905) hydrogen bonds : angle 6.56662 ( 2556) link_BETA1-4 : bond 0.00467 ( 10) link_BETA1-4 : angle 2.24734 ( 30) link_NAG-ASN : bond 0.00645 ( 31) link_NAG-ASN : angle 3.10837 ( 93) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6608 Ramachandran restraints generated. 3304 Oldfield, 0 Emsley, 3304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6608 Ramachandran restraints generated. 3304 Oldfield, 0 Emsley, 3304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 124 time to evaluate : 0.949 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 697 MET cc_start: 0.8698 (ppp) cc_final: 0.8317 (ppp) REVERT: A 869 MET cc_start: 0.8992 (mtm) cc_final: 0.8622 (mtp) REVERT: B 166 CYS cc_start: 0.7461 (OUTLIER) cc_final: 0.7122 (t) REVERT: B 395 VAL cc_start: 0.8293 (OUTLIER) cc_final: 0.7951 (t) REVERT: B 571 ASP cc_start: 0.8749 (p0) cc_final: 0.8514 (p0) REVERT: B 731 MET cc_start: 0.9092 (ptm) cc_final: 0.8888 (ptm) REVERT: B 950 ASP cc_start: 0.8903 (t0) cc_final: 0.8618 (t0) REVERT: B 1107 ARG cc_start: 0.7084 (ptp-170) cc_final: 0.6813 (ptp-170) REVERT: C 424 LYS cc_start: 0.8408 (ttpt) cc_final: 0.7887 (ptpp) REVERT: C 743 CYS cc_start: 0.7541 (OUTLIER) cc_final: 0.6932 (p) REVERT: C 1107 ARG cc_start: 0.7590 (mtt-85) cc_final: 0.6748 (mtt90) REVERT: H 4 LEU cc_start: 0.8157 (mm) cc_final: 0.7804 (tt) REVERT: H 109 VAL cc_start: 0.4328 (OUTLIER) cc_final: 0.3933 (t) REVERT: L 4 MET cc_start: 0.7435 (mtp) cc_final: 0.6470 (tpp) REVERT: L 90 GLN cc_start: 0.9111 (OUTLIER) cc_final: 0.8606 (pp30) REVERT: M 45 LEU cc_start: 0.4708 (mp) cc_final: 0.4337 (mt) REVERT: N 46 LEU cc_start: 0.4923 (OUTLIER) cc_final: 0.3592 (tt) outliers start: 87 outliers final: 47 residues processed: 199 average time/residue: 0.1511 time to fit residues: 49.7316 Evaluate side-chains 154 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 101 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 777 ASN Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1061 VAL Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 436 TRP Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 749 CYS Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain H residue 32 TYR Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain M residue 32 TYR Chi-restraints excluded: chain M residue 108 MET Chi-restraints excluded: chain N residue 46 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 77 optimal weight: 1.9990 chunk 169 optimal weight: 6.9990 chunk 139 optimal weight: 7.9990 chunk 289 optimal weight: 5.9990 chunk 271 optimal weight: 2.9990 chunk 82 optimal weight: 0.9990 chunk 229 optimal weight: 30.0000 chunk 106 optimal weight: 3.9990 chunk 74 optimal weight: 0.9980 chunk 201 optimal weight: 7.9990 chunk 51 optimal weight: 10.0000 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN ** B 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 953 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.068702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.044950 restraints weight = 154153.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.046372 restraints weight = 79418.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 63)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.047304 restraints weight = 51518.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 71)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.047935 restraints weight = 38603.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.048339 restraints weight = 32086.162| |-----------------------------------------------------------------------------| r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.4449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 26899 Z= 0.146 Angle : 0.626 12.397 36753 Z= 0.315 Chirality : 0.045 0.381 4351 Planarity : 0.004 0.063 4638 Dihedral : 6.010 65.785 4462 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.36 % Favored : 94.52 % Rotamer: Outliers : 2.16 % Allowed : 17.68 % Favored : 80.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.53 (0.14), residues: 3304 helix: 0.55 (0.20), residues: 651 sheet: -1.18 (0.18), residues: 712 loop : -1.53 (0.14), residues: 1941 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG N 18 TYR 0.027 0.001 TYR C 369 PHE 0.044 0.001 PHE C 759 TRP 0.012 0.001 TRP N 32 HIS 0.008 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00314 (26818) covalent geometry : angle 0.60234 (36550) SS BOND : bond 0.00440 ( 40) SS BOND : angle 1.95384 ( 80) hydrogen bonds : bond 0.04294 ( 905) hydrogen bonds : angle 6.17192 ( 2556) link_BETA1-4 : bond 0.00643 ( 10) link_BETA1-4 : angle 1.75771 ( 30) link_NAG-ASN : bond 0.00496 ( 31) link_NAG-ASN : angle 2.79624 ( 93) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6608 Ramachandran restraints generated. 3304 Oldfield, 0 Emsley, 3304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6608 Ramachandran restraints generated. 3304 Oldfield, 0 Emsley, 3304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 121 time to evaluate : 0.936 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 PHE cc_start: 0.8974 (m-80) cc_final: 0.8491 (m-80) REVERT: A 697 MET cc_start: 0.8660 (ppp) cc_final: 0.8375 (ppp) REVERT: A 740 MET cc_start: 0.8455 (tpp) cc_final: 0.8217 (tpp) REVERT: A 776 LYS cc_start: 0.9508 (tttt) cc_final: 0.9174 (tptt) REVERT: A 869 MET cc_start: 0.8992 (mtm) cc_final: 0.8624 (mtp) REVERT: B 166 CYS cc_start: 0.7301 (OUTLIER) cc_final: 0.6978 (t) REVERT: B 731 MET cc_start: 0.9058 (ptm) cc_final: 0.8811 (ptm) REVERT: B 1107 ARG cc_start: 0.7141 (ptp-170) cc_final: 0.6719 (ptp-170) REVERT: C 424 LYS cc_start: 0.8327 (ttpt) cc_final: 0.7799 (ptpp) REVERT: C 1107 ARG cc_start: 0.7819 (mtt-85) cc_final: 0.6573 (mtt-85) REVERT: H 4 LEU cc_start: 0.8138 (mm) cc_final: 0.7815 (tt) REVERT: H 109 VAL cc_start: 0.4254 (OUTLIER) cc_final: 0.3871 (t) REVERT: L 4 MET cc_start: 0.7450 (mtp) cc_final: 0.6413 (tpp) REVERT: M 45 LEU cc_start: 0.4697 (mp) cc_final: 0.4348 (mt) REVERT: N 46 LEU cc_start: 0.4716 (OUTLIER) cc_final: 0.3366 (tt) outliers start: 59 outliers final: 36 residues processed: 172 average time/residue: 0.1517 time to fit residues: 43.3169 Evaluate side-chains 147 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 108 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 749 CYS Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 896 ILE Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 1012 LEU Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain H residue 32 TYR Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain M residue 108 MET Chi-restraints excluded: chain N residue 46 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 225 optimal weight: 0.0870 chunk 82 optimal weight: 1.9990 chunk 34 optimal weight: 20.0000 chunk 84 optimal weight: 5.9990 chunk 98 optimal weight: 10.0000 chunk 304 optimal weight: 10.0000 chunk 175 optimal weight: 9.9990 chunk 193 optimal weight: 9.9990 chunk 233 optimal weight: 6.9990 chunk 311 optimal weight: 5.9990 chunk 60 optimal weight: 0.0570 overall best weight: 2.8282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 920 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1011 GLN ** B 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 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 = 0.3795 r_free = 0.3795 target = 0.068381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.044811 restraints weight = 153555.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.046234 restraints weight = 79677.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.047073 restraints weight = 51054.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 58)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.047749 restraints weight = 38801.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.048123 restraints weight = 32195.412| |-----------------------------------------------------------------------------| r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.4662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 26899 Z= 0.157 Angle : 0.624 13.461 36753 Z= 0.313 Chirality : 0.044 0.377 4351 Planarity : 0.004 0.064 4638 Dihedral : 5.621 50.242 4462 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.99 % Favored : 93.89 % Rotamer: Outliers : 2.13 % Allowed : 18.42 % Favored : 79.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.44 (0.14), residues: 3304 helix: 0.69 (0.20), residues: 649 sheet: -1.14 (0.18), residues: 714 loop : -1.50 (0.14), residues: 1941 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG L 24 TYR 0.022 0.001 TYR M 79 PHE 0.039 0.001 PHE C 759 TRP 0.012 0.001 TRP M 36 HIS 0.008 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00336 (26818) covalent geometry : angle 0.59595 (36550) SS BOND : bond 0.00451 ( 40) SS BOND : angle 2.50882 ( 80) hydrogen bonds : bond 0.04225 ( 905) hydrogen bonds : angle 5.99668 ( 2556) link_BETA1-4 : bond 0.00655 ( 10) link_BETA1-4 : angle 1.65324 ( 30) link_NAG-ASN : bond 0.00521 ( 31) link_NAG-ASN : angle 2.81777 ( 93) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6608 Ramachandran restraints generated. 3304 Oldfield, 0 Emsley, 3304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6608 Ramachandran restraints generated. 3304 Oldfield, 0 Emsley, 3304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 112 time to evaluate : 0.860 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 PHE cc_start: 0.8964 (m-80) cc_final: 0.8465 (m-80) REVERT: A 697 MET cc_start: 0.8651 (ppp) cc_final: 0.8283 (ppp) REVERT: A 776 LYS cc_start: 0.9523 (tttt) cc_final: 0.9196 (tptt) REVERT: A 869 MET cc_start: 0.9049 (mtm) cc_final: 0.8639 (mtp) REVERT: A 994 ASP cc_start: 0.9149 (t0) cc_final: 0.8771 (t0) REVERT: B 166 CYS cc_start: 0.7259 (OUTLIER) cc_final: 0.6918 (t) REVERT: B 731 MET cc_start: 0.9080 (ptm) cc_final: 0.8850 (ptm) REVERT: B 1050 MET cc_start: 0.7408 (ptp) cc_final: 0.7188 (ptp) REVERT: B 1107 ARG cc_start: 0.7176 (ptp-170) cc_final: 0.6763 (ptp-170) REVERT: C 424 LYS cc_start: 0.8263 (ttpt) cc_final: 0.7695 (ptpp) REVERT: C 663 ASP cc_start: 0.8828 (p0) cc_final: 0.8618 (p0) REVERT: C 902 MET cc_start: 0.8052 (mmp) cc_final: 0.7537 (mmt) REVERT: C 1029 MET cc_start: 0.9018 (mmm) cc_final: 0.8665 (tpp) REVERT: C 1107 ARG cc_start: 0.7802 (mtt-85) cc_final: 0.6579 (mtt-85) REVERT: C 1138 TYR cc_start: 0.8506 (t80) cc_final: 0.8202 (t80) REVERT: H 4 LEU cc_start: 0.8004 (mm) cc_final: 0.7700 (tt) REVERT: H 109 VAL cc_start: 0.4385 (OUTLIER) cc_final: 0.4006 (t) REVERT: M 45 LEU cc_start: 0.4757 (mp) cc_final: 0.4429 (mt) REVERT: N 46 LEU cc_start: 0.4966 (OUTLIER) cc_final: 0.3578 (tt) outliers start: 58 outliers final: 42 residues processed: 162 average time/residue: 0.1446 time to fit residues: 40.0054 Evaluate side-chains 155 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 110 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 437 ASN Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 436 TRP Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 749 CYS Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 896 ILE Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 1012 LEU Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain H residue 32 TYR Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain M residue 32 TYR Chi-restraints excluded: chain M residue 37 VAL Chi-restraints excluded: chain N residue 46 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 153 optimal weight: 4.9990 chunk 279 optimal weight: 2.9990 chunk 105 optimal weight: 30.0000 chunk 296 optimal weight: 40.0000 chunk 141 optimal weight: 10.0000 chunk 218 optimal weight: 3.9990 chunk 104 optimal weight: 7.9990 chunk 83 optimal weight: 0.9990 chunk 309 optimal weight: 20.0000 chunk 130 optimal weight: 30.0000 chunk 278 optimal weight: 0.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 764 ASN ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 920 GLN ** B 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 872 GLN ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.068301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.044606 restraints weight = 154769.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.046074 restraints weight = 79960.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.047034 restraints weight = 51812.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.047688 restraints weight = 38969.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.048087 restraints weight = 32386.446| |-----------------------------------------------------------------------------| r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.4903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 26899 Z= 0.151 Angle : 0.620 13.941 36753 Z= 0.310 Chirality : 0.044 0.374 4351 Planarity : 0.004 0.064 4638 Dihedral : 5.407 50.716 4462 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.66 % Favored : 94.22 % Rotamer: Outliers : 2.27 % Allowed : 18.64 % Favored : 79.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.40 (0.14), residues: 3304 helix: 0.65 (0.20), residues: 656 sheet: -1.11 (0.18), residues: 702 loop : -1.45 (0.14), residues: 1946 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG L 24 TYR 0.023 0.001 TYR B 369 PHE 0.037 0.001 PHE C 759 TRP 0.013 0.001 TRP M 36 HIS 0.008 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00323 (26818) covalent geometry : angle 0.59063 (36550) SS BOND : bond 0.00415 ( 40) SS BOND : angle 2.78592 ( 80) hydrogen bonds : bond 0.04127 ( 905) hydrogen bonds : angle 5.86209 ( 2556) link_BETA1-4 : bond 0.00529 ( 10) link_BETA1-4 : angle 1.52607 ( 30) link_NAG-ASN : bond 0.00516 ( 31) link_NAG-ASN : angle 2.75816 ( 93) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6608 Ramachandran restraints generated. 3304 Oldfield, 0 Emsley, 3304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6608 Ramachandran restraints generated. 3304 Oldfield, 0 Emsley, 3304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 113 time to evaluate : 1.022 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 697 MET cc_start: 0.8638 (ppp) cc_final: 0.8231 (ppp) REVERT: A 776 LYS cc_start: 0.9513 (tttt) cc_final: 0.9199 (tptt) REVERT: A 869 MET cc_start: 0.9029 (mtm) cc_final: 0.8634 (mtp) REVERT: A 994 ASP cc_start: 0.9139 (t0) cc_final: 0.8755 (t0) REVERT: B 166 CYS cc_start: 0.7273 (OUTLIER) cc_final: 0.6987 (t) REVERT: B 731 MET cc_start: 0.9039 (ptm) cc_final: 0.8806 (ptm) REVERT: B 869 MET cc_start: 0.8941 (ptp) cc_final: 0.8719 (ptp) REVERT: B 902 MET cc_start: 0.8070 (OUTLIER) cc_final: 0.7745 (mmp) REVERT: B 1050 MET cc_start: 0.7475 (ptp) cc_final: 0.7168 (ptp) REVERT: B 1107 ARG cc_start: 0.7125 (ptp-170) cc_final: 0.6740 (ptp-170) REVERT: C 424 LYS cc_start: 0.8235 (ttpt) cc_final: 0.7650 (ptpp) REVERT: C 902 MET cc_start: 0.8054 (mmp) cc_final: 0.7698 (mmt) REVERT: C 1029 MET cc_start: 0.8963 (mmm) cc_final: 0.8619 (tpp) REVERT: C 1107 ARG cc_start: 0.7800 (mtt-85) cc_final: 0.6924 (mtt90) REVERT: C 1138 TYR cc_start: 0.8450 (t80) cc_final: 0.8212 (t80) REVERT: H 109 VAL cc_start: 0.4226 (OUTLIER) cc_final: 0.3862 (t) REVERT: L 4 MET cc_start: 0.6432 (OUTLIER) cc_final: 0.5935 (ptp) REVERT: M 45 LEU cc_start: 0.4906 (mp) cc_final: 0.4591 (mt) REVERT: N 46 LEU cc_start: 0.4976 (OUTLIER) cc_final: 0.3584 (tt) outliers start: 62 outliers final: 46 residues processed: 162 average time/residue: 0.1405 time to fit residues: 38.2057 Evaluate side-chains 159 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 108 time to evaluate : 1.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 902 MET Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 436 TRP Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 749 CYS Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 896 ILE Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 1012 LEU Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain H residue 32 TYR Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain M residue 32 TYR Chi-restraints excluded: chain M residue 37 VAL Chi-restraints excluded: chain M residue 80 MET Chi-restraints excluded: chain M residue 108 MET Chi-restraints excluded: chain N residue 46 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 27 optimal weight: 4.9990 chunk 266 optimal weight: 4.9990 chunk 216 optimal weight: 8.9990 chunk 3 optimal weight: 0.9990 chunk 57 optimal weight: 0.7980 chunk 163 optimal weight: 7.9990 chunk 249 optimal weight: 9.9990 chunk 45 optimal weight: 1.9990 chunk 5 optimal weight: 5.9990 chunk 245 optimal weight: 10.0000 chunk 89 optimal weight: 2.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 784 GLN ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 64 GLN ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.068521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.045036 restraints weight = 153590.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.046466 restraints weight = 79153.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 73)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.047399 restraints weight = 51215.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.048053 restraints weight = 38275.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 63)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.048452 restraints weight = 31800.852| |-----------------------------------------------------------------------------| r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.5050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 26899 Z= 0.139 Angle : 0.627 13.456 36753 Z= 0.310 Chirality : 0.044 0.368 4351 Planarity : 0.004 0.065 4638 Dihedral : 5.297 51.332 4462 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.93 % Favored : 93.95 % Rotamer: Outliers : 2.09 % Allowed : 18.78 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.33 (0.14), residues: 3304 helix: 0.66 (0.20), residues: 668 sheet: -1.11 (0.18), residues: 719 loop : -1.37 (0.14), residues: 1917 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 24 TYR 0.018 0.001 TYR M 79 PHE 0.035 0.001 PHE C 759 TRP 0.016 0.001 TRP H 47 HIS 0.008 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00301 (26818) covalent geometry : angle 0.59891 (36550) SS BOND : bond 0.00384 ( 40) SS BOND : angle 2.77834 ( 80) hydrogen bonds : bond 0.04014 ( 905) hydrogen bonds : angle 5.74843 ( 2556) link_BETA1-4 : bond 0.00564 ( 10) link_BETA1-4 : angle 1.43392 ( 30) link_NAG-ASN : bond 0.00501 ( 31) link_NAG-ASN : angle 2.63847 ( 93) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6608 Ramachandran restraints generated. 3304 Oldfield, 0 Emsley, 3304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6608 Ramachandran restraints generated. 3304 Oldfield, 0 Emsley, 3304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 114 time to evaluate : 0.755 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 697 MET cc_start: 0.8686 (ppp) cc_final: 0.8275 (ppp) REVERT: A 869 MET cc_start: 0.9077 (mtm) cc_final: 0.8668 (mtp) REVERT: A 994 ASP cc_start: 0.9196 (t0) cc_final: 0.8806 (t0) REVERT: B 166 CYS cc_start: 0.7271 (OUTLIER) cc_final: 0.7011 (t) REVERT: B 731 MET cc_start: 0.9110 (ptm) cc_final: 0.8844 (ptm) REVERT: B 869 MET cc_start: 0.9007 (ptp) cc_final: 0.8789 (ptp) REVERT: B 1107 ARG cc_start: 0.7214 (ptp-170) cc_final: 0.6874 (ptp-170) REVERT: C 424 LYS cc_start: 0.8221 (ttpt) cc_final: 0.7627 (ptpp) REVERT: C 663 ASP cc_start: 0.8774 (p0) cc_final: 0.8565 (p0) REVERT: C 902 MET cc_start: 0.8000 (mmp) cc_final: 0.7679 (mmt) REVERT: C 1107 ARG cc_start: 0.7834 (mtt-85) cc_final: 0.6941 (mtt90) REVERT: C 1138 TYR cc_start: 0.8504 (t80) cc_final: 0.8303 (t80) REVERT: H 109 VAL cc_start: 0.4038 (OUTLIER) cc_final: 0.3625 (t) REVERT: M 45 LEU cc_start: 0.4864 (mp) cc_final: 0.4507 (mt) REVERT: N 46 LEU cc_start: 0.5011 (OUTLIER) cc_final: 0.3639 (tt) outliers start: 57 outliers final: 48 residues processed: 160 average time/residue: 0.1572 time to fit residues: 42.2104 Evaluate side-chains 157 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 106 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 437 ASN Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 902 MET Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 436 TRP Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 749 CYS Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 896 ILE Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 1012 LEU Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain H residue 32 TYR Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain M residue 32 TYR Chi-restraints excluded: chain M residue 37 VAL Chi-restraints excluded: chain N residue 46 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 145 optimal weight: 0.0370 chunk 99 optimal weight: 0.3980 chunk 237 optimal weight: 9.9990 chunk 16 optimal weight: 50.0000 chunk 261 optimal weight: 6.9990 chunk 103 optimal weight: 6.9990 chunk 108 optimal weight: 9.9990 chunk 78 optimal weight: 8.9990 chunk 298 optimal weight: 8.9990 chunk 280 optimal weight: 0.5980 chunk 225 optimal weight: 0.2980 overall best weight: 1.6660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 764 ASN A1036 GLN ** B 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.068806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.045421 restraints weight = 152380.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.046832 restraints weight = 78739.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.047780 restraints weight = 51151.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 60)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.048418 restraints weight = 38421.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.048779 restraints weight = 31913.835| |-----------------------------------------------------------------------------| r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.5144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 26899 Z= 0.122 Angle : 0.618 13.364 36753 Z= 0.306 Chirality : 0.044 0.363 4351 Planarity : 0.004 0.065 4638 Dihedral : 5.141 52.677 4461 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.24 % Favored : 94.64 % Rotamer: Outliers : 1.87 % Allowed : 19.19 % Favored : 78.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.25 (0.14), residues: 3304 helix: 0.70 (0.20), residues: 665 sheet: -1.05 (0.18), residues: 721 loop : -1.31 (0.14), residues: 1918 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 38 TYR 0.025 0.001 TYR B 369 PHE 0.034 0.001 PHE C 759 TRP 0.025 0.001 TRP H 47 HIS 0.007 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00266 (26818) covalent geometry : angle 0.59163 (36550) SS BOND : bond 0.00368 ( 40) SS BOND : angle 2.69882 ( 80) hydrogen bonds : bond 0.03888 ( 905) hydrogen bonds : angle 5.63839 ( 2556) link_BETA1-4 : bond 0.00487 ( 10) link_BETA1-4 : angle 1.34721 ( 30) link_NAG-ASN : bond 0.00500 ( 31) link_NAG-ASN : angle 2.58109 ( 93) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6608 Ramachandran restraints generated. 3304 Oldfield, 0 Emsley, 3304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6608 Ramachandran restraints generated. 3304 Oldfield, 0 Emsley, 3304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 111 time to evaluate : 1.016 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 PHE cc_start: 0.8918 (m-80) cc_final: 0.8383 (m-80) REVERT: A 697 MET cc_start: 0.8647 (ppp) cc_final: 0.8125 (ppp) REVERT: A 869 MET cc_start: 0.9003 (mtm) cc_final: 0.8633 (mtp) REVERT: A 994 ASP cc_start: 0.9113 (t0) cc_final: 0.8720 (t0) REVERT: B 166 CYS cc_start: 0.7254 (OUTLIER) cc_final: 0.6968 (t) REVERT: B 731 MET cc_start: 0.9064 (ptm) cc_final: 0.8798 (ptm) REVERT: B 869 MET cc_start: 0.8946 (ptp) cc_final: 0.8737 (ptp) REVERT: B 1107 ARG cc_start: 0.7174 (ptp-170) cc_final: 0.6834 (ptp-170) REVERT: C 424 LYS cc_start: 0.8282 (ttpt) cc_final: 0.7657 (ptpp) REVERT: C 740 MET cc_start: 0.8506 (mmm) cc_final: 0.8245 (mmm) REVERT: C 902 MET cc_start: 0.8040 (mmp) cc_final: 0.7736 (mmt) REVERT: C 1107 ARG cc_start: 0.7834 (mtt-85) cc_final: 0.6934 (mtt90) REVERT: H 109 VAL cc_start: 0.4178 (OUTLIER) cc_final: 0.3798 (t) REVERT: L 4 MET cc_start: 0.7189 (ptp) cc_final: 0.6917 (ptp) REVERT: M 45 LEU cc_start: 0.4879 (mp) cc_final: 0.4521 (mt) REVERT: N 46 LEU cc_start: 0.4992 (OUTLIER) cc_final: 0.3612 (tt) outliers start: 51 outliers final: 43 residues processed: 153 average time/residue: 0.1543 time to fit residues: 39.8076 Evaluate side-chains 150 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 104 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 749 CYS Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 896 ILE Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 1012 LEU Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain H residue 32 TYR Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain M residue 32 TYR Chi-restraints excluded: chain M residue 37 VAL Chi-restraints excluded: chain N residue 46 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 180 optimal weight: 1.9990 chunk 124 optimal weight: 20.0000 chunk 191 optimal weight: 5.9990 chunk 106 optimal weight: 0.0770 chunk 119 optimal weight: 20.0000 chunk 87 optimal weight: 9.9990 chunk 178 optimal weight: 6.9990 chunk 250 optimal weight: 7.9990 chunk 234 optimal weight: 8.9990 chunk 7 optimal weight: 2.9990 chunk 212 optimal weight: 4.9990 overall best weight: 3.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 GLN ** 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 = 0.3783 r_free = 0.3783 target = 0.067736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.044417 restraints weight = 153090.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.045720 restraints weight = 78831.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.046618 restraints weight = 51564.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.047293 restraints weight = 38779.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 66)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.047695 restraints weight = 32147.772| |-----------------------------------------------------------------------------| r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.5428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 26899 Z= 0.165 Angle : 0.639 12.889 36753 Z= 0.319 Chirality : 0.044 0.370 4351 Planarity : 0.004 0.063 4638 Dihedral : 5.210 59.762 4459 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.17 % Favored : 93.70 % Rotamer: Outliers : 2.13 % Allowed : 19.15 % Favored : 78.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.28 (0.14), residues: 3304 helix: 0.61 (0.20), residues: 673 sheet: -1.01 (0.19), residues: 699 loop : -1.34 (0.14), residues: 1932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 38 TYR 0.018 0.001 TYR M 79 PHE 0.033 0.001 PHE C 759 TRP 0.016 0.001 TRP H 47 HIS 0.008 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00353 (26818) covalent geometry : angle 0.61259 (36550) SS BOND : bond 0.00439 ( 40) SS BOND : angle 2.71299 ( 80) hydrogen bonds : bond 0.04122 ( 905) hydrogen bonds : angle 5.69359 ( 2556) link_BETA1-4 : bond 0.00409 ( 10) link_BETA1-4 : angle 1.42945 ( 30) link_NAG-ASN : bond 0.00538 ( 31) link_NAG-ASN : angle 2.63151 ( 93) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5759.35 seconds wall clock time: 99 minutes 44.87 seconds (5984.87 seconds total)