Starting phenix.real_space_refine on Sat Mar 7 05:37:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7e5s_30994/03_2026/7e5s_30994.cif Found real_map, /net/cci-nas-00/data/ceres_data/7e5s_30994/03_2026/7e5s_30994.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7e5s_30994/03_2026/7e5s_30994.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7e5s_30994/03_2026/7e5s_30994.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7e5s_30994/03_2026/7e5s_30994.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7e5s_30994/03_2026/7e5s_30994.map" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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 165 5.16 5 C 24696 2.51 5 N 6463 2.21 5 O 7592 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 189 residue(s): 0.04s 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: 38916 Number of models: 1 Model: "" Number of chains: 31 Chain: "A" Number of atoms: 8366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1072, 8366 Classifications: {'peptide': 1072} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 53, 'TRANS': 1018} Chain breaks: 4 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 1, 'TYR:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 15 Chain: "B" Number of atoms: 8334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1072, 8334 Classifications: {'peptide': 1072} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 53, 'TRANS': 1018} Chain breaks: 4 Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 3, 'ASP:plan': 3, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 44 Chain: "C" Number of atoms: 8354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1072, 8354 Classifications: {'peptide': 1072} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 53, 'TRANS': 1018} Chain breaks: 4 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 26 Chain: "D" Number of atoms: 704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 704 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 6, 'TRANS': 98} Unresolved non-hydrogen bonds: 126 Unresolved non-hydrogen angles: 158 Unresolved non-hydrogen dihedrals: 101 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 3, 'ARG:plan': 2, 'HIS:plan': 1, 'TYR:plan': 1, 'PHE:plan': 1, 'ASP:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 66 Chain: "E" Number of atoms: 903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 903 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 4, 'TRANS': 115} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "H" Number of atoms: 704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 704 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 6, 'TRANS': 98} Unresolved non-hydrogen bonds: 126 Unresolved non-hydrogen angles: 158 Unresolved non-hydrogen dihedrals: 101 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 3, 'ARG:plan': 2, 'HIS:plan': 1, 'TYR:plan': 1, 'PHE:plan': 1, 'ASP:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 66 Chain: "I" Number of atoms: 912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 912 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 117} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "J" Number of atoms: 912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 912 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 117} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "K" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 817 Classifications: {'peptide': 108} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 101} Chain: "L" Number of atoms: 903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 903 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 4, 'TRANS': 115} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "N" Number of atoms: 788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 788 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "O" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 806 Classifications: {'peptide': 110} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 7, 'TRANS': 102} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 2, 'PHE:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 16 Chain: "P" Number of atoms: 927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 927 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 113} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "Q" Number of atoms: 788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 788 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "R" Number of atoms: 899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 899 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 115} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "S" Number of atoms: 788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 788 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "T" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 817 Classifications: {'peptide': 108} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 101} Chain: "U" Number of atoms: 927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 927 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 113} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "V" Number of atoms: 931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 931 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 6, 'TRANS': 113} 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: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" 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: "X" 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: "Y" 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: "Z" 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 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: "c" 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: "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 Time building chain proxies: 8.28, per 1000 atoms: 0.21 Number of scatterers: 38916 At special positions: 0 Unit cell: (213.2, 221.52, 215.28, 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 165 16.00 O 7592 8.00 N 6463 7.00 C 24696 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=55, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=1.25 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=1.50 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.91 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 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.02 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=2.05 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=1.35 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=1.82 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.37 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=1.48 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.04 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=1.42 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=2.07 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=1.47 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 96 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 89 " distance=2.03 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 91 " distance=2.03 Simple disulfide: pdb=" SG CYS P 23 " - pdb=" SG CYS P 97 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 22 " - pdb=" SG CYS Q 89 " distance=2.03 Simple disulfide: pdb=" SG CYS R 22 " - pdb=" SG CYS R 96 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 89 " distance=2.03 Simple disulfide: pdb=" SG CYS T 23 " - pdb=" SG CYS T 88 " distance=2.03 Simple disulfide: pdb=" SG CYS U 23 " - pdb=" SG CYS U 97 " distance=2.03 Simple disulfide: pdb=" SG CYS V 23 " - pdb=" SG CYS V 97 " 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=1, symmetry=0 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG M 1 " - " NAG M 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " NAG-ASN " NAG F 1 " - " ASN A 717 " " NAG G 1 " - " ASN A 801 " " NAG M 1 " - " ASN A1098 " " NAG W 1 " - " ASN B 717 " " NAG X 1 " - " ASN B 801 " " NAG Y 1 " - " ASN B1098 " " NAG Z 1 " - " ASN B1134 " " NAG a 1 " - " ASN C 234 " " NAG b 1 " - " ASN C 717 " " NAG c 1 " - " ASN C 801 " " NAG d 1 " - " ASN C1098 " " NAG e 1 " - " ASN C1134 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.95 Conformation dependent library (CDL) restraints added in 1.6 seconds 9952 Ramachandran restraints generated. 4976 Oldfield, 0 Emsley, 4976 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9304 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 86 sheets defined 16.9% alpha, 28.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.70 Creating SS restraints... Processing helix chain 'A' and resid 156 through 158 No H-bonds generated for 'chain 'A' and resid 156 through 158' Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.600A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 372 Processing helix chain 'A' and resid 383 through 390 removed outlier: 3.576A pdb=" N ASN A 388 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ASP A 389 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 410 removed outlier: 3.957A pdb=" N ARG A 408 " --> pdb=" O GLY A 404 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLN A 409 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 421 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 757 Processing helix chain 'A' and resid 757 through 783 removed outlier: 4.253A pdb=" N THR A 761 " --> pdb=" O GLY A 757 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LEU A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASN A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) 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 removed outlier: 3.656A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 910 Processing helix chain 'A' and resid 912 through 919 removed outlier: 3.844A 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 945 through 968 Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.558A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1032 removed outlier: 3.617A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 3.905A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 158 No H-bonds generated for 'chain 'B' and resid 156 through 158' Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.843A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N PHE B 342 " --> pdb=" O PHE B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 Processing helix chain 'B' and resid 365 through 372 Processing helix chain 'B' and resid 383 through 390 Processing helix chain 'B' and resid 405 through 409 Processing helix chain 'B' and resid 416 through 421 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 757 Processing helix chain 'B' and resid 757 through 783 removed outlier: 4.219A pdb=" N THR B 761 " --> pdb=" O GLY B 757 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU B 763 " --> pdb=" O PHE B 759 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.518A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 910 Processing helix chain 'B' and resid 912 through 919 removed outlier: 3.751A 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 945 through 968 Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.549A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1032 removed outlier: 3.620A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 4.008A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.559A pdb=" N PHE C 342 " --> pdb=" O PHE C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 372 removed outlier: 3.794A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 390 removed outlier: 3.546A pdb=" N LEU C 390 " --> pdb=" O LYS C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 410 Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 757 Processing helix chain 'C' and resid 757 through 783 removed outlier: 4.220A pdb=" N THR C 761 " --> pdb=" O GLY C 757 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LEU C 763 " --> pdb=" O PHE C 759 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASN C 764 " --> pdb=" O CYS C 760 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.530A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 910 Processing helix chain 'C' and resid 912 through 919 removed outlier: 3.765A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 968 removed outlier: 3.672A pdb=" N SER C 967 " --> pdb=" O VAL C 963 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.510A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1032 removed outlier: 3.545A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 4.098A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'I' and resid 74 through 76 No H-bonds generated for 'chain 'I' and resid 74 through 76' Processing helix chain 'I' and resid 87 through 91 Processing helix chain 'J' and resid 87 through 91 Processing helix chain 'N' and resid 80 through 84 removed outlier: 4.333A pdb=" N GLU N 84 " --> pdb=" O THR N 81 " (cutoff:3.500A) Processing helix chain 'P' and resid 29 through 33 Processing helix chain 'Q' and resid 80 through 84 removed outlier: 4.334A pdb=" N GLU Q 84 " --> pdb=" O THR Q 81 " (cutoff:3.500A) Processing helix chain 'S' and resid 80 through 84 removed outlier: 4.333A pdb=" N GLU S 84 " --> pdb=" O THR S 81 " (cutoff:3.500A) Processing helix chain 'U' and resid 29 through 33 Processing helix chain 'V' and resid 29 through 33 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 31 removed outlier: 3.845A pdb=" N SER A 31 " --> pdb=" O SER A 60 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 9.471A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N ALA A 263 " --> pdb=" O ALA A 67 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LYS A 195 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ILE A 203 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.142A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.183A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 27 through 31 removed outlier: 3.845A pdb=" N SER A 31 " --> pdb=" O SER A 60 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 4.504A 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: 3.725A pdb=" N TRP A 104 " --> pdb=" O ILE A 119 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N GLN A 134 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 9.343A pdb=" N ASN A 164 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 152 through 155 removed outlier: 3.617A pdb=" N GLY A 142 " --> pdb=" O SER A 155 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 3.990A pdb=" N GLY A 311 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N THR A 599 " --> pdb=" O GLY A 311 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 327 removed outlier: 3.535A pdb=" N THR A 553 " --> pdb=" O ASP A 586 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.754A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ALA A 435 " --> pdb=" O THR A 376 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR A 376 " --> pdb=" O ALA A 435 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.662A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.410A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER A 673 " --> pdb=" O ILE A 693 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 702 through 703 Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 727 removed outlier: 6.332A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB5, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB6, first strand: chain 'A' and resid 1094 through 1096 Processing sheet with id=AB7, first strand: chain 'B' and resid 27 through 31 removed outlier: 3.682A pdb=" N SER B 31 " --> pdb=" O SER B 60 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ILE B 203 " --> pdb=" O VAL B 227 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.632A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.264A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 48 through 55 removed outlier: 4.019A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 68 through 70 Processing sheet with id=AC1, first strand: chain 'B' and resid 84 through 85 removed outlier: 4.166A pdb=" N TRP B 104 " --> pdb=" O ILE B 119 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ILE B 119 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N GLU B 132 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N CYS B 166 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N GLN B 134 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 9.191A pdb=" N ASN B 164 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 152 through 155 removed outlier: 3.594A pdb=" N GLY B 142 " --> pdb=" O SER B 155 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 319 removed outlier: 7.327A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 325 through 328 removed outlier: 3.617A pdb=" N THR B 553 " --> pdb=" O ASP B 586 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AC6, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC7, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.815A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.525A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER B 673 " --> pdb=" O ILE B 693 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 702 through 703 Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 727 removed outlier: 6.468A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.509A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD3, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AD4, first strand: chain 'C' and resid 27 through 31 removed outlier: 3.719A pdb=" N SER C 31 " --> pdb=" O SER C 60 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N ALA C 263 " --> pdb=" O ALA C 67 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU C 189 " --> pdb=" O THR C 208 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LYS C 195 " --> pdb=" O LYS C 202 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ILE C 203 " --> pdb=" O VAL C 227 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.743A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.320A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 27 through 31 removed outlier: 3.719A pdb=" N SER C 31 " --> pdb=" O SER C 60 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 48 through 55 removed outlier: 7.516A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AD8, first strand: chain 'C' and resid 115 through 120 removed outlier: 3.592A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N GLU C 132 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N CYS C 166 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N GLN C 134 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 9.476A pdb=" N ASN C 164 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 152 through 155 Processing sheet with id=AE1, first strand: chain 'C' and resid 311 through 319 removed outlier: 3.556A pdb=" N THR C 315 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 325 through 328 removed outlier: 5.959A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.974A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE5, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE6, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.917A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.614A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N SER C 673 " --> pdb=" O ILE C 693 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 711 through 727 removed outlier: 6.529A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.369A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AF1, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AF2, first strand: chain 'D' and resid 21 through 22 removed outlier: 3.593A pdb=" N PHE D 70 " --> pdb=" O CYS D 22 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'D' and resid 52 through 53 removed outlier: 5.154A pdb=" N SER D 42 " --> pdb=" O LYS D 38 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N LYS D 38 " --> pdb=" O SER D 42 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N TRP D 34 " --> pdb=" O LEU D 46 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'E' and resid 4 through 6 removed outlier: 3.977A pdb=" N THR E 78 " --> pdb=" O ASP E 73 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ASP E 73 " --> pdb=" O THR E 78 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'E' and resid 10 through 12 removed outlier: 3.517A pdb=" N ILE E 34 " --> pdb=" O ILE E 51 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLY E 49 " --> pdb=" O TRP E 36 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N LYS E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N TRP E 47 " --> pdb=" O LYS E 38 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'E' and resid 10 through 12 removed outlier: 4.434A pdb=" N TYR E 109 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'H' and resid 18 through 22 removed outlier: 3.559A pdb=" N PHE H 70 " --> pdb=" O CYS H 22 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'H' and resid 52 through 53 removed outlier: 5.155A pdb=" N SER H 42 " --> pdb=" O LYS H 38 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N LYS H 38 " --> pdb=" O SER H 42 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N TRP H 34 " --> pdb=" O LEU H 46 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'I' and resid 3 through 6 Processing sheet with id=AG1, first strand: chain 'I' and resid 10 through 12 removed outlier: 3.550A pdb=" N THR I 113 " --> pdb=" O TYR I 94 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N MET I 34 " --> pdb=" O VAL I 50 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N VAL I 50 " --> pdb=" O MET I 34 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N TRP I 36 " --> pdb=" O VAL I 48 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'J' and resid 3 through 6 Processing sheet with id=AG3, first strand: chain 'J' and resid 10 through 12 removed outlier: 3.551A pdb=" N THR J 113 " --> pdb=" O TYR J 94 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N MET J 34 " --> pdb=" O VAL J 50 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N VAL J 50 " --> pdb=" O MET J 34 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N TRP J 36 " --> pdb=" O VAL J 48 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'K' and resid 4 through 7 removed outlier: 3.615A pdb=" N PHE K 71 " --> pdb=" O CYS K 23 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'K' and resid 10 through 13 removed outlier: 3.606A pdb=" N GLU K 105 " --> pdb=" O LEU K 11 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N LEU K 33 " --> pdb=" O TYR K 49 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N TYR K 49 " --> pdb=" O LEU K 33 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'L' and resid 4 through 6 removed outlier: 4.278A pdb=" N THR L 78 " --> pdb=" O ASP L 73 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ASP L 73 " --> pdb=" O THR L 78 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'L' and resid 10 through 12 removed outlier: 7.253A pdb=" N ILE L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N TYR L 50 " --> pdb=" O ILE L 34 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N TRP L 36 " --> pdb=" O ILE L 48 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N SER L 59 " --> pdb=" O TYR L 50 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'L' and resid 10 through 12 removed outlier: 4.466A pdb=" N TYR L 109 " --> pdb=" O ARG L 98 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'N' and resid 9 through 12 removed outlier: 3.689A pdb=" N ASP N 86 " --> pdb=" O GLN N 39 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N VAL N 34 " --> pdb=" O TYR N 50 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N TYR N 50 " --> pdb=" O VAL N 34 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N TRP N 36 " --> pdb=" O LEU N 48 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'N' and resid 9 through 12 removed outlier: 3.733A pdb=" N THR N 91 " --> pdb=" O VAL N 100 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL N 100 " --> pdb=" O THR N 91 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'N' and resid 20 through 23 Processing sheet with id=AH3, first strand: chain 'O' and resid 4 through 6 removed outlier: 3.886A pdb=" N CYS O 22 " --> pdb=" O PHE O 74 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER O 70 " --> pdb=" O ASP O 73 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'O' and resid 39 through 41 removed outlier: 4.022A pdb=" N VAL O 88 " --> pdb=" O GLN O 41 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'P' and resid 3 through 4 removed outlier: 3.835A pdb=" N GLN P 3 " --> pdb=" O SER P 26 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'P' and resid 22 through 23 removed outlier: 3.601A pdb=" N ALA P 80 " --> pdb=" O CYS P 23 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'P' and resid 46 through 49 Processing sheet with id=AH8, first strand: chain 'Q' and resid 9 through 12 removed outlier: 3.689A pdb=" N ASP Q 86 " --> pdb=" O GLN Q 39 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N VAL Q 34 " --> pdb=" O TYR Q 50 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N TYR Q 50 " --> pdb=" O VAL Q 34 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N TRP Q 36 " --> pdb=" O LEU Q 48 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'Q' and resid 9 through 12 removed outlier: 3.734A pdb=" N THR Q 91 " --> pdb=" O VAL Q 100 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL Q 100 " --> pdb=" O THR Q 91 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'Q' and resid 20 through 23 Processing sheet with id=AI2, first strand: chain 'R' and resid 3 through 4 removed outlier: 3.502A pdb=" N LEU R 18 " --> pdb=" O MET R 83 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N THR R 78 " --> pdb=" O ASP R 73 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ASP R 73 " --> pdb=" O THR R 78 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'R' and resid 11 through 12 Processing sheet with id=AI4, first strand: chain 'R' and resid 45 through 50 removed outlier: 7.418A pdb=" N TRP R 36 " --> pdb=" O VAL R 48 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N GLU R 50 " --> pdb=" O MET R 34 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N MET R 34 " --> pdb=" O GLU R 50 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N TYR R 109 " --> pdb=" O ARG R 98 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'S' and resid 9 through 12 removed outlier: 3.688A pdb=" N ASP S 86 " --> pdb=" O GLN S 39 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N VAL S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N TYR S 50 " --> pdb=" O VAL S 34 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N TRP S 36 " --> pdb=" O LEU S 48 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'S' and resid 9 through 12 removed outlier: 3.734A pdb=" N THR S 91 " --> pdb=" O VAL S 100 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL S 100 " --> pdb=" O THR S 91 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'S' and resid 20 through 23 Processing sheet with id=AI8, first strand: chain 'T' and resid 4 through 7 removed outlier: 3.622A pdb=" N PHE T 71 " --> pdb=" O CYS T 23 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'T' and resid 10 through 13 removed outlier: 3.606A pdb=" N GLU T 105 " --> pdb=" O LEU T 11 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N LEU T 33 " --> pdb=" O TYR T 49 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N TYR T 49 " --> pdb=" O LEU T 33 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N TRP T 35 " --> pdb=" O LEU T 47 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'U' and resid 3 through 4 removed outlier: 3.838A pdb=" N GLN U 3 " --> pdb=" O SER U 26 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER U 26 " --> pdb=" O GLN U 3 " (cutoff:3.500A) No H-bonds generated for sheet with id=AJ1 Processing sheet with id=AJ2, first strand: chain 'U' and resid 22 through 23 removed outlier: 3.601A pdb=" N ALA U 80 " --> pdb=" O CYS U 23 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'U' and resid 46 through 49 Processing sheet with id=AJ4, first strand: chain 'V' and resid 22 through 23 removed outlier: 3.601A pdb=" N ALA V 80 " --> pdb=" O CYS V 23 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'V' and resid 46 through 49 removed outlier: 3.838A pdb=" N VAL V 38 " --> pdb=" O TYR V 96 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N TYR V 96 " --> pdb=" O VAL V 38 " (cutoff:3.500A) 1439 hydrogen bonds defined for protein. 3822 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: 10.15 Time building geometry restraints manager: 4.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 8215 1.33 - 1.45: 9826 1.45 - 1.58: 21555 1.58 - 1.70: 1 1.70 - 1.82: 216 Bond restraints: 39813 Sorted by residual: bond pdb=" C1 NAG Y 1 " pdb=" C2 NAG Y 1 " ideal model delta sigma weight residual 1.532 1.638 -0.106 2.00e-02 2.50e+03 2.83e+01 bond pdb=" N ILE B 332 " pdb=" CA ILE B 332 " ideal model delta sigma weight residual 1.460 1.499 -0.039 8.60e-03 1.35e+04 2.05e+01 bond pdb=" N GLN K 79 " pdb=" CA GLN K 79 " ideal model delta sigma weight residual 1.453 1.489 -0.036 8.30e-03 1.45e+04 1.88e+01 bond pdb=" N GLN T 79 " pdb=" CA GLN T 79 " ideal model delta sigma weight residual 1.453 1.489 -0.036 8.30e-03 1.45e+04 1.87e+01 bond pdb=" N ILE B 664 " pdb=" CA ILE B 664 " ideal model delta sigma weight residual 1.457 1.495 -0.038 9.00e-03 1.23e+04 1.77e+01 ... (remaining 39808 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.03: 52165 3.03 - 6.06: 1984 6.06 - 9.09: 44 9.09 - 12.12: 4 12.12 - 15.15: 3 Bond angle restraints: 54200 Sorted by residual: angle pdb=" N THR B 523 " pdb=" CA THR B 523 " pdb=" C THR B 523 " ideal model delta sigma weight residual 111.28 123.58 -12.30 1.09e+00 8.42e-01 1.27e+02 angle pdb=" C GLY C 526 " pdb=" N PRO C 527 " pdb=" CA PRO C 527 " ideal model delta sigma weight residual 119.05 128.03 -8.98 1.11e+00 8.12e-01 6.54e+01 angle pdb=" N CYS A 131 " pdb=" CA CYS A 131 " pdb=" CB CYS A 131 " ideal model delta sigma weight residual 111.69 125.33 -13.64 1.74e+00 3.30e-01 6.15e+01 angle pdb=" C ASP P 110 " pdb=" CA ASP P 110 " pdb=" CB ASP P 110 " ideal model delta sigma weight residual 110.17 125.32 -15.15 1.97e+00 2.58e-01 5.91e+01 angle pdb=" CA GLY B 184 " pdb=" C GLY B 184 " pdb=" O GLY B 184 " ideal model delta sigma weight residual 122.22 117.33 4.89 6.50e-01 2.37e+00 5.66e+01 ... (remaining 54195 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 22450 17.87 - 35.75: 1172 35.75 - 53.62: 216 53.62 - 71.50: 26 71.50 - 89.37: 20 Dihedral angle restraints: 23884 sinusoidal: 9334 harmonic: 14550 Sorted by residual: dihedral pdb=" CB CYS C 336 " pdb=" SG CYS C 336 " pdb=" SG CYS C 361 " pdb=" CB CYS C 361 " ideal model delta sinusoidal sigma weight residual 93.00 -177.63 -89.37 1 1.00e+01 1.00e-02 9.49e+01 dihedral pdb=" CB CYS B 379 " pdb=" SG CYS B 379 " pdb=" SG CYS B 432 " pdb=" CB CYS B 432 " ideal model delta sinusoidal sigma weight residual 93.00 3.69 89.31 1 1.00e+01 1.00e-02 9.48e+01 dihedral pdb=" C ASP P 110 " pdb=" N ASP P 110 " pdb=" CA ASP P 110 " pdb=" CB ASP P 110 " ideal model delta harmonic sigma weight residual -122.60 -145.36 22.76 0 2.50e+00 1.60e-01 8.28e+01 ... (remaining 23881 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.194: 5866 0.194 - 0.387: 302 0.387 - 0.581: 4 0.581 - 0.774: 1 0.774 - 0.968: 1 Chirality restraints: 6174 Sorted by residual: chirality pdb=" C1 NAG Y 2 " pdb=" O4 NAG Y 1 " pdb=" C2 NAG Y 2 " pdb=" O5 NAG Y 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.24 -0.16 2.00e-02 2.50e+03 6.01e+01 chirality pdb=" C1 NAG M 2 " pdb=" O4 NAG M 1 " pdb=" C2 NAG M 2 " pdb=" O5 NAG M 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.26 -0.14 2.00e-02 2.50e+03 4.63e+01 chirality pdb=" C1 NAG W 2 " pdb=" O4 NAG W 1 " pdb=" C2 NAG W 2 " pdb=" O5 NAG W 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.27 -0.13 2.00e-02 2.50e+03 4.01e+01 ... (remaining 6171 not shown) Planarity restraints: 6985 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG e 2 " 0.353 2.00e-02 2.50e+03 3.04e-01 1.16e+03 pdb=" C7 NAG e 2 " -0.085 2.00e-02 2.50e+03 pdb=" C8 NAG e 2 " 0.125 2.00e-02 2.50e+03 pdb=" N2 NAG e 2 " -0.542 2.00e-02 2.50e+03 pdb=" O7 NAG e 2 " 0.149 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG Z 2 " 0.353 2.00e-02 2.50e+03 3.04e-01 1.16e+03 pdb=" C7 NAG Z 2 " -0.085 2.00e-02 2.50e+03 pdb=" C8 NAG Z 2 " 0.123 2.00e-02 2.50e+03 pdb=" N2 NAG Z 2 " -0.541 2.00e-02 2.50e+03 pdb=" O7 NAG Z 2 " 0.151 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG c 1 " 0.351 2.00e-02 2.50e+03 3.03e-01 1.15e+03 pdb=" C7 NAG c 1 " -0.083 2.00e-02 2.50e+03 pdb=" C8 NAG c 1 " 0.098 2.00e-02 2.50e+03 pdb=" N2 NAG c 1 " -0.539 2.00e-02 2.50e+03 pdb=" O7 NAG c 1 " 0.172 2.00e-02 2.50e+03 ... (remaining 6982 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.25: 34 2.25 - 2.91: 16276 2.91 - 3.58: 55197 3.58 - 4.24: 93324 4.24 - 4.90: 154991 Nonbonded interactions: 319822 Sorted by model distance: nonbonded pdb=" OG1 THR B1100 " pdb=" C1 NAG Y 1 " model vdw 1.589 3.470 nonbonded pdb=" OD1 ASN B 331 " pdb=" O THR B 523 " model vdw 1.881 3.040 nonbonded pdb=" OH TYR C 473 " pdb=" CB TYR C 489 " model vdw 1.966 3.440 nonbonded pdb=" C LEU B 452 " pdb=" CE2 TYR B 495 " model vdw 1.971 3.570 nonbonded pdb=" NE2 HIS A1048 " pdb=" OG SER A1051 " model vdw 2.013 3.120 ... (remaining 319817 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 245 or (resid 246 and (name N or name CA or nam \ e C or name O or name CB )) or resid 247 through 404 or (resid 405 through 406 a \ nd (name N or name CA or name C or name O or name CB )) or resid 407 or (resid 4 \ 08 through 409 and (name N or name CA or name C or name O or name CB )) or resid \ 410 through 426 or (resid 427 through 428 and (name N or name CA or name C or n \ ame O or name CB )) or resid 429 through 508 or (resid 509 and (name N or name C \ A or name C or name O or name CB )) or resid 510 through 515 or (resid 516 and ( \ name N or name CA or name C or name O or name CB )) or resid 517 through 1013 or \ (resid 1014 through 1016 and (name N or name CA or name C or name O or name CB \ )) or resid 1017 through 1147)) selection = (chain 'B' and (resid 14 through 494 or (resid 495 and (name N or name CA or nam \ e C or name O or name CB )) or resid 496 through 508 or (resid 509 and (name N o \ r name CA or name C or name O or name CB )) or resid 510 through 1147)) selection = (chain 'C' and (resid 14 through 245 or (resid 246 and (name N or name CA or nam \ e C or name O or name CB )) or resid 247 through 407 or (resid 408 through 409 a \ nd (name N or name CA or name C or name O or name CB )) or resid 410 through 494 \ or (resid 495 and (name N or name CA or name C or name O or name CB )) or resid \ 496 through 1013 or (resid 1014 through 1016 and (name N or name CA or name C o \ r name O or name CB )) or resid 1017 through 1105 or (resid 1106 and (name N or \ name CA or name C or name O or name CB )) or resid 1107 through 1147)) } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'L' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'M' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' } ncs_group { reference = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'K' selection = chain 'T' } ncs_group { reference = chain 'N' selection = chain 'Q' selection = chain 'S' } ncs_group { reference = chain 'P' selection = chain 'U' selection = (chain 'V' and (resid 1 through 6 or (resid 7 and (name N or name CA or name C o \ r name O or name CB )) or resid 8 through 120)) } 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: 5.670 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.670 Check model and map are aligned: 0.120 Set scattering table: 0.100 Process input model: 35.970 Find NCS groups from input model: 0.760 Set up NCS constraints: 0.120 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:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4519 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 : 0.015 0.879 39893 Z= 0.990 Angle : 1.530 62.941 54382 Z= 1.099 Chirality : 0.101 0.968 6174 Planarity : 0.010 0.304 6973 Dihedral : 10.849 80.795 14415 Min Nonbonded Distance : 1.589 Molprobity Statistics. All-atom Clashscore : 21.26 Ramachandran Plot: Outliers : 0.30 % Allowed : 4.48 % Favored : 95.22 % Rotamer: Outliers : 1.35 % Allowed : 5.77 % Favored : 92.87 % Cbeta Deviations : 0.49 % Peptide Plane: Cis-proline : 1.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.12), residues: 4976 helix: 4.22 (0.18), residues: 745 sheet: 0.45 (0.14), residues: 1280 loop : -0.54 (0.11), residues: 2951 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG K 96 TYR 0.030 0.002 TYR J 94 PHE 0.023 0.002 PHE D 82 TRP 0.026 0.002 TRP J 47 HIS 0.008 0.001 HIS V 36 Details of bonding type rmsd covalent geometry : bond 0.01163 (39813) covalent geometry : angle 1.40695 (54200) SS BOND : bond 0.24433 ( 55) SS BOND : angle 13.25353 ( 110) hydrogen bonds : bond 0.21045 ( 1406) hydrogen bonds : angle 9.64897 ( 3822) Misc. bond : bond 0.08278 ( 1) link_BETA1-4 : bond 0.00105 ( 12) link_BETA1-4 : angle 0.49316 ( 36) link_NAG-ASN : bond 0.01311 ( 12) link_NAG-ASN : angle 4.53757 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9952 Ramachandran restraints generated. 4976 Oldfield, 0 Emsley, 4976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9952 Ramachandran restraints generated. 4976 Oldfield, 0 Emsley, 4976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 4338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 400 time to evaluate : 1.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 434 ILE cc_start: 0.4448 (OUTLIER) cc_final: 0.4184 (mt) REVERT: D 46 LEU cc_start: 0.4214 (mt) cc_final: 0.2679 (mm) REVERT: P 71 MET cc_start: 0.0054 (mtm) cc_final: -0.0500 (mmt) outliers start: 57 outliers final: 5 residues processed: 447 average time/residue: 0.2577 time to fit residues: 181.9671 Evaluate side-chains 176 residues out of total 4338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 170 time to evaluate : 1.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 965 GLN Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain L residue 43 LYS Chi-restraints excluded: chain O residue 97 VAL Chi-restraints excluded: chain R residue 91 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 497 random chunks: chunk 432 optimal weight: 40.0000 chunk 197 optimal weight: 0.9980 chunk 388 optimal weight: 30.0000 chunk 455 optimal weight: 50.0000 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 0.8980 chunk 494 optimal weight: 20.0000 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 2.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS A 52 GLN A 66 HIS A 69 HIS A 165 ASN A 211 ASN A 331 ASN A 394 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 481 ASN A 655 HIS A 675 GLN A 872 GLN ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 165 ASN B 211 ASN B 282 ASN B 370 ASN B 487 ASN ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 655 HIS B 675 GLN B 804 GLN B 901 GLN B 935 GLN B1011 GLN B1088 HIS C 49 HIS C 52 GLN C 165 ASN C 211 ASN C 370 ASN C 487 ASN C 493 GLN C 655 HIS C 675 GLN C 901 GLN D 91 ASN ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 55 ASN H 91 ASN H 99 GLN I 84 ASN ** J 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 84 ASN ** K 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 6 GLN L 55 ASN L 112 GLN N 6 GLN P 40 GLN P 66 GLN Q 6 GLN R 77 ASN S 6 GLN U 40 GLN U 114 GLN V 114 GLN Total number of N/Q/H flips: 52 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4513 r_free = 0.4513 target = 0.093213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.070475 restraints weight = 331306.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.070397 restraints weight = 156048.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.071073 restraints weight = 95576.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.070917 restraints weight = 61249.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.071070 restraints weight = 67952.031| |-----------------------------------------------------------------------------| r_work (final): 0.3824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7243 moved from start: 0.2736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 39893 Z= 0.194 Angle : 0.716 15.029 54382 Z= 0.373 Chirality : 0.047 0.372 6174 Planarity : 0.005 0.086 6973 Dihedral : 5.272 45.943 5921 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.59 % Favored : 97.23 % Rotamer: Outliers : 2.16 % Allowed : 9.76 % Favored : 88.07 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 1.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.12), residues: 4976 helix: 2.65 (0.18), residues: 751 sheet: 0.30 (0.13), residues: 1438 loop : -0.54 (0.11), residues: 2787 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG V 68 TYR 0.030 0.002 TYR R 94 PHE 0.034 0.002 PHE V 109 TRP 0.023 0.002 TRP P 112 HIS 0.008 0.002 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00419 (39813) covalent geometry : angle 0.71082 (54200) SS BOND : bond 0.00462 ( 55) SS BOND : angle 1.41860 ( 110) hydrogen bonds : bond 0.04938 ( 1406) hydrogen bonds : angle 7.28817 ( 3822) Misc. bond : bond 0.00023 ( 1) link_BETA1-4 : bond 0.00629 ( 12) link_BETA1-4 : angle 1.66858 ( 36) link_NAG-ASN : bond 0.00672 ( 12) link_NAG-ASN : angle 2.12209 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9952 Ramachandran restraints generated. 4976 Oldfield, 0 Emsley, 4976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9952 Ramachandran restraints generated. 4976 Oldfield, 0 Emsley, 4976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 4338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 201 time to evaluate : 1.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: J 79 LEU cc_start: -0.2327 (OUTLIER) cc_final: -0.3408 (mt) REVERT: L 43 LYS cc_start: 0.5102 (OUTLIER) cc_final: 0.4784 (mppt) REVERT: P 58 GLU cc_start: 0.8928 (mm-30) cc_final: 0.8479 (tm-30) REVERT: P 71 MET cc_start: 0.7454 (mtm) cc_final: 0.7114 (tmm) REVERT: U 49 MET cc_start: 0.7269 (OUTLIER) cc_final: 0.6366 (ptt) REVERT: U 65 PHE cc_start: 0.7588 (m-80) cc_final: 0.7315 (m-80) REVERT: U 71 MET cc_start: 0.5450 (tpt) cc_final: 0.4856 (tpt) REVERT: U 82 MET cc_start: 0.1714 (tpt) cc_final: 0.1308 (tpt) REVERT: V 39 ARG cc_start: 0.4320 (OUTLIER) cc_final: 0.3873 (ptp90) REVERT: V 81 TYR cc_start: 0.9017 (m-80) cc_final: 0.8665 (m-80) outliers start: 91 outliers final: 36 residues processed: 281 average time/residue: 0.2407 time to fit residues: 110.4316 Evaluate side-chains 193 residues out of total 4338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 153 time to evaluate : 1.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 965 GLN Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 1064 HIS Chi-restraints excluded: chain B residue 1127 ASP Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 40 ASP Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain I residue 101 THR Chi-restraints excluded: chain J residue 79 LEU Chi-restraints excluded: chain K residue 65 SER Chi-restraints excluded: chain L residue 43 LYS Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain O residue 97 VAL Chi-restraints excluded: chain R residue 5 VAL Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 44 ARG Chi-restraints excluded: chain R residue 108 ASP Chi-restraints excluded: chain U residue 49 MET Chi-restraints excluded: chain V residue 39 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 497 random chunks: chunk 454 optimal weight: 20.0000 chunk 38 optimal weight: 8.9990 chunk 110 optimal weight: 2.9990 chunk 317 optimal weight: 1.9990 chunk 408 optimal weight: 50.0000 chunk 392 optimal weight: 50.0000 chunk 395 optimal weight: 40.0000 chunk 111 optimal weight: 1.9990 chunk 146 optimal weight: 50.0000 chunk 126 optimal weight: 8.9990 chunk 217 optimal weight: 10.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN A 965 GLN ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 185 ASN ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1101 HIS C 66 HIS C 185 ASN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 282 ASN C 414 GLN ** C 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 99 GLN ** J 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 104 ASN ** K 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 57 GLN U 3 GLN ** V 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.088780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.063560 restraints weight = 316502.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.065140 restraints weight = 162698.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.064081 restraints weight = 95466.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.064178 restraints weight = 113036.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.064211 restraints weight = 89947.346| |-----------------------------------------------------------------------------| r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.4701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.081 39893 Z= 0.301 Angle : 0.768 11.022 54382 Z= 0.405 Chirality : 0.049 0.401 6174 Planarity : 0.006 0.125 6973 Dihedral : 5.696 55.644 5917 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 15.25 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.02 % Favored : 95.82 % Rotamer: Outliers : 2.19 % Allowed : 10.93 % Favored : 86.89 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 1.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.11), residues: 4976 helix: 1.62 (0.18), residues: 763 sheet: -0.06 (0.13), residues: 1402 loop : -0.75 (0.11), residues: 2811 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG I 98 TYR 0.043 0.002 TYR C 904 PHE 0.037 0.002 PHE B 797 TRP 0.029 0.002 TRP V 37 HIS 0.007 0.002 HIS B 69 Details of bonding type rmsd covalent geometry : bond 0.00665 (39813) covalent geometry : angle 0.76035 (54200) SS BOND : bond 0.00529 ( 55) SS BOND : angle 1.58168 ( 110) hydrogen bonds : bond 0.05186 ( 1406) hydrogen bonds : angle 7.07841 ( 3822) Misc. bond : bond 0.00092 ( 1) link_BETA1-4 : bond 0.01262 ( 12) link_BETA1-4 : angle 1.64797 ( 36) link_NAG-ASN : bond 0.00955 ( 12) link_NAG-ASN : angle 3.32052 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9952 Ramachandran restraints generated. 4976 Oldfield, 0 Emsley, 4976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9952 Ramachandran restraints generated. 4976 Oldfield, 0 Emsley, 4976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 4338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 172 time to evaluate : 1.443 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: B 97 LYS cc_start: 0.6362 (OUTLIER) cc_final: 0.6015 (mmtm) REVERT: B 1064 HIS cc_start: 0.8583 (OUTLIER) cc_final: 0.7567 (p90) REVERT: C 557 LYS cc_start: 0.3203 (OUTLIER) cc_final: 0.2984 (tttt) REVERT: J 60 TYR cc_start: 0.7053 (m-10) cc_final: 0.6697 (t80) REVERT: J 79 LEU cc_start: -0.1785 (OUTLIER) cc_final: -0.2058 (pp) REVERT: K 34 ASN cc_start: 0.3786 (m-40) cc_final: 0.2994 (m110) REVERT: P 49 MET cc_start: 0.9191 (OUTLIER) cc_final: 0.8927 (ppp) REVERT: P 71 MET cc_start: 0.6865 (mtm) cc_final: 0.6069 (tmm) REVERT: P 82 MET cc_start: 0.1435 (tpt) cc_final: -0.1121 (tpt) REVERT: U 49 MET cc_start: 0.7097 (OUTLIER) cc_final: 0.6546 (ptt) outliers start: 92 outliers final: 49 residues processed: 251 average time/residue: 0.2334 time to fit residues: 97.5031 Evaluate side-chains 188 residues out of total 4338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 133 time to evaluate : 1.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 79 PHE Chi-restraints excluded: chain B residue 97 LYS Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 1064 HIS Chi-restraints excluded: chain B residue 1082 CYS Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1127 ASP Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 40 ASP Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 185 ASN Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 557 LYS Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 945 LEU Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain H residue 99 GLN Chi-restraints excluded: chain J residue 79 LEU Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain O residue 9 THR Chi-restraints excluded: chain O residue 97 VAL Chi-restraints excluded: chain P residue 49 MET Chi-restraints excluded: chain P residue 60 MET Chi-restraints excluded: chain Q residue 96 LEU Chi-restraints excluded: chain R residue 5 VAL Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 73 ASP Chi-restraints excluded: chain R residue 108 ASP Chi-restraints excluded: chain T residue 58 VAL Chi-restraints excluded: chain U residue 49 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 497 random chunks: chunk 354 optimal weight: 30.0000 chunk 160 optimal weight: 10.0000 chunk 485 optimal weight: 30.0000 chunk 314 optimal weight: 0.9980 chunk 154 optimal weight: 7.9990 chunk 262 optimal weight: 30.0000 chunk 316 optimal weight: 0.7980 chunk 270 optimal weight: 0.8980 chunk 200 optimal weight: 1.9990 chunk 484 optimal weight: 40.0000 chunk 391 optimal weight: 2.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 955 ASN ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1101 HIS ** C 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 185 ASN C 207 HIS C 271 GLN C 414 GLN ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 35 HIS H 99 GLN J 82 GLN ** K 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 28 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4416 r_free = 0.4416 target = 0.089463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.064695 restraints weight = 317716.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.065548 restraints weight = 159073.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.065459 restraints weight = 100899.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.065415 restraints weight = 103788.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.066413 restraints weight = 95037.819| |-----------------------------------------------------------------------------| r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.4865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 39893 Z= 0.139 Angle : 0.585 13.501 54382 Z= 0.305 Chirality : 0.044 0.574 6174 Planarity : 0.004 0.052 6973 Dihedral : 5.118 52.565 5910 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.28 % Favored : 96.58 % Rotamer: Outliers : 1.88 % Allowed : 11.64 % Favored : 86.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.12), residues: 4976 helix: 2.05 (0.18), residues: 759 sheet: 0.05 (0.13), residues: 1414 loop : -0.74 (0.11), residues: 2803 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B1107 TYR 0.020 0.001 TYR C 904 PHE 0.025 0.001 PHE V 109 TRP 0.021 0.001 TRP I 36 HIS 0.006 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00300 (39813) covalent geometry : angle 0.57804 (54200) SS BOND : bond 0.00328 ( 55) SS BOND : angle 1.31354 ( 110) hydrogen bonds : bond 0.03980 ( 1406) hydrogen bonds : angle 6.51836 ( 3822) Misc. bond : bond 0.00028 ( 1) link_BETA1-4 : bond 0.00344 ( 12) link_BETA1-4 : angle 1.27679 ( 36) link_NAG-ASN : bond 0.00490 ( 12) link_NAG-ASN : angle 2.50577 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9952 Ramachandran restraints generated. 4976 Oldfield, 0 Emsley, 4976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9952 Ramachandran restraints generated. 4976 Oldfield, 0 Emsley, 4976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 4338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 153 time to evaluate : 1.489 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: B 97 LYS cc_start: 0.6254 (OUTLIER) cc_final: 0.5883 (mmtm) REVERT: B 869 MET cc_start: 0.8682 (tpp) cc_final: 0.8287 (tpp) REVERT: B 1064 HIS cc_start: 0.8228 (OUTLIER) cc_final: 0.7513 (p90) REVERT: C 697 MET cc_start: 0.8289 (OUTLIER) cc_final: 0.8035 (ppp) REVERT: C 988 GLU cc_start: 0.7655 (OUTLIER) cc_final: 0.7345 (pm20) REVERT: I 103 MET cc_start: 0.2912 (ttp) cc_final: 0.2492 (tmm) REVERT: J 60 TYR cc_start: 0.6879 (m-10) cc_final: 0.6571 (t80) REVERT: J 79 LEU cc_start: -0.2723 (OUTLIER) cc_final: -0.3316 (pp) REVERT: J 103 MET cc_start: 0.6692 (tpt) cc_final: 0.6480 (tpt) REVERT: P 49 MET cc_start: 0.9109 (tmm) cc_final: 0.8530 (ppp) REVERT: P 71 MET cc_start: 0.6210 (mtm) cc_final: 0.5734 (ttt) REVERT: P 82 MET cc_start: 0.0230 (tpt) cc_final: -0.0960 (tpt) REVERT: V 82 MET cc_start: -0.0927 (tpt) cc_final: -0.1605 (tpp) outliers start: 79 outliers final: 44 residues processed: 223 average time/residue: 0.2315 time to fit residues: 86.1437 Evaluate side-chains 186 residues out of total 4338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 137 time to evaluate : 1.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 79 PHE Chi-restraints excluded: chain B residue 97 LYS Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 1064 HIS Chi-restraints excluded: chain B residue 1127 ASP Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 40 ASP Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain I residue 79 LEU Chi-restraints excluded: chain J residue 79 LEU Chi-restraints excluded: chain K residue 65 SER Chi-restraints excluded: chain L residue 24 VAL Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain O residue 42 LYS Chi-restraints excluded: chain O residue 51 ILE Chi-restraints excluded: chain O residue 97 VAL Chi-restraints excluded: chain P residue 60 MET Chi-restraints excluded: chain P residue 116 THR Chi-restraints excluded: chain Q residue 96 LEU Chi-restraints excluded: chain R residue 5 VAL Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 73 ASP Chi-restraints excluded: chain R residue 108 ASP Chi-restraints excluded: chain U residue 92 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 497 random chunks: chunk 66 optimal weight: 3.9990 chunk 45 optimal weight: 20.0000 chunk 160 optimal weight: 0.7980 chunk 10 optimal weight: 9.9990 chunk 343 optimal weight: 7.9990 chunk 274 optimal weight: 5.9990 chunk 313 optimal weight: 0.9990 chunk 56 optimal weight: 4.9990 chunk 179 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 383 optimal weight: 7.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 703 ASN ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 HIS ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 122 ASN C 185 ASN ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 3 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.088666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.063472 restraints weight = 314765.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.064564 restraints weight = 160675.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.064245 restraints weight = 98414.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.064101 restraints weight = 100721.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.064577 restraints weight = 93809.202| |-----------------------------------------------------------------------------| r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.5337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 39893 Z= 0.177 Angle : 0.587 9.509 54382 Z= 0.305 Chirality : 0.043 0.324 6174 Planarity : 0.004 0.071 6973 Dihedral : 4.985 58.442 5910 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.80 % Favored : 96.06 % Rotamer: Outliers : 1.97 % Allowed : 12.57 % Favored : 85.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.12), residues: 4976 helix: 2.14 (0.18), residues: 749 sheet: 0.05 (0.13), residues: 1423 loop : -0.77 (0.11), residues: 2804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG V 20 TYR 0.033 0.001 TYR N 50 PHE 0.023 0.001 PHE V 109 TRP 0.019 0.001 TRP P 112 HIS 0.009 0.001 HIS U 36 Details of bonding type rmsd covalent geometry : bond 0.00388 (39813) covalent geometry : angle 0.58162 (54200) SS BOND : bond 0.00287 ( 55) SS BOND : angle 1.10650 ( 110) hydrogen bonds : bond 0.03908 ( 1406) hydrogen bonds : angle 6.29581 ( 3822) Misc. bond : bond 0.00013 ( 1) link_BETA1-4 : bond 0.00413 ( 12) link_BETA1-4 : angle 1.17182 ( 36) link_NAG-ASN : bond 0.00569 ( 12) link_NAG-ASN : angle 2.29989 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9952 Ramachandran restraints generated. 4976 Oldfield, 0 Emsley, 4976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9952 Ramachandran restraints generated. 4976 Oldfield, 0 Emsley, 4976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 4338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 154 time to evaluate : 1.099 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: A 1126 CYS cc_start: 0.4661 (p) cc_final: 0.4387 (p) REVERT: B 97 LYS cc_start: 0.6497 (OUTLIER) cc_final: 0.6237 (mmtm) REVERT: B 1064 HIS cc_start: 0.8193 (OUTLIER) cc_final: 0.7472 (p90) REVERT: C 697 MET cc_start: 0.8339 (OUTLIER) cc_final: 0.7998 (ppp) REVERT: C 988 GLU cc_start: 0.8031 (OUTLIER) cc_final: 0.7681 (pm20) REVERT: I 34 MET cc_start: -0.1672 (mtp) cc_final: -0.2654 (mmp) REVERT: I 103 MET cc_start: 0.3317 (ttp) cc_final: 0.3023 (tmm) REVERT: J 60 TYR cc_start: 0.6998 (m-10) cc_final: 0.6727 (t80) REVERT: P 49 MET cc_start: 0.9147 (OUTLIER) cc_final: 0.8851 (ppp) REVERT: P 71 MET cc_start: 0.6671 (mtm) cc_final: 0.6374 (ttt) REVERT: P 82 MET cc_start: 0.0479 (tpt) cc_final: -0.0622 (mmt) REVERT: P 110 ASP cc_start: 0.2579 (OUTLIER) cc_final: 0.2353 (p0) REVERT: Q 33 TYR cc_start: 0.8549 (m-80) cc_final: 0.7728 (p90) REVERT: U 49 MET cc_start: 0.6592 (ppp) cc_final: 0.6310 (ppp) outliers start: 83 outliers final: 54 residues processed: 226 average time/residue: 0.2308 time to fit residues: 86.9125 Evaluate side-chains 201 residues out of total 4338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 141 time to evaluate : 1.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 451 TYR Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 79 PHE Chi-restraints excluded: chain B residue 97 LYS Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1064 HIS Chi-restraints excluded: chain B residue 1127 ASP Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 40 ASP Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 185 ASN Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain K residue 65 SER Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain N residue 50 TYR Chi-restraints excluded: chain O residue 42 LYS Chi-restraints excluded: chain O residue 51 ILE Chi-restraints excluded: chain O residue 97 VAL Chi-restraints excluded: chain O residue 105 THR Chi-restraints excluded: chain P residue 49 MET Chi-restraints excluded: chain P residue 60 MET Chi-restraints excluded: chain P residue 110 ASP Chi-restraints excluded: chain Q residue 96 LEU Chi-restraints excluded: chain R residue 5 VAL Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 73 ASP Chi-restraints excluded: chain R residue 108 ASP Chi-restraints excluded: chain T residue 5 THR Chi-restraints excluded: chain U residue 92 THR Chi-restraints excluded: chain V residue 60 MET Chi-restraints excluded: chain V residue 81 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 497 random chunks: chunk 302 optimal weight: 5.9990 chunk 198 optimal weight: 6.9990 chunk 57 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 308 optimal weight: 1.9990 chunk 288 optimal weight: 3.9990 chunk 51 optimal weight: 7.9990 chunk 338 optimal weight: 7.9990 chunk 237 optimal weight: 20.0000 chunk 196 optimal weight: 0.7980 chunk 173 optimal weight: 5.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 185 ASN ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 580 GLN ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.088127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.063226 restraints weight = 313728.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.063904 restraints weight = 168153.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.063551 restraints weight = 111545.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.063601 restraints weight = 96275.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.063614 restraints weight = 83741.833| |-----------------------------------------------------------------------------| r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.5702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 39893 Z= 0.187 Angle : 0.585 10.970 54382 Z= 0.304 Chirality : 0.043 0.349 6174 Planarity : 0.004 0.053 6973 Dihedral : 5.019 59.284 5910 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.80 % Favored : 96.06 % Rotamer: Outliers : 2.35 % Allowed : 12.66 % Favored : 84.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.12), residues: 4976 helix: 2.23 (0.18), residues: 729 sheet: -0.03 (0.13), residues: 1440 loop : -0.81 (0.11), residues: 2807 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG R 67 TYR 0.028 0.001 TYR V 61 PHE 0.022 0.001 PHE V 109 TRP 0.018 0.001 TRP I 36 HIS 0.005 0.001 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00410 (39813) covalent geometry : angle 0.57820 (54200) SS BOND : bond 0.00387 ( 55) SS BOND : angle 1.53659 ( 110) hydrogen bonds : bond 0.03809 ( 1406) hydrogen bonds : angle 6.17093 ( 3822) Misc. bond : bond 0.00009 ( 1) link_BETA1-4 : bond 0.00414 ( 12) link_BETA1-4 : angle 1.21655 ( 36) link_NAG-ASN : bond 0.00562 ( 12) link_NAG-ASN : angle 2.32781 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9952 Ramachandran restraints generated. 4976 Oldfield, 0 Emsley, 4976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9952 Ramachandran restraints generated. 4976 Oldfield, 0 Emsley, 4976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 4338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 149 time to evaluate : 1.462 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: A 869 MET cc_start: 0.8033 (ttm) cc_final: 0.7612 (ttp) REVERT: B 97 LYS cc_start: 0.6824 (OUTLIER) cc_final: 0.6601 (mmtm) REVERT: B 166 CYS cc_start: 0.8301 (OUTLIER) cc_final: 0.7630 (m) REVERT: B 740 MET cc_start: 0.8474 (tpp) cc_final: 0.8257 (tpp) REVERT: B 1064 HIS cc_start: 0.8188 (OUTLIER) cc_final: 0.7507 (p90) REVERT: C 63 THR cc_start: 0.8655 (OUTLIER) cc_final: 0.8261 (p) REVERT: C 329 PHE cc_start: 0.8601 (OUTLIER) cc_final: 0.8048 (m-80) REVERT: I 34 MET cc_start: -0.2242 (mtp) cc_final: -0.2713 (mmp) REVERT: I 103 MET cc_start: 0.2372 (ttp) cc_final: 0.1924 (tmm) REVERT: P 49 MET cc_start: 0.9171 (OUTLIER) cc_final: 0.8793 (ppp) REVERT: P 58 GLU cc_start: 0.9167 (mm-30) cc_final: 0.8717 (pm20) REVERT: P 71 MET cc_start: 0.5666 (mtm) cc_final: 0.5068 (ttt) REVERT: P 82 MET cc_start: -0.0300 (tpt) cc_final: -0.1167 (mmt) REVERT: P 112 TRP cc_start: 0.8081 (p90) cc_final: 0.7598 (p90) REVERT: Q 33 TYR cc_start: 0.8579 (m-80) cc_final: 0.7566 (p90) REVERT: V 49 MET cc_start: 0.7084 (ppp) cc_final: 0.6367 (tpt) outliers start: 99 outliers final: 62 residues processed: 236 average time/residue: 0.2276 time to fit residues: 89.8073 Evaluate side-chains 203 residues out of total 4338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 135 time to evaluate : 1.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 451 TYR Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 79 PHE Chi-restraints excluded: chain B residue 97 LYS Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 967 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1064 HIS Chi-restraints excluded: chain B residue 1127 ASP Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 40 ASP Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 557 LYS Chi-restraints excluded: chain C residue 945 LEU Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain I residue 101 THR Chi-restraints excluded: chain K residue 65 SER Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain N residue 50 TYR Chi-restraints excluded: chain O residue 42 LYS Chi-restraints excluded: chain O residue 51 ILE Chi-restraints excluded: chain O residue 97 VAL Chi-restraints excluded: chain O residue 105 THR Chi-restraints excluded: chain P residue 49 MET Chi-restraints excluded: chain P residue 60 MET Chi-restraints excluded: chain P residue 110 ASP Chi-restraints excluded: chain P residue 116 THR Chi-restraints excluded: chain Q residue 96 LEU Chi-restraints excluded: chain R residue 5 VAL Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 73 ASP Chi-restraints excluded: chain R residue 108 ASP Chi-restraints excluded: chain T residue 58 VAL Chi-restraints excluded: chain U residue 92 THR Chi-restraints excluded: chain V residue 81 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 497 random chunks: chunk 381 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 413 optimal weight: 0.0670 chunk 187 optimal weight: 0.9990 chunk 95 optimal weight: 5.9990 chunk 97 optimal weight: 0.6980 chunk 21 optimal weight: 0.9980 chunk 203 optimal weight: 3.9990 chunk 337 optimal weight: 40.0000 chunk 374 optimal weight: 9.9990 chunk 241 optimal weight: 1.9990 overall best weight: 0.9522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 901 GLN ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 52 ASN S 52 ASN U 66 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4399 r_free = 0.4399 target = 0.088730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.063620 restraints weight = 313418.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.065603 restraints weight = 150771.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.063995 restraints weight = 85825.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.064212 restraints weight = 90793.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.064087 restraints weight = 83318.134| |-----------------------------------------------------------------------------| r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.5800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.095 39893 Z= 0.114 Angle : 0.546 12.488 54382 Z= 0.283 Chirality : 0.042 0.307 6174 Planarity : 0.004 0.053 6973 Dihedral : 4.704 58.617 5910 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.52 % Favored : 96.34 % Rotamer: Outliers : 1.85 % Allowed : 13.09 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.12), residues: 4976 helix: 2.40 (0.19), residues: 729 sheet: 0.07 (0.13), residues: 1427 loop : -0.79 (0.11), residues: 2820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG T 24 TYR 0.029 0.001 TYR S 33 PHE 0.020 0.001 PHE V 109 TRP 0.019 0.001 TRP I 36 HIS 0.004 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00251 (39813) covalent geometry : angle 0.53933 (54200) SS BOND : bond 0.00379 ( 55) SS BOND : angle 1.63008 ( 110) hydrogen bonds : bond 0.03491 ( 1406) hydrogen bonds : angle 5.87158 ( 3822) Misc. bond : bond 0.00031 ( 1) link_BETA1-4 : bond 0.00357 ( 12) link_BETA1-4 : angle 1.12404 ( 36) link_NAG-ASN : bond 0.00196 ( 12) link_NAG-ASN : angle 1.72554 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9952 Ramachandran restraints generated. 4976 Oldfield, 0 Emsley, 4976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9952 Ramachandran restraints generated. 4976 Oldfield, 0 Emsley, 4976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 4338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 149 time to evaluate : 1.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 422 ASN cc_start: 0.7632 (OUTLIER) cc_final: 0.6848 (p0) REVERT: A 740 MET cc_start: 0.8526 (mmm) cc_final: 0.8198 (mmm) REVERT: B 166 CYS cc_start: 0.8139 (OUTLIER) cc_final: 0.7401 (m) REVERT: B 740 MET cc_start: 0.8502 (tpp) cc_final: 0.8248 (tpp) REVERT: B 1064 HIS cc_start: 0.7942 (OUTLIER) cc_final: 0.7457 (p90) REVERT: C 63 THR cc_start: 0.8499 (OUTLIER) cc_final: 0.8111 (t) REVERT: C 329 PHE cc_start: 0.8704 (OUTLIER) cc_final: 0.8193 (m-80) REVERT: I 34 MET cc_start: -0.1766 (mtp) cc_final: -0.2527 (mmp) REVERT: P 49 MET cc_start: 0.9109 (OUTLIER) cc_final: 0.8829 (ppp) REVERT: P 58 GLU cc_start: 0.9121 (mm-30) cc_final: 0.8779 (tm-30) REVERT: P 82 MET cc_start: 0.0326 (tpt) cc_final: -0.0966 (mmt) REVERT: Q 33 TYR cc_start: 0.8597 (m-80) cc_final: 0.7848 (p90) outliers start: 78 outliers final: 57 residues processed: 216 average time/residue: 0.2295 time to fit residues: 82.5844 Evaluate side-chains 199 residues out of total 4338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 136 time to evaluate : 1.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 451 TYR Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 79 PHE Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1064 HIS Chi-restraints excluded: chain B residue 1127 ASP Chi-restraints excluded: chain C residue 40 ASP Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 185 ASN Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 557 LYS Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 945 LEU Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain K residue 65 SER Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain N residue 50 TYR Chi-restraints excluded: chain O residue 42 LYS Chi-restraints excluded: chain O residue 51 ILE Chi-restraints excluded: chain O residue 97 VAL Chi-restraints excluded: chain O residue 105 THR Chi-restraints excluded: chain P residue 49 MET Chi-restraints excluded: chain P residue 60 MET Chi-restraints excluded: chain P residue 110 ASP Chi-restraints excluded: chain P residue 116 THR Chi-restraints excluded: chain Q residue 96 LEU Chi-restraints excluded: chain R residue 5 VAL Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 73 ASP Chi-restraints excluded: chain R residue 108 ASP Chi-restraints excluded: chain S residue 33 TYR Chi-restraints excluded: chain T residue 58 VAL Chi-restraints excluded: chain U residue 92 THR Chi-restraints excluded: chain V residue 61 TYR Chi-restraints excluded: chain V residue 81 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 497 random chunks: chunk 132 optimal weight: 6.9990 chunk 253 optimal weight: 40.0000 chunk 362 optimal weight: 6.9990 chunk 325 optimal weight: 8.9990 chunk 240 optimal weight: 8.9990 chunk 10 optimal weight: 0.9980 chunk 86 optimal weight: 2.9990 chunk 232 optimal weight: 9.9990 chunk 408 optimal weight: 50.0000 chunk 288 optimal weight: 6.9990 chunk 207 optimal weight: 3.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 GLN A 872 GLN A 901 GLN ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1088 HIS B 185 ASN B 360 ASN ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 690 GLN C 414 GLN C 450 ASN D 99 GLN ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 104 ASN ** K 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.086704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.061181 restraints weight = 310850.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.061788 restraints weight = 162834.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.061674 restraints weight = 111141.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.061705 restraints weight = 113234.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.061606 restraints weight = 98647.101| |-----------------------------------------------------------------------------| r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.6588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.088 39893 Z= 0.267 Angle : 0.688 11.301 54382 Z= 0.355 Chirality : 0.045 0.396 6174 Planarity : 0.005 0.076 6973 Dihedral : 5.397 56.804 5910 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 14.28 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.30 % Favored : 95.56 % Rotamer: Outliers : 2.09 % Allowed : 13.16 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.12), residues: 4976 helix: 1.80 (0.18), residues: 732 sheet: -0.27 (0.13), residues: 1409 loop : -0.86 (0.11), residues: 2835 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG R 19 TYR 0.027 0.002 TYR D 85 PHE 0.029 0.002 PHE A 186 TRP 0.024 0.002 TRP I 36 HIS 0.010 0.002 HIS B1083 Details of bonding type rmsd covalent geometry : bond 0.00590 (39813) covalent geometry : angle 0.67714 (54200) SS BOND : bond 0.00463 ( 55) SS BOND : angle 2.02963 ( 110) hydrogen bonds : bond 0.04306 ( 1406) hydrogen bonds : angle 6.30118 ( 3822) Misc. bond : bond 0.00002 ( 1) link_BETA1-4 : bond 0.00479 ( 12) link_BETA1-4 : angle 1.67640 ( 36) link_NAG-ASN : bond 0.00943 ( 12) link_NAG-ASN : angle 3.19459 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9952 Ramachandran restraints generated. 4976 Oldfield, 0 Emsley, 4976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9952 Ramachandran restraints generated. 4976 Oldfield, 0 Emsley, 4976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 4338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 145 time to evaluate : 1.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 976 VAL cc_start: 0.9220 (OUTLIER) cc_final: 0.8934 (p) REVERT: B 1064 HIS cc_start: 0.8294 (OUTLIER) cc_final: 0.7577 (p90) REVERT: C 153 MET cc_start: 0.8101 (tpt) cc_final: 0.7880 (tpt) REVERT: C 329 PHE cc_start: 0.8820 (OUTLIER) cc_final: 0.8567 (m-80) REVERT: C 697 MET cc_start: 0.8261 (ptm) cc_final: 0.8033 (ptm) REVERT: E 31 ASN cc_start: 0.8742 (t0) cc_final: 0.8534 (p0) REVERT: L 83 LEU cc_start: 0.4968 (tp) cc_final: 0.4347 (mp) REVERT: L 86 LEU cc_start: 0.3640 (OUTLIER) cc_final: 0.3069 (mm) REVERT: P 49 MET cc_start: 0.9120 (tmm) cc_final: 0.8830 (ppp) REVERT: P 58 GLU cc_start: 0.9162 (mm-30) cc_final: 0.8715 (pm20) REVERT: P 71 MET cc_start: 0.2752 (ttt) cc_final: 0.1764 (tmm) REVERT: Q 33 TYR cc_start: 0.8603 (m-80) cc_final: 0.7681 (p90) REVERT: R 34 MET cc_start: 0.6716 (mmt) cc_final: 0.6346 (mmt) REVERT: R 67 ARG cc_start: 0.8414 (mmm160) cc_final: 0.8173 (mmp-170) REVERT: T 24 ARG cc_start: 0.7365 (ptm-80) cc_final: 0.7053 (tpt90) outliers start: 88 outliers final: 66 residues processed: 221 average time/residue: 0.2306 time to fit residues: 86.2039 Evaluate side-chains 198 residues out of total 4338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 128 time to evaluate : 1.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 79 PHE Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 967 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1064 HIS Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1127 ASP Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 185 ASN Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 214 ARG Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 557 LYS Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 945 LEU Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain I residue 101 THR Chi-restraints excluded: chain K residue 65 SER Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain L residue 86 LEU Chi-restraints excluded: chain N residue 50 TYR Chi-restraints excluded: chain O residue 42 LYS Chi-restraints excluded: chain O residue 51 ILE Chi-restraints excluded: chain O residue 97 VAL Chi-restraints excluded: chain O residue 105 THR Chi-restraints excluded: chain P residue 60 MET Chi-restraints excluded: chain P residue 110 ASP Chi-restraints excluded: chain Q residue 96 LEU Chi-restraints excluded: chain R residue 5 VAL Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 73 ASP Chi-restraints excluded: chain R residue 108 ASP Chi-restraints excluded: chain S residue 33 TYR Chi-restraints excluded: chain T residue 58 VAL Chi-restraints excluded: chain V residue 60 MET Chi-restraints excluded: chain V residue 61 TYR Chi-restraints excluded: chain V residue 81 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 497 random chunks: chunk 136 optimal weight: 2.9990 chunk 142 optimal weight: 7.9990 chunk 47 optimal weight: 10.0000 chunk 196 optimal weight: 0.9990 chunk 134 optimal weight: 0.9990 chunk 287 optimal weight: 0.9980 chunk 330 optimal weight: 7.9990 chunk 452 optimal weight: 20.0000 chunk 214 optimal weight: 40.0000 chunk 10 optimal weight: 9.9990 chunk 293 optimal weight: 1.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 GLN ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 185 ASN ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 414 GLN ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 52 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.087589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.062133 restraints weight = 311685.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.063296 restraints weight = 154058.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.062909 restraints weight = 92445.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.062871 restraints weight = 96506.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.062800 restraints weight = 89487.070| |-----------------------------------------------------------------------------| r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.6616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 39893 Z= 0.131 Angle : 0.567 11.749 54382 Z= 0.291 Chirality : 0.043 0.328 6174 Planarity : 0.004 0.057 6973 Dihedral : 4.973 59.674 5910 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.52 % Favored : 96.34 % Rotamer: Outliers : 1.78 % Allowed : 13.83 % Favored : 84.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.12), residues: 4976 helix: 2.26 (0.19), residues: 734 sheet: -0.19 (0.13), residues: 1404 loop : -0.81 (0.11), residues: 2838 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG P 68 TYR 0.023 0.001 TYR S 33 PHE 0.023 0.001 PHE D 86 TRP 0.025 0.001 TRP V 112 HIS 0.005 0.001 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00289 (39813) covalent geometry : angle 0.56122 (54200) SS BOND : bond 0.00221 ( 55) SS BOND : angle 1.39610 ( 110) hydrogen bonds : bond 0.03513 ( 1406) hydrogen bonds : angle 5.89414 ( 3822) Misc. bond : bond 0.00028 ( 1) link_BETA1-4 : bond 0.00542 ( 12) link_BETA1-4 : angle 1.28048 ( 36) link_NAG-ASN : bond 0.00294 ( 12) link_NAG-ASN : angle 2.04847 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9952 Ramachandran restraints generated. 4976 Oldfield, 0 Emsley, 4976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9952 Ramachandran restraints generated. 4976 Oldfield, 0 Emsley, 4976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 4338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 135 time to evaluate : 1.256 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: B 740 MET cc_start: 0.8449 (OUTLIER) cc_final: 0.8122 (tpp) REVERT: B 1064 HIS cc_start: 0.7982 (OUTLIER) cc_final: 0.7416 (p90) REVERT: C 329 PHE cc_start: 0.8809 (OUTLIER) cc_final: 0.8569 (m-80) REVERT: C 557 LYS cc_start: 0.3909 (OUTLIER) cc_final: 0.1812 (mmtt) REVERT: L 83 LEU cc_start: 0.5033 (tp) cc_final: 0.4628 (mp) REVERT: L 86 LEU cc_start: 0.3929 (OUTLIER) cc_final: 0.3374 (mm) REVERT: P 71 MET cc_start: 0.3722 (ttt) cc_final: 0.3181 (tmm) REVERT: Q 33 TYR cc_start: 0.8578 (m-80) cc_final: 0.7795 (p90) REVERT: R 34 MET cc_start: 0.6891 (mmt) cc_final: 0.6637 (mmt) outliers start: 75 outliers final: 64 residues processed: 198 average time/residue: 0.2374 time to fit residues: 78.6362 Evaluate side-chains 195 residues out of total 4338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 126 time to evaluate : 1.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 451 TYR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 79 PHE Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 967 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1064 HIS Chi-restraints excluded: chain B residue 1127 ASP Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 185 ASN Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 557 LYS Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 945 LEU Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain E residue 44 SER Chi-restraints excluded: chain I residue 101 THR Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain K residue 65 SER Chi-restraints excluded: chain L residue 86 LEU Chi-restraints excluded: chain N residue 50 TYR Chi-restraints excluded: chain O residue 51 ILE Chi-restraints excluded: chain O residue 97 VAL Chi-restraints excluded: chain O residue 105 THR Chi-restraints excluded: chain P residue 60 MET Chi-restraints excluded: chain P residue 110 ASP Chi-restraints excluded: chain P residue 116 THR Chi-restraints excluded: chain Q residue 96 LEU Chi-restraints excluded: chain R residue 5 VAL Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 73 ASP Chi-restraints excluded: chain R residue 108 ASP Chi-restraints excluded: chain S residue 33 TYR Chi-restraints excluded: chain T residue 58 VAL Chi-restraints excluded: chain U residue 92 THR Chi-restraints excluded: chain V residue 60 MET Chi-restraints excluded: chain V residue 61 TYR Chi-restraints excluded: chain V residue 81 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 497 random chunks: chunk 150 optimal weight: 30.0000 chunk 97 optimal weight: 0.9980 chunk 67 optimal weight: 7.9990 chunk 453 optimal weight: 2.9990 chunk 285 optimal weight: 0.6980 chunk 495 optimal weight: 10.0000 chunk 62 optimal weight: 2.9990 chunk 265 optimal weight: 0.0020 chunk 121 optimal weight: 10.0000 chunk 205 optimal weight: 0.9980 chunk 243 optimal weight: 3.9990 overall best weight: 1.1390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 901 GLN ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 185 ASN ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 965 GLN ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 52 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.087719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.062455 restraints weight = 309422.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.063884 restraints weight = 153877.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.062936 restraints weight = 96069.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.063308 restraints weight = 107391.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.062956 restraints weight = 88631.292| |-----------------------------------------------------------------------------| r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.6687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 39893 Z= 0.119 Angle : 0.551 12.460 54382 Z= 0.282 Chirality : 0.042 0.317 6174 Planarity : 0.004 0.056 6973 Dihedral : 4.717 58.275 5910 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.96 % Favored : 95.90 % Rotamer: Outliers : 1.62 % Allowed : 14.02 % Favored : 84.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.12), residues: 4976 helix: 2.37 (0.19), residues: 735 sheet: -0.07 (0.13), residues: 1419 loop : -0.79 (0.12), residues: 2822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG T 24 TYR 0.021 0.001 TYR S 33 PHE 0.022 0.001 PHE A 464 TRP 0.022 0.001 TRP V 112 HIS 0.007 0.001 HIS I 99 Details of bonding type rmsd covalent geometry : bond 0.00262 (39813) covalent geometry : angle 0.54631 (54200) SS BOND : bond 0.00219 ( 55) SS BOND : angle 1.22759 ( 110) hydrogen bonds : bond 0.03385 ( 1406) hydrogen bonds : angle 5.71395 ( 3822) Misc. bond : bond 0.00017 ( 1) link_BETA1-4 : bond 0.00420 ( 12) link_BETA1-4 : angle 1.24566 ( 36) link_NAG-ASN : bond 0.00269 ( 12) link_NAG-ASN : angle 1.84691 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9952 Ramachandran restraints generated. 4976 Oldfield, 0 Emsley, 4976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9952 Ramachandran restraints generated. 4976 Oldfield, 0 Emsley, 4976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 4338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 129 time to evaluate : 1.014 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 422 ASN cc_start: 0.7717 (OUTLIER) cc_final: 0.6987 (p0) REVERT: B 166 CYS cc_start: 0.8125 (OUTLIER) cc_final: 0.7418 (m) REVERT: B 740 MET cc_start: 0.8492 (tpp) cc_final: 0.8199 (mmm) REVERT: B 1064 HIS cc_start: 0.7893 (OUTLIER) cc_final: 0.7396 (p90) REVERT: C 329 PHE cc_start: 0.8793 (OUTLIER) cc_final: 0.8549 (m-80) REVERT: C 557 LYS cc_start: 0.3797 (OUTLIER) cc_final: 0.1918 (mmtt) REVERT: J 103 MET cc_start: 0.6939 (tpt) cc_final: 0.6615 (tpt) REVERT: L 58 THR cc_start: 0.6472 (m) cc_final: 0.6019 (t) REVERT: L 83 LEU cc_start: 0.4905 (tp) cc_final: 0.4458 (mp) REVERT: L 86 LEU cc_start: 0.3986 (OUTLIER) cc_final: 0.3474 (mm) REVERT: P 71 MET cc_start: 0.3729 (ttt) cc_final: 0.2959 (tmm) REVERT: Q 33 TYR cc_start: 0.8569 (m-80) cc_final: 0.7785 (p90) REVERT: R 34 MET cc_start: 0.7017 (mmt) cc_final: 0.6727 (mmt) outliers start: 68 outliers final: 58 residues processed: 188 average time/residue: 0.2242 time to fit residues: 70.9537 Evaluate side-chains 185 residues out of total 4338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 121 time to evaluate : 1.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 451 TYR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 79 PHE Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 967 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1064 HIS Chi-restraints excluded: chain B residue 1127 ASP Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 185 ASN Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 557 LYS Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 945 LEU Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain E residue 44 SER Chi-restraints excluded: chain I residue 101 THR Chi-restraints excluded: chain K residue 65 SER Chi-restraints excluded: chain L residue 86 LEU Chi-restraints excluded: chain N residue 50 TYR Chi-restraints excluded: chain O residue 51 ILE Chi-restraints excluded: chain O residue 97 VAL Chi-restraints excluded: chain O residue 105 THR Chi-restraints excluded: chain P residue 60 MET Chi-restraints excluded: chain P residue 110 ASP Chi-restraints excluded: chain P residue 116 THR Chi-restraints excluded: chain Q residue 96 LEU Chi-restraints excluded: chain R residue 5 VAL Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 73 ASP Chi-restraints excluded: chain R residue 108 ASP Chi-restraints excluded: chain S residue 33 TYR Chi-restraints excluded: chain T residue 58 VAL Chi-restraints excluded: chain U residue 92 THR Chi-restraints excluded: chain V residue 60 MET Chi-restraints excluded: chain V residue 61 TYR Chi-restraints excluded: chain V residue 81 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 497 random chunks: chunk 328 optimal weight: 3.9990 chunk 280 optimal weight: 0.7980 chunk 317 optimal weight: 0.1980 chunk 431 optimal weight: 9.9990 chunk 56 optimal weight: 6.9990 chunk 426 optimal weight: 6.9990 chunk 82 optimal weight: 3.9990 chunk 367 optimal weight: 40.0000 chunk 120 optimal weight: 3.9990 chunk 404 optimal weight: 1.9990 chunk 269 optimal weight: 3.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 872 GLN A 901 GLN ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 185 ASN ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 34 ASN ** 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 = 0.4362 r_free = 0.4362 target = 0.087283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.061756 restraints weight = 311626.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.062307 restraints weight = 158222.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.063006 restraints weight = 101489.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.062517 restraints weight = 92555.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.062480 restraints weight = 88022.244| |-----------------------------------------------------------------------------| r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.6862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 39893 Z= 0.154 Angle : 0.569 12.337 54382 Z= 0.291 Chirality : 0.043 0.330 6174 Planarity : 0.004 0.055 6973 Dihedral : 4.757 58.712 5910 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.90 % Favored : 95.96 % Rotamer: Outliers : 1.69 % Allowed : 14.11 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.12), residues: 4976 helix: 2.33 (0.19), residues: 735 sheet: -0.15 (0.13), residues: 1446 loop : -0.77 (0.12), residues: 2795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG P 68 TYR 0.020 0.001 TYR S 33 PHE 0.019 0.001 PHE V 109 TRP 0.023 0.001 TRP I 36 HIS 0.007 0.001 HIS I 99 Details of bonding type rmsd covalent geometry : bond 0.00340 (39813) covalent geometry : angle 0.56344 (54200) SS BOND : bond 0.00254 ( 55) SS BOND : angle 1.26698 ( 110) hydrogen bonds : bond 0.03487 ( 1406) hydrogen bonds : angle 5.72084 ( 3822) Misc. bond : bond 0.00007 ( 1) link_BETA1-4 : bond 0.00424 ( 12) link_BETA1-4 : angle 1.29129 ( 36) link_NAG-ASN : bond 0.00442 ( 12) link_NAG-ASN : angle 2.13086 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10720.19 seconds wall clock time: 184 minutes 6.63 seconds (11046.63 seconds total)