Starting phenix.real_space_refine on Fri Mar 6 22:38:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ldd_23283/03_2026/7ldd_23283_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ldd_23283/03_2026/7ldd_23283.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7ldd_23283/03_2026/7ldd_23283_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ldd_23283/03_2026/7ldd_23283_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ldd_23283/03_2026/7ldd_23283.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ldd_23283/03_2026/7ldd_23283.map" } resolution = 3.4 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= 0.017 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: 7 Type Number sf(0) Gaussians P 4 5.49 5 S 148 5.16 5 Cl 2 4.86 5 C 22160 2.51 5 N 5796 2.21 5 O 6400 1.98 5 F 18 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 118 residue(s): 0.02s 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: 34528 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 5868 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 776, 5867 Classifications: {'peptide': 776} Incomplete info: {'truncation_to_alanine': 83} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 749} Chain breaks: 2 Unresolved non-hydrogen bonds: 318 Unresolved non-hydrogen angles: 379 Unresolved non-hydrogen dihedrals: 261 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'ASN:plan1': 4, 'PHE:plan': 2, 'GLN:plan1': 4, 'ASP:plan': 14, 'ARG:plan': 12, 'GLU:plan': 12} Unresolved non-hydrogen planarities: 190 Conformer: "B" Number of residues, atoms: 776, 5867 Classifications: {'peptide': 776} Incomplete info: {'truncation_to_alanine': 83} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 749} Chain breaks: 2 Unresolved non-hydrogen bonds: 318 Unresolved non-hydrogen angles: 379 Unresolved non-hydrogen dihedrals: 261 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'ASN:plan1': 4, 'PHE:plan': 2, 'GLN:plan1': 4, 'ASP:plan': 14, 'ARG:plan': 12, 'GLU:plan': 12} Unresolved non-hydrogen planarities: 190 bond proxies already assigned to first conformer: 5999 Chain: "B" Number of atoms: 5687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 778, 5687 Classifications: {'peptide': 778} Incomplete info: {'truncation_to_alanine': 111} Link IDs: {'PCIS': 3, 'PTRANS': 18, 'TRANS': 756} Chain breaks: 2 Unresolved non-hydrogen bonds: 454 Unresolved non-hydrogen angles: 527 Unresolved non-hydrogen dihedrals: 390 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 7, 'ARG:plan': 18, 'GLU:plan': 21, 'PHE:plan': 2, 'ASN:plan1': 2, 'HIS:plan': 1, 'ASP:plan': 6, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 250 Chain: "C" Number of atoms: 5868 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 776, 5867 Classifications: {'peptide': 776} Incomplete info: {'truncation_to_alanine': 83} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 749} Chain breaks: 2 Unresolved non-hydrogen bonds: 318 Unresolved non-hydrogen angles: 379 Unresolved non-hydrogen dihedrals: 261 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'ASN:plan1': 4, 'PHE:plan': 2, 'GLN:plan1': 4, 'ASP:plan': 14, 'ARG:plan': 12, 'GLU:plan': 12} Unresolved non-hydrogen planarities: 190 Conformer: "B" Number of residues, atoms: 776, 5867 Classifications: {'peptide': 776} Incomplete info: {'truncation_to_alanine': 83} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 749} Chain breaks: 2 Unresolved non-hydrogen bonds: 318 Unresolved non-hydrogen angles: 379 Unresolved non-hydrogen dihedrals: 261 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'ASN:plan1': 4, 'PHE:plan': 2, 'GLN:plan1': 4, 'ASP:plan': 14, 'ARG:plan': 12, 'GLU:plan': 12} Unresolved non-hydrogen planarities: 190 bond proxies already assigned to first conformer: 5999 Chain: "D" Number of atoms: 5687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 778, 5687 Classifications: {'peptide': 778} Incomplete info: {'truncation_to_alanine': 111} Link IDs: {'PCIS': 3, 'PTRANS': 18, 'TRANS': 756} Chain breaks: 2 Unresolved non-hydrogen bonds: 454 Unresolved non-hydrogen angles: 527 Unresolved non-hydrogen dihedrals: 390 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 7, 'ARG:plan': 18, 'GLU:plan': 21, 'PHE:plan': 2, 'ASN:plan1': 2, 'HIS:plan': 1, 'ASP:plan': 6, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 250 Chain: "E" Number of atoms: 974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 974 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain breaks: 2 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 110 Unresolved non-hydrogen dihedrals: 72 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'TYR:plan': 2, 'HIS:plan': 2, 'GLU:plan': 4, 'ASP:plan': 1, 'ASN:plan1': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 64 Chain: "F" Number of atoms: 978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 978 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain breaks: 2 Unresolved non-hydrogen bonds: 82 Unresolved non-hydrogen angles: 105 Unresolved non-hydrogen dihedrals: 69 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'TYR:plan': 2, 'HIS:plan': 2, 'GLU:plan': 3, 'ASP:plan': 1, 'ASN:plan1': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 60 Chain: "G" Number of atoms: 1134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1134 Classifications: {'peptide': 162} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 1, 'TRANS': 160} Chain breaks: 3 Unresolved non-hydrogen bonds: 115 Unresolved non-hydrogen angles: 142 Unresolved non-hydrogen dihedrals: 97 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'TYR:plan': 3, 'ARG:plan': 7, 'GLU:plan': 2, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 77 Chain: "H" Number of atoms: 1134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1134 Classifications: {'peptide': 162} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 1, 'TRANS': 160} Chain breaks: 3 Unresolved non-hydrogen bonds: 115 Unresolved non-hydrogen angles: 142 Unresolved non-hydrogen dihedrals: 97 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'TYR:plan': 3, 'ARG:plan': 7, 'GLU:plan': 2, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 77 Chain: "I" Number of atoms: 1124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1124 Classifications: {'peptide': 229} Incomplete info: {'truncation_to_alanine': 193} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 216} Chain breaks: 1 Unresolved chain link angles: 12 Unresolved non-hydrogen bonds: 683 Unresolved non-hydrogen angles: 881 Unresolved non-hydrogen dihedrals: 584 Unresolved non-hydrogen chiralities: 59 Planarities with less than four sites: {'GLU:plan': 11, 'GLN:plan1': 11, 'PHE:plan': 7, 'ASP:plan': 13, 'TYR:plan': 12, 'TRP:plan': 5, 'ARG:plan': 10, 'ASN:plan1': 5, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 368 Chain: "J" Number of atoms: 1042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1042 Classifications: {'peptide': 211} Incomplete info: {'truncation_to_alanine': 189} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 202} Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 636 Unresolved non-hydrogen angles: 820 Unresolved non-hydrogen dihedrals: 533 Unresolved non-hydrogen chiralities: 58 Planarities with less than four sites: {'GLU:plan': 9, 'GLN:plan1': 11, 'ASP:plan': 12, 'ARG:plan': 8, 'ASN:plan1': 11, 'TYR:plan': 10, 'TRP:plan': 3, 'HIS:plan': 3, 'PHE:plan': 8} Unresolved non-hydrogen planarities: 349 Chain: "K" Number of atoms: 1059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1059 Classifications: {'peptide': 215} Incomplete info: {'truncation_to_alanine': 186} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 200} Unresolved chain link angles: 14 Unresolved non-hydrogen bonds: 606 Unresolved non-hydrogen angles: 797 Unresolved non-hydrogen dihedrals: 523 Unresolved non-hydrogen chiralities: 64 Planarities with less than four sites: {'GLN:plan1': 8, 'GLU:plan': 5, 'PHE:plan': 5, 'ASN:plan1': 8, 'TYR:plan': 9, 'HIS:plan': 4, 'TRP:plan': 7, 'ARG:plan': 3, 'ASP:plan': 9} Unresolved non-hydrogen planarities: 294 Chain: "L" Number of atoms: 1124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1124 Classifications: {'peptide': 229} Incomplete info: {'truncation_to_alanine': 193} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 216} Chain breaks: 1 Unresolved chain link angles: 12 Unresolved non-hydrogen bonds: 683 Unresolved non-hydrogen angles: 881 Unresolved non-hydrogen dihedrals: 584 Unresolved non-hydrogen chiralities: 59 Planarities with less than four sites: {'GLU:plan': 11, 'GLN:plan1': 11, 'PHE:plan': 7, 'ASP:plan': 13, 'TYR:plan': 12, 'TRP:plan': 5, 'ARG:plan': 10, 'ASN:plan1': 5, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 368 Chain: "M" Number of atoms: 1042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1042 Classifications: {'peptide': 211} Incomplete info: {'truncation_to_alanine': 189} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 202} Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 636 Unresolved non-hydrogen angles: 820 Unresolved non-hydrogen dihedrals: 533 Unresolved non-hydrogen chiralities: 58 Planarities with less than four sites: {'GLU:plan': 9, 'GLN:plan1': 11, 'ASP:plan': 12, 'ARG:plan': 8, 'ASN:plan1': 11, 'TYR:plan': 10, 'TRP:plan': 3, 'HIS:plan': 3, 'PHE:plan': 8} Unresolved non-hydrogen planarities: 349 Chain: "N" Number of atoms: 1059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1059 Classifications: {'peptide': 215} Incomplete info: {'truncation_to_alanine': 186} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 200} Unresolved chain link angles: 14 Unresolved non-hydrogen bonds: 606 Unresolved non-hydrogen angles: 797 Unresolved non-hydrogen dihedrals: 523 Unresolved non-hydrogen chiralities: 64 Planarities with less than four sites: {'GLN:plan1': 8, 'GLU:plan': 5, 'PHE:plan': 5, 'ASN:plan1': 8, 'TYR:plan': 9, 'HIS:plan': 4, 'TRP:plan': 7, 'ARG:plan': 3, 'ASP:plan': 9} Unresolved non-hydrogen planarities: 294 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" 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: "S" 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: "T" 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: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 100 Unusual residues: {'D10': 1, 'HP6': 2, 'NAG': 2, 'OCT': 1, 'R16': 1, 'ZK1': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 92 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 92 Unusual residues: {'C14': 1, 'D12': 1, 'DD9': 2, 'NAG': 1, 'OCT': 1, 'ZK1': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 100 Unusual residues: {'D10': 1, 'HP6': 2, 'NAG': 2, 'OCT': 1, 'R16': 1, 'ZK1': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 92 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 92 Unusual residues: {'C14': 1, 'D12': 1, 'DD9': 2, 'NAG': 1, 'OCT': 1, 'ZK1': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 21 Unusual residues: {'C14': 1, 'D10': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "F" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 21 Unusual residues: {'C14': 1, 'D10': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "G" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 77 Unusual residues: {'C14': 1, 'D10': 1, 'D12': 2, 'OCT': 1, 'XVD': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "H" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 77 Unusual residues: {'C14': 1, 'D10': 1, 'D12': 2, 'OCT': 1, 'XVD': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Time building chain proxies: 9.19, per 1000 atoms: 0.27 Number of scatterers: 34528 At special positions: 0 Unit cell: (124.852, 228.559, 270.848, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Cl 2 17.00 S 148 16.00 P 4 15.00 F 18 9.00 O 6400 8.00 N 5796 7.00 C 22160 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 57 " - pdb=" SG CYS A 305 " distance=2.03 Simple disulfide: pdb=" SG CYS A 714 " - pdb=" SG CYS A 769 " distance=2.03 Simple disulfide: pdb=" SG CYS B 57 " - pdb=" SG CYS B 309 " distance=2.03 Simple disulfide: pdb=" SG CYS B 718 " - pdb=" SG CYS B 773 " distance=2.03 Simple disulfide: pdb=" SG CYS C 57 " - pdb=" SG CYS C 305 " distance=2.03 Simple disulfide: pdb=" SG CYS C 714 " - pdb=" SG CYS C 769 " distance=2.03 Simple disulfide: pdb=" SG CYS D 57 " - pdb=" SG CYS D 309 " distance=2.03 Simple disulfide: pdb=" SG CYS D 718 " - pdb=" SG CYS D 773 " distance=2.03 Simple disulfide: pdb=" SG CYS G 90 " - pdb=" SG CYS G 100 " distance=2.04 Simple disulfide: pdb=" SG CYS H 90 " - pdb=" SG CYS H 100 " distance=2.04 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=2, symmetry=0 Links applied BETA1-4 " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " NAG-ASN " NAG A 906 " - " ASN A 231 " " NAG A 907 " - " ASN A 239 " " NAG B 902 " - " ASN B 349 " " NAG C 906 " - " ASN C 231 " " NAG C 907 " - " ASN C 239 " " NAG D 907 " - " ASN D 349 " " NAG O 1 " - " ASN A 45 " " NAG P 1 " - " ASN A 345 " " NAG Q 1 " - " ASN B 235 " " NAG R 1 " - " ASN C 45 " " NAG S 1 " - " ASN C 345 " " NAG T 1 " - " ASN D 235 " Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.90 Conformation dependent library (CDL) restraints added in 2.2 seconds 9844 Ramachandran restraints generated. 4922 Oldfield, 0 Emsley, 4922 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9216 Finding SS restraints... Secondary structure from input PDB file: 144 helices and 60 sheets defined 39.8% alpha, 14.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.49 Creating SS restraints... Processing helix chain 'A' and resid 18 through 31 removed outlier: 3.688A pdb=" N LEU A 31 " --> pdb=" O ALA A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 61 Processing helix chain 'A' and resid 75 through 87 removed outlier: 3.837A pdb=" N SER A 81 " --> pdb=" O ASN A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 123 Processing helix chain 'A' and resid 137 through 151 removed outlier: 3.816A pdb=" N ARG A 142 " --> pdb=" O SER A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 175 Processing helix chain 'A' and resid 187 through 199 removed outlier: 3.834A pdb=" N GLY A 196 " --> pdb=" O ASN A 192 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N GLN A 197 " --> pdb=" O ALA A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 202 No H-bonds generated for 'chain 'A' and resid 200 through 202' Processing helix chain 'A' and resid 242 through 259 Processing helix chain 'A' and resid 270 through 292 Processing helix chain 'A' and resid 315 through 326 Processing helix chain 'A' and resid 412 through 415 removed outlier: 3.614A pdb=" N ASP A 415 " --> pdb=" O GLU A 412 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 412 through 415' Processing helix chain 'A' and resid 419 through 433 Processing helix chain 'A' and resid 458 through 465 Processing helix chain 'A' and resid 478 through 483 Processing helix chain 'A' and resid 511 through 515 Processing helix chain 'A' and resid 518 through 540 Processing helix chain 'A' and resid 569 through 581 removed outlier: 3.873A pdb=" N LEU A 573 " --> pdb=" O ILE A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 625 removed outlier: 3.512A pdb=" N ARG A 595 " --> pdb=" O SER A 591 " (cutoff:3.500A) Processing helix chain 'A' and resid 631 through 638 Processing helix chain 'A' and resid 649 through 657 Processing helix chain 'A' and resid 660 through 672 removed outlier: 3.608A pdb=" N LYS A 665 " --> pdb=" O ALA A 661 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N MET A 666 " --> pdb=" O VAL A 662 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER A 672 " --> pdb=" O THR A 668 " (cutoff:3.500A) Processing helix chain 'A' and resid 681 through 693 Processing helix chain 'A' and resid 702 through 711 Processing helix chain 'A' and resid 739 through 752 Processing helix chain 'A' and resid 754 through 764 Processing helix chain 'A' and resid 785 through 787 No H-bonds generated for 'chain 'A' and resid 785 through 787' Processing helix chain 'A' and resid 788 through 812 removed outlier: 3.848A pdb=" N PHE A 792 " --> pdb=" O VAL A 788 " (cutoff:3.500A) Processing helix chain 'B' and resid 16 through 30 removed outlier: 3.643A pdb=" N TYR B 20 " --> pdb=" O ALA B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 61 Processing helix chain 'B' and resid 75 through 87 Processing helix chain 'B' and resid 111 through 123 Processing helix chain 'B' and resid 132 through 136 removed outlier: 4.283A pdb=" N ARG B 135 " --> pdb=" O ASP B 132 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLY B 136 " --> pdb=" O SER B 133 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 132 through 136' Processing helix chain 'B' and resid 137 through 151 Processing helix chain 'B' and resid 166 through 181 removed outlier: 3.517A pdb=" N THR B 170 " --> pdb=" O LYS B 166 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS B 181 " --> pdb=" O ASP B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 206 Processing helix chain 'B' and resid 246 through 255 removed outlier: 3.585A pdb=" N ARG B 255 " --> pdb=" O LYS B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 296 Processing helix chain 'B' and resid 319 through 329 Processing helix chain 'B' and resid 423 through 436 Processing helix chain 'B' and resid 461 through 469 removed outlier: 3.615A pdb=" N TYR B 469 " --> pdb=" O GLY B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 487 removed outlier: 3.651A pdb=" N GLU B 487 " --> pdb=" O LEU B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 519 removed outlier: 3.751A pdb=" N LEU B 518 " --> pdb=" O PHE B 515 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASP B 519 " --> pdb=" O SER B 516 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 515 through 519' Processing helix chain 'B' and resid 522 through 547 removed outlier: 3.683A pdb=" N PHE B 531 " --> pdb=" O MET B 527 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N PHE B 546 " --> pdb=" O LEU B 542 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N SER B 547 " --> pdb=" O VAL B 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 574 through 585 Processing helix chain 'B' and resid 595 through 626 removed outlier: 4.288A pdb=" N VAL B 601 " --> pdb=" O SER B 597 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL B 626 " --> pdb=" O ALA B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 635 through 643 removed outlier: 3.691A pdb=" N LEU B 639 " --> pdb=" O SER B 635 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N LYS B 641 " --> pdb=" O GLU B 637 " (cutoff:3.500A) Processing helix chain 'B' and resid 653 through 661 Processing helix chain 'B' and resid 664 through 676 removed outlier: 3.814A pdb=" N SER B 676 " --> pdb=" O THR B 672 " (cutoff:3.500A) Processing helix chain 'B' and resid 685 through 696 Processing helix chain 'B' and resid 706 through 714 Processing helix chain 'B' and resid 742 through 756 removed outlier: 4.307A pdb=" N LEU B 748 " --> pdb=" O ASN B 744 " (cutoff:3.500A) Processing helix chain 'B' and resid 757 through 767 Processing helix chain 'B' and resid 788 through 819 removed outlier: 3.754A pdb=" N VAL B 792 " --> pdb=" O SER B 788 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N GLY B 794 " --> pdb=" O SER B 790 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N VAL B 795 " --> pdb=" O ASN B 791 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N PHE B 796 " --> pdb=" O VAL B 792 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ILE B 798 " --> pdb=" O GLY B 794 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 31 removed outlier: 3.687A pdb=" N LEU C 31 " --> pdb=" O ALA C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 61 Processing helix chain 'C' and resid 75 through 87 removed outlier: 3.838A pdb=" N SER C 81 " --> pdb=" O ASN C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 123 Processing helix chain 'C' and resid 137 through 151 removed outlier: 3.815A pdb=" N ARG C 142 " --> pdb=" O SER C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 163 through 175 Processing helix chain 'C' and resid 187 through 199 removed outlier: 3.834A pdb=" N GLY C 196 " --> pdb=" O ASN C 192 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N GLN C 197 " --> pdb=" O ALA C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 200 through 202 No H-bonds generated for 'chain 'C' and resid 200 through 202' Processing helix chain 'C' and resid 242 through 259 Processing helix chain 'C' and resid 270 through 292 Processing helix chain 'C' and resid 315 through 326 Processing helix chain 'C' and resid 412 through 415 removed outlier: 3.611A pdb=" N ASP C 415 " --> pdb=" O GLU C 412 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 412 through 415' Processing helix chain 'C' and resid 419 through 433 Processing helix chain 'C' and resid 457 through 465 removed outlier: 3.738A pdb=" N GLY C 461 " --> pdb=" O ASN C 457 " (cutoff:3.500A) Processing helix chain 'C' and resid 478 through 483 Processing helix chain 'C' and resid 511 through 515 Processing helix chain 'C' and resid 518 through 540 Processing helix chain 'C' and resid 568 through 581 removed outlier: 3.569A pdb=" N SER C 572 " --> pdb=" O GLY C 568 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N LEU C 573 " --> pdb=" O ILE C 569 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TRP C 574 " --> pdb=" O PHE C 570 " (cutoff:3.500A) Processing helix chain 'C' and resid 591 through 625 removed outlier: 3.665A pdb=" N ARG C 595 " --> pdb=" O SER C 591 " (cutoff:3.500A) Processing helix chain 'C' and resid 631 through 638 Processing helix chain 'C' and resid 649 through 657 Processing helix chain 'C' and resid 660 through 672 removed outlier: 3.689A pdb=" N LYS C 665 " --> pdb=" O ALA C 661 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N MET C 666 " --> pdb=" O VAL C 662 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N SER C 672 " --> pdb=" O THR C 668 " (cutoff:3.500A) Processing helix chain 'C' and resid 681 through 693 removed outlier: 3.529A pdb=" N LYS C 693 " --> pdb=" O VAL C 689 " (cutoff:3.500A) Processing helix chain 'C' and resid 702 through 711 Processing helix chain 'C' and resid 739 through 752 Processing helix chain 'C' and resid 753 through 764 removed outlier: 3.866A pdb=" N LYS C 757 " --> pdb=" O GLY C 753 " (cutoff:3.500A) Processing helix chain 'C' and resid 771 through 775 removed outlier: 3.526A pdb=" N SER C 774 " --> pdb=" O SER C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 784 through 787 Processing helix chain 'C' and resid 788 through 813 removed outlier: 3.805A pdb=" N PHE C 792 " --> pdb=" O VAL C 788 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LYS C 813 " --> pdb=" O GLU C 809 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 30 removed outlier: 3.643A pdb=" N TYR D 20 " --> pdb=" O ALA D 16 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 61 Processing helix chain 'D' and resid 75 through 87 Processing helix chain 'D' and resid 111 through 123 Processing helix chain 'D' and resid 132 through 136 removed outlier: 4.283A pdb=" N ARG D 135 " --> pdb=" O ASP D 132 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLY D 136 " --> pdb=" O SER D 133 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 132 through 136' Processing helix chain 'D' and resid 137 through 151 Processing helix chain 'D' and resid 166 through 181 removed outlier: 3.516A pdb=" N THR D 170 " --> pdb=" O LYS D 166 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS D 181 " --> pdb=" O ASP D 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 206 Processing helix chain 'D' and resid 246 through 255 removed outlier: 3.585A pdb=" N ARG D 255 " --> pdb=" O LYS D 251 " (cutoff:3.500A) Processing helix chain 'D' and resid 273 through 296 Processing helix chain 'D' and resid 319 through 329 Processing helix chain 'D' and resid 423 through 436 Processing helix chain 'D' and resid 461 through 469 Processing helix chain 'D' and resid 482 through 487 removed outlier: 3.651A pdb=" N GLU D 487 " --> pdb=" O LEU D 483 " (cutoff:3.500A) Processing helix chain 'D' and resid 515 through 519 removed outlier: 3.743A pdb=" N LEU D 518 " --> pdb=" O PHE D 515 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ASP D 519 " --> pdb=" O SER D 516 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 515 through 519' Processing helix chain 'D' and resid 522 through 547 removed outlier: 3.652A pdb=" N PHE D 531 " --> pdb=" O MET D 527 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N PHE D 546 " --> pdb=" O LEU D 542 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N SER D 547 " --> pdb=" O VAL D 543 " (cutoff:3.500A) Processing helix chain 'D' and resid 574 through 585 Processing helix chain 'D' and resid 595 through 626 removed outlier: 4.167A pdb=" N VAL D 601 " --> pdb=" O SER D 597 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL D 626 " --> pdb=" O ALA D 622 " (cutoff:3.500A) Processing helix chain 'D' and resid 635 through 643 removed outlier: 3.686A pdb=" N LEU D 639 " --> pdb=" O SER D 635 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N LYS D 641 " --> pdb=" O GLU D 637 " (cutoff:3.500A) Processing helix chain 'D' and resid 653 through 661 Processing helix chain 'D' and resid 664 through 676 removed outlier: 3.830A pdb=" N SER D 676 " --> pdb=" O THR D 672 " (cutoff:3.500A) Processing helix chain 'D' and resid 685 through 696 Processing helix chain 'D' and resid 706 through 714 Processing helix chain 'D' and resid 742 through 756 removed outlier: 4.393A pdb=" N LEU D 748 " --> pdb=" O ASN D 744 " (cutoff:3.500A) Processing helix chain 'D' and resid 757 through 767 removed outlier: 3.521A pdb=" N LYS D 761 " --> pdb=" O GLY D 757 " (cutoff:3.500A) Processing helix chain 'D' and resid 774 through 779 Processing helix chain 'D' and resid 788 through 819 removed outlier: 3.832A pdb=" N VAL D 792 " --> pdb=" O SER D 788 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N GLY D 794 " --> pdb=" O SER D 790 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N VAL D 795 " --> pdb=" O ASN D 791 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N PHE D 796 " --> pdb=" O VAL D 792 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE D 798 " --> pdb=" O GLY D 794 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 37 removed outlier: 3.810A pdb=" N LEU E 14 " --> pdb=" O TYR E 10 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL E 15 " --> pdb=" O MET E 11 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA E 18 " --> pdb=" O LEU E 14 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N SER E 19 " --> pdb=" O VAL E 15 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE E 22 " --> pdb=" O ALA E 18 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N PHE E 23 " --> pdb=" O SER E 19 " (cutoff:3.500A) Processing helix chain 'E' and resid 57 through 85 removed outlier: 3.931A pdb=" N VAL E 69 " --> pdb=" O ARG E 65 " (cutoff:3.500A) Proline residue: E 70 - end of helix removed outlier: 3.502A pdb=" N HIS E 75 " --> pdb=" O GLU E 71 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU E 77 " --> pdb=" O SER E 73 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N PHE E 82 " --> pdb=" O PHE E 78 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LEU E 83 " --> pdb=" O CYS E 79 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 92 removed outlier: 3.585A pdb=" N GLY E 92 " --> pdb=" O TRP E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 94 through 108 removed outlier: 3.605A pdb=" N HIS E 101 " --> pdb=" O LEU E 97 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N TRP E 103 " --> pdb=" O PHE E 99 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ARG E 104 " --> pdb=" O TYR E 100 " (cutoff:3.500A) Processing helix chain 'E' and resid 127 through 153 removed outlier: 3.902A pdb=" N CYS E 137 " --> pdb=" O LYS E 133 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N LYS E 138 " --> pdb=" O GLU E 134 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N PHE E 146 " --> pdb=" O TYR E 142 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N TYR E 148 " --> pdb=" O LEU E 144 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N TYR E 149 " --> pdb=" O SER E 145 " (cutoff:3.500A) Processing helix chain 'E' and resid 153 through 158 removed outlier: 3.572A pdb=" N VAL E 158 " --> pdb=" O VAL E 154 " (cutoff:3.500A) Processing helix chain 'F' and resid 4 through 37 removed outlier: 3.804A pdb=" N LEU F 14 " --> pdb=" O TYR F 10 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N VAL F 15 " --> pdb=" O MET F 11 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA F 18 " --> pdb=" O LEU F 14 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N SER F 19 " --> pdb=" O VAL F 15 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE F 22 " --> pdb=" O ALA F 18 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N PHE F 23 " --> pdb=" O SER F 19 " (cutoff:3.500A) Processing helix chain 'F' and resid 57 through 85 removed outlier: 3.821A pdb=" N LEU F 64 " --> pdb=" O ILE F 60 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N VAL F 69 " --> pdb=" O ARG F 65 " (cutoff:3.500A) Proline residue: F 70 - end of helix removed outlier: 3.566A pdb=" N LEU F 77 " --> pdb=" O SER F 73 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N PHE F 82 " --> pdb=" O PHE F 78 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LEU F 83 " --> pdb=" O CYS F 79 " (cutoff:3.500A) Processing helix chain 'F' and resid 87 through 92 removed outlier: 3.570A pdb=" N GLY F 92 " --> pdb=" O TRP F 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 94 through 107 removed outlier: 3.647A pdb=" N HIS F 101 " --> pdb=" O LEU F 97 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU F 102 " --> pdb=" O LEU F 98 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N TRP F 103 " --> pdb=" O PHE F 99 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ARG F 104 " --> pdb=" O TYR F 100 " (cutoff:3.500A) Processing helix chain 'F' and resid 127 through 153 removed outlier: 3.510A pdb=" N LYS F 133 " --> pdb=" O ASN F 129 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N CYS F 137 " --> pdb=" O LYS F 133 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N LYS F 138 " --> pdb=" O GLU F 134 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N PHE F 146 " --> pdb=" O TYR F 142 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N TYR F 148 " --> pdb=" O LEU F 144 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N TYR F 149 " --> pdb=" O SER F 145 " (cutoff:3.500A) Processing helix chain 'F' and resid 153 through 158 removed outlier: 3.511A pdb=" N VAL F 158 " --> pdb=" O VAL F 154 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 39 removed outlier: 4.383A pdb=" N THR G 25 " --> pdb=" O VAL G 21 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLY G 27 " --> pdb=" O LEU G 23 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLY G 33 " --> pdb=" O PHE G 29 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LEU G 34 " --> pdb=" O SER G 30 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ILE G 37 " --> pdb=" O GLY G 33 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA G 38 " --> pdb=" O LEU G 34 " (cutoff:3.500A) Processing helix chain 'G' and resid 118 through 127 removed outlier: 3.801A pdb=" N ARG G 122 " --> pdb=" O GLU G 118 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL G 124 " --> pdb=" O LEU G 120 " (cutoff:3.500A) Processing helix chain 'G' and resid 129 through 145 removed outlier: 4.311A pdb=" N ALA G 135 " --> pdb=" O PRO G 131 " (cutoff:3.500A) Processing helix chain 'G' and resid 146 through 149 removed outlier: 4.019A pdb=" N ARG G 149 " --> pdb=" O ALA G 146 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 146 through 149' Processing helix chain 'G' and resid 156 through 185 removed outlier: 3.844A pdb=" N GLY G 160 " --> pdb=" O ASN G 156 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA G 161 " --> pdb=" O ILE G 157 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU G 164 " --> pdb=" O GLY G 160 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL G 166 " --> pdb=" O GLY G 162 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N GLY G 169 " --> pdb=" O PHE G 165 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL G 176 " --> pdb=" O ASN G 172 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N TYR G 179 " --> pdb=" O GLY G 175 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA G 182 " --> pdb=" O VAL G 178 " (cutoff:3.500A) Processing helix chain 'G' and resid 202 through 231 removed outlier: 3.581A pdb=" N TYR G 206 " --> pdb=" O GLY G 202 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHE G 207 " --> pdb=" O TRP G 203 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N GLY G 208 " --> pdb=" O SER G 204 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLY G 209 " --> pdb=" O PHE G 205 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHE G 212 " --> pdb=" O GLY G 208 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ALA G 215 " --> pdb=" O SER G 211 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N VAL G 223 " --> pdb=" O GLY G 219 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ILE G 225 " --> pdb=" O LEU G 221 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N TYR G 226 " --> pdb=" O ALA G 222 " (cutoff:3.500A) Processing helix chain 'H' and resid 21 through 39 removed outlier: 4.384A pdb=" N THR H 25 " --> pdb=" O VAL H 21 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLY H 27 " --> pdb=" O LEU H 23 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLY H 33 " --> pdb=" O PHE H 29 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N LEU H 34 " --> pdb=" O SER H 30 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ILE H 37 " --> pdb=" O GLY H 33 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA H 38 " --> pdb=" O LEU H 34 " (cutoff:3.500A) Processing helix chain 'H' and resid 118 through 127 removed outlier: 3.802A pdb=" N ARG H 122 " --> pdb=" O GLU H 118 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL H 124 " --> pdb=" O LEU H 120 " (cutoff:3.500A) Processing helix chain 'H' and resid 129 through 145 removed outlier: 4.311A pdb=" N ALA H 135 " --> pdb=" O PRO H 131 " (cutoff:3.500A) Processing helix chain 'H' and resid 146 through 149 removed outlier: 4.020A pdb=" N ARG H 149 " --> pdb=" O ALA H 146 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 146 through 149' Processing helix chain 'H' and resid 156 through 185 removed outlier: 3.844A pdb=" N GLY H 160 " --> pdb=" O ASN H 156 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ALA H 161 " --> pdb=" O ILE H 157 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU H 164 " --> pdb=" O GLY H 160 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL H 166 " --> pdb=" O GLY H 162 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N GLY H 169 " --> pdb=" O PHE H 165 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL H 176 " --> pdb=" O ASN H 172 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N TYR H 179 " --> pdb=" O GLY H 175 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA H 182 " --> pdb=" O VAL H 178 " (cutoff:3.500A) Processing helix chain 'H' and resid 202 through 231 removed outlier: 3.580A pdb=" N TYR H 206 " --> pdb=" O GLY H 202 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE H 207 " --> pdb=" O TRP H 203 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N GLY H 208 " --> pdb=" O SER H 204 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLY H 209 " --> pdb=" O PHE H 205 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE H 212 " --> pdb=" O GLY H 208 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ALA H 215 " --> pdb=" O SER H 211 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N VAL H 223 " --> pdb=" O GLY H 219 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ILE H 225 " --> pdb=" O LEU H 221 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N TYR H 226 " --> pdb=" O ALA H 222 " (cutoff:3.500A) Processing helix chain 'I' and resid 217 through 221 removed outlier: 3.976A pdb=" N ALA I 221 " --> pdb=" O ALA I 218 " (cutoff:3.500A) Processing helix chain 'J' and resid 122 through 129 removed outlier: 4.108A pdb=" N GLY J 129 " --> pdb=" O GLN J 125 " (cutoff:3.500A) Processing helix chain 'J' and resid 183 through 188 removed outlier: 3.556A pdb=" N GLU J 188 " --> pdb=" O LYS J 184 " (cutoff:3.500A) Processing helix chain 'K' and resid 63 through 67 removed outlier: 4.371A pdb=" N SER K 66 " --> pdb=" O ALA K 63 " (cutoff:3.500A) Processing helix chain 'K' and resid 161 through 165 Processing helix chain 'L' and resid 217 through 221 removed outlier: 3.976A pdb=" N ALA L 221 " --> pdb=" O ALA L 218 " (cutoff:3.500A) Processing helix chain 'M' and resid 122 through 129 removed outlier: 4.107A pdb=" N GLY M 129 " --> pdb=" O GLN M 125 " (cutoff:3.500A) Processing helix chain 'M' and resid 183 through 188 removed outlier: 3.555A pdb=" N GLU M 188 " --> pdb=" O LYS M 184 " (cutoff:3.500A) Processing helix chain 'N' and resid 63 through 67 removed outlier: 4.371A pdb=" N SER N 66 " --> pdb=" O ALA N 63 " (cutoff:3.500A) Processing helix chain 'N' and resid 161 through 165 Processing sheet with id=AA1, first strand: chain 'A' and resid 36 through 43 removed outlier: 4.038A pdb=" N ALA A 66 " --> pdb=" O GLN A 8 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 153 through 158 removed outlier: 7.563A pdb=" N THR A 126 " --> pdb=" O LEU A 181 " (cutoff:3.500A) removed outlier: 8.715A pdb=" N VAL A 183 " --> pdb=" O THR A 126 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N VAL A 128 " --> pdb=" O VAL A 183 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N ASP A 185 " --> pdb=" O VAL A 128 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N ILE A 130 " --> pdb=" O ASP A 185 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N TYR A 208 " --> pdb=" O ASN A 231 " (cutoff:3.500A) removed outlier: 8.155A pdb=" N THR A 233 " --> pdb=" O TYR A 208 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N TYR A 210 " --> pdb=" O THR A 233 " (cutoff:3.500A) removed outlier: 8.680A pdb=" N PHE A 235 " --> pdb=" O TYR A 210 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N LEU A 212 " --> pdb=" O PHE A 235 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N VAL A 350 " --> pdb=" O ILE A 361 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LYS A 354 " --> pdb=" O GLY A 357 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 327 through 328 Processing sheet with id=AA4, first strand: chain 'A' and resid 437 through 440 removed outlier: 5.737A pdb=" N VAL A 393 " --> pdb=" O GLU A 439 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 403 through 404 Processing sheet with id=AA6, first strand: chain 'A' and resid 486 through 487 Processing sheet with id=AA7, first strand: chain 'A' and resid 493 through 494 removed outlier: 3.632A pdb=" N LEU A 494 " --> pdb=" O LYS A 726 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 678 through 679 removed outlier: 9.036A pdb=" N VAL A 679 " --> pdb=" O TYR A 643 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N THR A 645 " --> pdb=" O VAL A 679 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ALA A 642 " --> pdb=" O ALA A 697 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N LEU A 699 " --> pdb=" O ALA A 642 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N GLY A 644 " --> pdb=" O LEU A 699 " (cutoff:3.500A) removed outlier: 9.417A pdb=" N GLU A 701 " --> pdb=" O GLY A 644 " (cutoff:3.500A) removed outlier: 11.093A pdb=" N LEU A 646 " --> pdb=" O GLU A 701 " (cutoff:3.500A) removed outlier: 8.548A pdb=" N TYR A 696 " --> pdb=" O LYS A 501 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N LYS A 501 " --> pdb=" O TYR A 696 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ILE A 498 " --> pdb=" O VAL A 719 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 37 through 44 removed outlier: 6.749A pdb=" N ILE B 6 " --> pdb=" O THR B 38 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N HIS B 40 " --> pdb=" O ILE B 6 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N ILE B 8 " --> pdb=" O HIS B 40 " (cutoff:3.500A) removed outlier: 8.342A pdb=" N ASP B 42 " --> pdb=" O ILE B 8 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N GLY B 10 " --> pdb=" O ASP B 42 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N LEU B 44 " --> pdb=" O GLY B 10 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N PHE B 12 " --> pdb=" O LEU B 44 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 91 through 92 Processing sheet with id=AB2, first strand: chain 'B' and resid 153 through 158 removed outlier: 5.093A pdb=" N ARG B 185 " --> pdb=" O LYS B 126 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N TYR B 214 " --> pdb=" O SER B 237 " (cutoff:3.500A) removed outlier: 8.379A pdb=" N PHE B 239 " --> pdb=" O TYR B 214 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N ILE B 216 " --> pdb=" O PHE B 239 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N VAL B 236 " --> pdb=" O LEU B 357 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLY B 366 " --> pdb=" O ILE B 354 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N GLU B 356 " --> pdb=" O LYS B 364 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N LYS B 364 " --> pdb=" O GLU B 356 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N LYS B 358 " --> pdb=" O PRO B 362 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 331 through 334 removed outlier: 4.150A pdb=" N LYS B 340 " --> pdb=" O ILE B 348 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 397 through 398 removed outlier: 3.507A pdb=" N ILE B 476 " --> pdb=" O THR B 398 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N ALA B 477 " --> pdb=" O ALA B 735 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N ALA B 735 " --> pdb=" O ALA B 477 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N LEU B 479 " --> pdb=" O GLY B 733 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 646 through 648 removed outlier: 3.635A pdb=" N ALA B 701 " --> pdb=" O ALA B 646 " (cutoff:3.500A) removed outlier: 8.778A pdb=" N TYR B 700 " --> pdb=" O LYS B 505 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N LYS B 505 " --> pdb=" O TYR B 700 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ILE B 502 " --> pdb=" O VAL B 723 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 36 through 43 removed outlier: 4.039A pdb=" N ALA C 66 " --> pdb=" O GLN C 8 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 153 through 158 removed outlier: 7.563A pdb=" N THR C 126 " --> pdb=" O LEU C 181 " (cutoff:3.500A) removed outlier: 8.717A pdb=" N VAL C 183 " --> pdb=" O THR C 126 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N VAL C 128 " --> pdb=" O VAL C 183 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N ASP C 185 " --> pdb=" O VAL C 128 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N ILE C 130 " --> pdb=" O ASP C 185 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N TYR C 208 " --> pdb=" O ASN C 231 " (cutoff:3.500A) removed outlier: 8.155A pdb=" N THR C 233 " --> pdb=" O TYR C 208 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N TYR C 210 " --> pdb=" O THR C 233 " (cutoff:3.500A) removed outlier: 8.680A pdb=" N PHE C 235 " --> pdb=" O TYR C 210 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N LEU C 212 " --> pdb=" O PHE C 235 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N VAL C 350 " --> pdb=" O ILE C 361 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LYS C 354 " --> pdb=" O GLY C 357 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 327 through 328 Processing sheet with id=AB9, first strand: chain 'C' and resid 437 through 440 removed outlier: 5.736A pdb=" N VAL C 393 " --> pdb=" O GLU C 439 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 403 through 404 Processing sheet with id=AC2, first strand: chain 'C' and resid 486 through 487 Processing sheet with id=AC3, first strand: chain 'C' and resid 493 through 494 removed outlier: 3.633A pdb=" N LEU C 494 " --> pdb=" O LYS C 726 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 678 through 679 removed outlier: 9.051A pdb=" N VAL C 679 " --> pdb=" O TYR C 643 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N THR C 645 " --> pdb=" O VAL C 679 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ALA C 642 " --> pdb=" O ALA C 697 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N LEU C 699 " --> pdb=" O ALA C 642 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N GLY C 644 " --> pdb=" O LEU C 699 " (cutoff:3.500A) removed outlier: 9.437A pdb=" N GLU C 701 " --> pdb=" O GLY C 644 " (cutoff:3.500A) removed outlier: 11.104A pdb=" N LEU C 646 " --> pdb=" O GLU C 701 " (cutoff:3.500A) removed outlier: 8.565A pdb=" N TYR C 696 " --> pdb=" O LYS C 501 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N LYS C 501 " --> pdb=" O TYR C 696 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ILE C 498 " --> pdb=" O VAL C 719 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 37 through 44 removed outlier: 6.748A pdb=" N ILE D 6 " --> pdb=" O THR D 38 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N HIS D 40 " --> pdb=" O ILE D 6 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N ILE D 8 " --> pdb=" O HIS D 40 " (cutoff:3.500A) removed outlier: 8.341A pdb=" N ASP D 42 " --> pdb=" O ILE D 8 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N GLY D 10 " --> pdb=" O ASP D 42 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N LEU D 44 " --> pdb=" O GLY D 10 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N PHE D 12 " --> pdb=" O LEU D 44 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 91 through 92 Processing sheet with id=AC7, first strand: chain 'D' and resid 153 through 158 removed outlier: 5.093A pdb=" N ARG D 185 " --> pdb=" O LYS D 126 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N TYR D 214 " --> pdb=" O SER D 237 " (cutoff:3.500A) removed outlier: 8.379A pdb=" N PHE D 239 " --> pdb=" O TYR D 214 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N ILE D 216 " --> pdb=" O PHE D 239 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N VAL D 236 " --> pdb=" O LEU D 357 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLY D 366 " --> pdb=" O ILE D 354 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N GLU D 356 " --> pdb=" O LYS D 364 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N LYS D 364 " --> pdb=" O GLU D 356 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N LYS D 358 " --> pdb=" O PRO D 362 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 331 through 334 removed outlier: 4.149A pdb=" N LYS D 340 " --> pdb=" O ILE D 348 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 397 through 398 removed outlier: 3.519A pdb=" N ILE D 476 " --> pdb=" O THR D 398 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N ALA D 477 " --> pdb=" O ALA D 735 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N ALA D 735 " --> pdb=" O ALA D 477 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N LEU D 479 " --> pdb=" O GLY D 733 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 646 through 648 removed outlier: 3.646A pdb=" N ALA D 701 " --> pdb=" O ALA D 646 " (cutoff:3.500A) removed outlier: 8.786A pdb=" N TYR D 700 " --> pdb=" O LYS D 505 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N LYS D 505 " --> pdb=" O TYR D 700 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE D 502 " --> pdb=" O VAL D 723 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 82 through 83 removed outlier: 3.577A pdb=" N THR G 47 " --> pdb=" O THR G 82 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 88 through 89 removed outlier: 3.605A pdb=" N ILE G 89 " --> pdb=" O VAL G 101 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 82 through 83 removed outlier: 3.577A pdb=" N THR H 47 " --> pdb=" O THR H 82 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 88 through 89 removed outlier: 3.606A pdb=" N ILE H 89 " --> pdb=" O VAL H 101 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 3 through 7 removed outlier: 3.631A pdb=" N LYS I 3 " --> pdb=" O SER I 25 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N SER I 7 " --> pdb=" O SER I 21 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N SER I 21 " --> pdb=" O SER I 7 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 45 through 50 removed outlier: 6.493A pdb=" N TRP I 36 " --> pdb=" O ILE I 48 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 138 through 141 removed outlier: 3.981A pdb=" N ILE I 155 " --> pdb=" O LEU I 211 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LEU I 211 " --> pdb=" O ILE I 155 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 144 through 147 removed outlier: 6.519A pdb=" N LYS I 241 " --> pdb=" O LEU I 145 " (cutoff:3.500A) removed outlier: 8.080A pdb=" N VAL I 147 " --> pdb=" O LYS I 241 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N GLU I 243 " --> pdb=" O VAL I 147 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'I' and resid 180 through 187 removed outlier: 5.508A pdb=" N LYS I 177 " --> pdb=" O PRO I 181 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N TRP I 173 " --> pdb=" O LEU I 185 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 6 through 7 Processing sheet with id=AE3, first strand: chain 'J' and resid 12 through 13 removed outlier: 7.299A pdb=" N LEU J 12 " --> pdb=" O GLU J 106 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N THR J 103 " --> pdb=" O TYR J 87 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N LEU J 34 " --> pdb=" O TYR J 50 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N TYR J 50 " --> pdb=" O LEU J 34 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N TRP J 36 " --> pdb=" O LEU J 48 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 133 through 137 Processing sheet with id=AE5, first strand: chain 'J' and resid 154 through 155 removed outlier: 3.555A pdb=" N ILE J 151 " --> pdb=" O SER J 154 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ILE J 206 " --> pdb=" O ALA J 197 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'K' and resid 4 through 8 removed outlier: 3.806A pdb=" N LYS K 6 " --> pdb=" O THR K 24 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N THR K 24 " --> pdb=" O LYS K 6 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'K' and resid 58 through 60 removed outlier: 5.509A pdb=" N TRP K 48 " --> pdb=" O ARG K 39 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ARG K 39 " --> pdb=" O TRP K 48 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLY K 50 " --> pdb=" O TRP K 37 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL K 109 " --> pdb=" O ARG K 98 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'K' and resid 127 through 131 Processing sheet with id=AE9, first strand: chain 'K' and resid 158 through 160 Processing sheet with id=AF1, first strand: chain 'K' and resid 176 through 178 removed outlier: 4.061A pdb=" N VAL K 176 " --> pdb=" O THR K 183 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N THR K 183 " --> pdb=" O VAL K 176 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'L' and resid 3 through 7 removed outlier: 3.631A pdb=" N LYS L 3 " --> pdb=" O SER L 25 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N SER L 7 " --> pdb=" O SER L 21 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N SER L 21 " --> pdb=" O SER L 7 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'L' and resid 45 through 50 removed outlier: 6.493A pdb=" N TRP L 36 " --> pdb=" O ILE L 48 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'L' and resid 138 through 141 removed outlier: 3.981A pdb=" N ILE L 155 " --> pdb=" O LEU L 211 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LEU L 211 " --> pdb=" O ILE L 155 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'L' and resid 144 through 147 removed outlier: 6.519A pdb=" N LYS L 241 " --> pdb=" O LEU L 145 " (cutoff:3.500A) removed outlier: 8.080A pdb=" N VAL L 147 " --> pdb=" O LYS L 241 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N GLU L 243 " --> pdb=" O VAL L 147 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF5 Processing sheet with id=AF6, first strand: chain 'L' and resid 180 through 187 removed outlier: 5.509A pdb=" N LYS L 177 " --> pdb=" O PRO L 181 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N TRP L 173 " --> pdb=" O LEU L 185 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'M' and resid 6 through 7 Processing sheet with id=AF8, first strand: chain 'M' and resid 12 through 13 removed outlier: 7.299A pdb=" N LEU M 12 " --> pdb=" O GLU M 106 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N THR M 103 " --> pdb=" O TYR M 87 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N LEU M 34 " --> pdb=" O TYR M 50 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N TYR M 50 " --> pdb=" O LEU M 34 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N TRP M 36 " --> pdb=" O LEU M 48 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'M' and resid 133 through 137 Processing sheet with id=AG1, first strand: chain 'M' and resid 154 through 155 removed outlier: 3.555A pdb=" N ILE M 151 " --> pdb=" O SER M 154 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ILE M 206 " --> pdb=" O ALA M 197 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'N' and resid 4 through 8 removed outlier: 3.806A pdb=" N LYS N 6 " --> pdb=" O THR N 24 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N THR N 24 " --> pdb=" O LYS N 6 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'N' and resid 58 through 60 removed outlier: 5.508A pdb=" N TRP N 48 " --> pdb=" O ARG N 39 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ARG N 39 " --> pdb=" O TRP N 48 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLY N 50 " --> pdb=" O TRP N 37 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL N 109 " --> pdb=" O ARG N 98 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'N' and resid 127 through 131 Processing sheet with id=AG5, first strand: chain 'N' and resid 158 through 160 Processing sheet with id=AG6, first strand: chain 'N' and resid 176 through 178 removed outlier: 4.061A pdb=" N VAL N 176 " --> pdb=" O THR N 183 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR N 183 " --> pdb=" O VAL N 176 " (cutoff:3.500A) 1674 hydrogen bonds defined for protein. 4752 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: 7.81 Time building geometry restraints manager: 3.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.36: 11362 1.36 - 1.49: 8999 1.49 - 1.62: 14523 1.62 - 1.75: 0 1.75 - 1.88: 234 Bond restraints: 35118 Sorted by residual: bond pdb=" CAU ZK1 C 901 " pdb=" OAB ZK1 C 901 " ideal model delta sigma weight residual 1.215 1.403 -0.188 2.00e-02 2.50e+03 8.85e+01 bond pdb=" CAU ZK1 B 901 " pdb=" OAB ZK1 B 901 " ideal model delta sigma weight residual 1.215 1.403 -0.188 2.00e-02 2.50e+03 8.85e+01 bond pdb=" CAU ZK1 A 901 " pdb=" OAB ZK1 A 901 " ideal model delta sigma weight residual 1.215 1.403 -0.188 2.00e-02 2.50e+03 8.81e+01 bond pdb=" CAU ZK1 D 906 " pdb=" OAB ZK1 D 906 " ideal model delta sigma weight residual 1.215 1.402 -0.187 2.00e-02 2.50e+03 8.77e+01 bond pdb=" CAT ZK1 C 901 " pdb=" OAA ZK1 C 901 " ideal model delta sigma weight residual 1.214 1.394 -0.180 2.00e-02 2.50e+03 8.13e+01 ... (remaining 35113 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.77: 47320 1.77 - 3.54: 475 3.54 - 5.32: 74 5.32 - 7.09: 26 7.09 - 8.86: 8 Bond angle restraints: 47903 Sorted by residual: angle pdb=" N VAL B 159 " pdb=" CA VAL B 159 " pdb=" C VAL B 159 " ideal model delta sigma weight residual 112.29 109.48 2.81 9.40e-01 1.13e+00 8.93e+00 angle pdb=" N VAL D 159 " pdb=" CA VAL D 159 " pdb=" C VAL D 159 " ideal model delta sigma weight residual 112.29 109.50 2.79 9.40e-01 1.13e+00 8.82e+00 angle pdb=" CAM ZK1 B 901 " pdb=" NAX ZK1 B 901 " pdb=" CAN ZK1 B 901 " ideal model delta sigma weight residual 111.06 119.92 -8.86 3.00e+00 1.11e-01 8.72e+00 angle pdb=" CAM ZK1 D 906 " pdb=" NAX ZK1 D 906 " pdb=" CAN ZK1 D 906 " ideal model delta sigma weight residual 111.06 119.89 -8.83 3.00e+00 1.11e-01 8.66e+00 angle pdb=" CAM ZK1 A 901 " pdb=" NAX ZK1 A 901 " pdb=" CAN ZK1 A 901 " ideal model delta sigma weight residual 111.06 119.88 -8.82 3.00e+00 1.11e-01 8.64e+00 ... (remaining 47898 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.74: 19792 23.74 - 47.49: 629 47.49 - 71.23: 80 71.23 - 94.97: 42 94.97 - 118.72: 34 Dihedral angle restraints: 20577 sinusoidal: 6243 harmonic: 14334 Sorted by residual: dihedral pdb=" CB CYS G 90 " pdb=" SG CYS G 90 " pdb=" SG CYS G 100 " pdb=" CB CYS G 100 " ideal model delta sinusoidal sigma weight residual -86.00 -27.43 -58.57 1 1.00e+01 1.00e-02 4.59e+01 dihedral pdb=" CB CYS H 90 " pdb=" SG CYS H 90 " pdb=" SG CYS H 100 " pdb=" CB CYS H 100 " ideal model delta sinusoidal sigma weight residual -86.00 -27.44 -58.56 1 1.00e+01 1.00e-02 4.59e+01 dihedral pdb=" CB CYS C 714 " pdb=" SG CYS C 714 " pdb=" SG CYS C 769 " pdb=" CB CYS C 769 " ideal model delta sinusoidal sigma weight residual 93.00 131.76 -38.76 1 1.00e+01 1.00e-02 2.11e+01 ... (remaining 20574 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.256: 5720 0.256 - 0.511: 2 0.511 - 0.767: 0 0.767 - 1.022: 0 1.022 - 1.278: 2 Chirality restraints: 5724 Sorted by residual: chirality pdb=" C1 NAG P 2 " pdb=" O4 NAG P 1 " pdb=" C2 NAG P 2 " pdb=" O5 NAG P 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.12 -1.28 2.00e-02 2.50e+03 4.08e+03 chirality pdb=" C1 NAG S 2 " pdb=" O4 NAG S 1 " pdb=" C2 NAG S 2 " pdb=" O5 NAG S 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.12 -1.28 2.00e-02 2.50e+03 4.08e+03 chirality pdb=" C1 NAG T 2 " pdb=" O4 NAG T 1 " pdb=" C2 NAG T 2 " pdb=" O5 NAG T 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.77 0.37 2.00e-02 2.50e+03 3.42e+02 ... (remaining 5721 not shown) Planarity restraints: 6137 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR C 92 " 0.022 5.00e-02 4.00e+02 3.34e-02 1.79e+00 pdb=" N PRO C 93 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO C 93 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO C 93 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 92 " -0.022 5.00e-02 4.00e+02 3.33e-02 1.77e+00 pdb=" N PRO A 93 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO A 93 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 93 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY C 740 " 0.018 5.00e-02 4.00e+02 2.75e-02 1.21e+00 pdb=" N PRO C 741 " -0.048 5.00e-02 4.00e+02 pdb=" CA PRO C 741 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO C 741 " 0.015 5.00e-02 4.00e+02 ... (remaining 6134 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 1645 2.73 - 3.27: 34518 3.27 - 3.81: 54143 3.81 - 4.36: 61055 4.36 - 4.90: 107339 Nonbonded interactions: 258700 Sorted by model distance: nonbonded pdb=" O4 NAG S 1 " pdb=" O7 NAG S 1 " model vdw 2.187 3.040 nonbonded pdb=" O4 NAG P 1 " pdb=" O7 NAG P 1 " model vdw 2.187 3.040 nonbonded pdb=" OH TYR D 122 " pdb=" OE2 GLU D 356 " model vdw 2.199 3.040 nonbonded pdb=" OH TYR B 122 " pdb=" OE2 GLU B 356 " model vdw 2.199 3.040 nonbonded pdb=" OD2 ASP C 277 " pdb=" OG1 THR C 332 " model vdw 2.215 3.040 ... (remaining 258695 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 1 through 649 or resid 651 through 908)) selection = (chain 'C' and (resid 1 through 649 or resid 651 through 908)) } ncs_group { reference = (chain 'B' and (resid 4 through 819 or resid 905)) selection = (chain 'D' and (resid 4 through 819 or (resid 905 and (name C2 or name C3 or nam \ e C4 or name C5 or name C6 or name C7 or name C8 or name C9 )))) } ncs_group { reference = chain 'E' selection = (chain 'F' and (resid 2 through 133 or (resid 134 and (name N or name CA or name \ C or name O or name CB )) or resid 135 through 202)) } ncs_group { reference = (chain 'G' and (resid 19 through 231 or resid 502 or resid 504 through 506)) selection = (chain 'H' and (resid 19 through 231 or resid 502 or resid 504 through 506)) } ncs_group { reference = chain 'I' selection = chain 'L' } ncs_group { reference = chain 'J' selection = chain 'M' } ncs_group { reference = chain 'K' selection = chain 'N' } ncs_group { reference = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 12.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.540 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 33.280 Find NCS groups from input model: 0.790 Set up NCS constraints: 0.130 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:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5767 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 : 0.005 0.188 35148 Z= 0.228 Angle : 0.645 44.750 47977 Z= 0.290 Chirality : 0.047 1.278 5724 Planarity : 0.002 0.033 6125 Dihedral : 13.687 118.717 11331 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 0.45 % Allowed : 7.19 % Favored : 92.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.38 (0.10), residues: 4922 helix: -1.53 (0.10), residues: 1862 sheet: -2.42 (0.15), residues: 892 loop : -2.74 (0.11), residues: 2168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 599 TYR 0.012 0.001 TYR B 280 PHE 0.011 0.001 PHE C 127 TRP 0.008 0.001 TRP C 252 HIS 0.002 0.000 HIS C 209 Details of bonding type rmsd covalent geometry : bond 0.00447 (35118) covalent geometry : angle 0.49251 (47903) SS BOND : bond 0.00405 ( 10) SS BOND : angle 1.06305 ( 20) hydrogen bonds : bond 0.20723 ( 1674) hydrogen bonds : angle 6.99959 ( 4752) Misc. bond : bond 0.00042 ( 2) link_BETA1-4 : bond 0.06462 ( 6) link_BETA1-4 : angle 21.17090 ( 18) link_NAG-ASN : bond 0.00381 ( 12) link_NAG-ASN : angle 2.47463 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9844 Ramachandran restraints generated. 4922 Oldfield, 0 Emsley, 4922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9844 Ramachandran restraints generated. 4922 Oldfield, 0 Emsley, 4922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 4276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 337 time to evaluate : 1.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 249 MET cc_start: 0.6931 (mmm) cc_final: 0.6003 (ttp) REVERT: A 620 LEU cc_start: 0.8023 (mt) cc_final: 0.7468 (mm) REVERT: B 700 TYR cc_start: 0.2799 (t80) cc_final: 0.2290 (t80) REVERT: C 249 MET cc_start: 0.6924 (mmm) cc_final: 0.6030 (ttp) REVERT: D 700 TYR cc_start: 0.2730 (t80) cc_final: 0.2328 (t80) REVERT: F 154 VAL cc_start: 0.6107 (t) cc_final: 0.5832 (p) outliers start: 12 outliers final: 6 residues processed: 349 average time/residue: 0.2017 time to fit residues: 117.5017 Evaluate side-chains 218 residues out of total 4276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 212 time to evaluate : 1.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain B residue 257 SER Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain D residue 257 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 432 optimal weight: 7.9990 chunk 197 optimal weight: 10.0000 chunk 388 optimal weight: 20.0000 chunk 455 optimal weight: 9.9990 chunk 215 optimal weight: 0.3980 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 30.0000 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 7.9990 chunk 470 optimal weight: 3.9990 overall best weight: 3.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN A 153 GLN A 349 HIS A 571 ASN A 722 ASN B 18 GLN ** B 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 161 ASN B 312 ASN B 714 GLN C 8 GLN ** C 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 153 GLN C 308 ASN C 583 GLN C 722 ASN D 18 GLN ** D 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 161 ASN D 312 ASN D 714 GLN ** E 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 132 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4982 r_free = 0.4982 target = 0.199451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4674 r_free = 0.4674 target = 0.171003 restraints weight = 72318.406| |-----------------------------------------------------------------------------| r_work (start): 0.4646 rms_B_bonded: 3.50 r_work: 0.4191 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.4191 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4139 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4139 r_free = 0.4139 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4139 r_free = 0.4139 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.4139 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6892 moved from start: 0.2654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.115 35148 Z= 0.399 Angle : 0.826 12.595 47977 Z= 0.423 Chirality : 0.051 0.336 5724 Planarity : 0.005 0.078 6125 Dihedral : 9.755 93.480 5948 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.57 % Favored : 94.39 % Rotamer: Outliers : 2.32 % Allowed : 13.04 % Favored : 84.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.50 (0.11), residues: 4922 helix: -0.48 (0.11), residues: 1932 sheet: -2.06 (0.16), residues: 886 loop : -2.58 (0.12), residues: 2104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 62 TYR 0.050 0.002 TYR A 71 PHE 0.036 0.003 PHE A 95 TRP 0.053 0.002 TRP D 606 HIS 0.011 0.002 HIS C 260 Details of bonding type rmsd covalent geometry : bond 0.00962 (35118) covalent geometry : angle 0.81736 (47903) SS BOND : bond 0.00598 ( 10) SS BOND : angle 1.23037 ( 20) hydrogen bonds : bond 0.05904 ( 1674) hydrogen bonds : angle 5.32559 ( 4752) Misc. bond : bond 0.00023 ( 2) link_BETA1-4 : bond 0.00666 ( 6) link_BETA1-4 : angle 3.59665 ( 18) link_NAG-ASN : bond 0.00460 ( 12) link_NAG-ASN : angle 3.47309 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9844 Ramachandran restraints generated. 4922 Oldfield, 0 Emsley, 4922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9844 Ramachandran restraints generated. 4922 Oldfield, 0 Emsley, 4922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 4276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 249 time to evaluate : 1.161 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 ARG cc_start: 0.8713 (OUTLIER) cc_final: 0.8329 (tpm-80) REVERT: A 195 LEU cc_start: 0.6582 (OUTLIER) cc_final: 0.6055 (mp) REVERT: A 249 MET cc_start: 0.7764 (mmm) cc_final: 0.7298 (ttp) REVERT: A 252 TRP cc_start: 0.5435 (t60) cc_final: 0.4989 (t60) REVERT: A 281 VAL cc_start: 0.8570 (OUTLIER) cc_final: 0.8060 (t) REVERT: B 29 GLN cc_start: 0.8784 (OUTLIER) cc_final: 0.7620 (tp40) REVERT: B 700 TYR cc_start: 0.3118 (t80) cc_final: 0.2387 (t80) REVERT: C 142 ARG cc_start: 0.8718 (OUTLIER) cc_final: 0.8337 (tpm-80) REVERT: C 195 LEU cc_start: 0.6552 (OUTLIER) cc_final: 0.6011 (mp) REVERT: C 252 TRP cc_start: 0.5455 (t60) cc_final: 0.5023 (t60) REVERT: C 281 VAL cc_start: 0.8571 (OUTLIER) cc_final: 0.8063 (t) REVERT: C 670 MET cc_start: 0.5291 (ptm) cc_final: 0.4835 (ttm) REVERT: D 29 GLN cc_start: 0.8774 (OUTLIER) cc_final: 0.7569 (tp40) REVERT: D 700 TYR cc_start: 0.2696 (t80) cc_final: 0.2249 (t80) outliers start: 62 outliers final: 40 residues processed: 303 average time/residue: 0.1887 time to fit residues: 96.9959 Evaluate side-chains 263 residues out of total 4276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 215 time to evaluate : 1.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 142 ARG Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 349 HIS Chi-restraints excluded: chain A residue 366 GLU Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain B residue 29 GLN Chi-restraints excluded: chain B residue 70 PHE Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 235 ASN Chi-restraints excluded: chain B residue 257 SER Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 353 ASN Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 142 ARG Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 308 ASN Chi-restraints excluded: chain C residue 349 HIS Chi-restraints excluded: chain C residue 366 GLU Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 781 SER Chi-restraints excluded: chain C residue 783 LEU Chi-restraints excluded: chain D residue 29 GLN Chi-restraints excluded: chain D residue 70 PHE Chi-restraints excluded: chain D residue 79 ILE Chi-restraints excluded: chain D residue 89 SER Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 235 ASN Chi-restraints excluded: chain D residue 257 SER Chi-restraints excluded: chain D residue 269 THR Chi-restraints excluded: chain D residue 330 VAL Chi-restraints excluded: chain D residue 353 ASN Chi-restraints excluded: chain D residue 442 LEU Chi-restraints excluded: chain E residue 151 TYR Chi-restraints excluded: chain E residue 156 THR Chi-restraints excluded: chain G residue 91 CYS Chi-restraints excluded: chain H residue 91 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 221 optimal weight: 8.9990 chunk 3 optimal weight: 0.8980 chunk 441 optimal weight: 40.0000 chunk 48 optimal weight: 10.0000 chunk 109 optimal weight: 0.1980 chunk 411 optimal weight: 10.0000 chunk 331 optimal weight: 20.0000 chunk 340 optimal weight: 0.9990 chunk 368 optimal weight: 7.9990 chunk 62 optimal weight: 5.9990 chunk 24 optimal weight: 0.9980 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 582 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 619 ASN C 19 GLN ** C 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 705 ASN ** D 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5012 r_free = 0.5012 target = 0.202465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4708 r_free = 0.4708 target = 0.173712 restraints weight = 71930.232| |-----------------------------------------------------------------------------| r_work (start): 0.4667 rms_B_bonded: 3.42 r_work: 0.4207 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.4207 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4143 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4143 r_free = 0.4143 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4143 r_free = 0.4143 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4143 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6897 moved from start: 0.2904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 35148 Z= 0.206 Angle : 0.627 14.024 47977 Z= 0.312 Chirality : 0.044 0.332 5724 Planarity : 0.004 0.207 6125 Dihedral : 8.563 88.686 5948 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.14 % Allowed : 16.07 % Favored : 81.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.91 (0.12), residues: 4922 helix: 0.30 (0.12), residues: 1932 sheet: -1.93 (0.16), residues: 942 loop : -2.46 (0.12), residues: 2048 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.027 0.001 ARG C 168 TYR 0.028 0.002 TYR A 71 PHE 0.029 0.002 PHE C 527 TRP 0.030 0.001 TRP B 606 HIS 0.018 0.001 HIS A 349 Details of bonding type rmsd covalent geometry : bond 0.00489 (35118) covalent geometry : angle 0.61658 (47903) SS BOND : bond 0.00922 ( 10) SS BOND : angle 1.36965 ( 20) hydrogen bonds : bond 0.04504 ( 1674) hydrogen bonds : angle 4.69451 ( 4752) Misc. bond : bond 0.00011 ( 2) link_BETA1-4 : bond 0.00401 ( 6) link_BETA1-4 : angle 3.43191 ( 18) link_NAG-ASN : bond 0.00287 ( 12) link_NAG-ASN : angle 3.43248 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9844 Ramachandran restraints generated. 4922 Oldfield, 0 Emsley, 4922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9844 Ramachandran restraints generated. 4922 Oldfield, 0 Emsley, 4922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 4276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 222 time to evaluate : 1.061 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 ARG cc_start: 0.8611 (OUTLIER) cc_final: 0.8248 (tpm-80) REVERT: A 249 MET cc_start: 0.7518 (mmm) cc_final: 0.7043 (ttp) REVERT: A 281 VAL cc_start: 0.8472 (OUTLIER) cc_final: 0.7938 (t) REVERT: A 666 MET cc_start: 0.6907 (mpp) cc_final: 0.6554 (mpp) REVERT: B 178 LEU cc_start: 0.9164 (OUTLIER) cc_final: 0.8956 (mp) REVERT: B 467 LEU cc_start: 0.2747 (OUTLIER) cc_final: 0.2197 (mt) REVERT: B 700 TYR cc_start: 0.3362 (t80) cc_final: 0.2418 (t80) REVERT: C 142 ARG cc_start: 0.8636 (OUTLIER) cc_final: 0.8276 (tpm-80) REVERT: C 249 MET cc_start: 0.7566 (mmm) cc_final: 0.7048 (ttp) REVERT: C 281 VAL cc_start: 0.8406 (OUTLIER) cc_final: 0.7870 (t) REVERT: C 670 MET cc_start: 0.5465 (ptm) cc_final: 0.4807 (ttp) REVERT: D 467 LEU cc_start: 0.2732 (OUTLIER) cc_final: 0.2262 (mt) REVERT: D 700 TYR cc_start: 0.2935 (t80) cc_final: 0.2310 (t80) outliers start: 57 outliers final: 37 residues processed: 270 average time/residue: 0.1860 time to fit residues: 85.9585 Evaluate side-chains 252 residues out of total 4276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 208 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 142 ARG Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 349 HIS Chi-restraints excluded: chain A residue 366 GLU Chi-restraints excluded: chain A residue 714 CYS Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 87 HIS Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 168 ASP Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 257 SER Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 619 ASN Chi-restraints excluded: chain B residue 629 MET Chi-restraints excluded: chain B residue 785 SER Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 142 ARG Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 349 HIS Chi-restraints excluded: chain C residue 366 GLU Chi-restraints excluded: chain C residue 783 LEU Chi-restraints excluded: chain D residue 44 LEU Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 79 ILE Chi-restraints excluded: chain D residue 87 HIS Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 168 ASP Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 257 SER Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 467 LEU Chi-restraints excluded: chain E residue 149 TYR Chi-restraints excluded: chain F residue 149 TYR Chi-restraints excluded: chain F residue 154 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 77 optimal weight: 0.0970 chunk 340 optimal weight: 8.9990 chunk 396 optimal weight: 30.0000 chunk 152 optimal weight: 10.0000 chunk 312 optimal weight: 7.9990 chunk 94 optimal weight: 1.9990 chunk 393 optimal weight: 20.0000 chunk 46 optimal weight: 7.9990 chunk 205 optimal weight: 10.0000 chunk 229 optimal weight: 8.9990 chunk 135 optimal weight: 20.0000 overall best weight: 5.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 331 GLN B 435 HIS C 571 ASN ** C 583 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 787 ASN D 208 HIS D 331 GLN ** E 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4978 r_free = 0.4978 target = 0.199423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4653 r_free = 0.4653 target = 0.169579 restraints weight = 70594.110| |-----------------------------------------------------------------------------| r_work (start): 0.4607 rms_B_bonded: 3.53 r_work: 0.4151 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.4151 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4063 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4063 r_free = 0.4063 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4063 r_free = 0.4063 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4063 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7008 moved from start: 0.4011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.170 35148 Z= 0.533 Angle : 0.960 15.385 47977 Z= 0.489 Chirality : 0.056 0.288 5724 Planarity : 0.006 0.141 6125 Dihedral : 9.323 92.211 5948 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.87 % Favored : 93.07 % Rotamer: Outliers : 4.23 % Allowed : 15.70 % Favored : 80.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.16 (0.11), residues: 4922 helix: 0.05 (0.12), residues: 1894 sheet: -1.89 (0.17), residues: 848 loop : -2.61 (0.12), residues: 2180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 258 TYR 0.049 0.003 TYR A 71 PHE 0.029 0.003 PHE C 24 TRP 0.024 0.003 TRP B 605 HIS 0.015 0.003 HIS A 21 Details of bonding type rmsd covalent geometry : bond 0.01298 (35118) covalent geometry : angle 0.95009 (47903) SS BOND : bond 0.01332 ( 10) SS BOND : angle 2.08142 ( 20) hydrogen bonds : bond 0.06073 ( 1674) hydrogen bonds : angle 5.52333 ( 4752) Misc. bond : bond 0.00036 ( 2) link_BETA1-4 : bond 0.00404 ( 6) link_BETA1-4 : angle 3.49976 ( 18) link_NAG-ASN : bond 0.01311 ( 12) link_NAG-ASN : angle 4.36483 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9844 Ramachandran restraints generated. 4922 Oldfield, 0 Emsley, 4922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9844 Ramachandran restraints generated. 4922 Oldfield, 0 Emsley, 4922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 4276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 222 time to evaluate : 1.102 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 106 GLN cc_start: 0.8864 (OUTLIER) cc_final: 0.8196 (mm-40) REVERT: A 142 ARG cc_start: 0.8718 (OUTLIER) cc_final: 0.8409 (tpm-80) REVERT: A 195 LEU cc_start: 0.6585 (OUTLIER) cc_final: 0.5998 (mp) REVERT: A 249 MET cc_start: 0.7812 (mmm) cc_final: 0.7346 (tmm) REVERT: A 403 MET cc_start: 0.4077 (mpp) cc_final: 0.3844 (mpp) REVERT: B 29 GLN cc_start: 0.8875 (OUTLIER) cc_final: 0.7363 (tp40) REVERT: B 106 GLN cc_start: 0.8569 (OUTLIER) cc_final: 0.7203 (mp10) REVERT: B 248 LEU cc_start: 0.8644 (OUTLIER) cc_final: 0.8427 (tp) REVERT: B 467 LEU cc_start: 0.2533 (OUTLIER) cc_final: 0.1825 (mt) REVERT: B 700 TYR cc_start: 0.3198 (t80) cc_final: 0.2331 (t80) REVERT: C 106 GLN cc_start: 0.8907 (OUTLIER) cc_final: 0.8254 (mm-40) REVERT: C 142 ARG cc_start: 0.8741 (OUTLIER) cc_final: 0.8431 (tpm-80) REVERT: C 195 LEU cc_start: 0.6500 (OUTLIER) cc_final: 0.5879 (mp) REVERT: C 249 MET cc_start: 0.7841 (mmm) cc_final: 0.7368 (tmm) REVERT: C 403 MET cc_start: 0.4094 (mpp) cc_final: 0.3853 (mpp) REVERT: C 670 MET cc_start: 0.5194 (ptm) cc_final: 0.4755 (ttp) REVERT: D 29 GLN cc_start: 0.8881 (OUTLIER) cc_final: 0.7368 (tp40) REVERT: D 106 GLN cc_start: 0.8532 (OUTLIER) cc_final: 0.7202 (mp10) REVERT: D 248 LEU cc_start: 0.8592 (OUTLIER) cc_final: 0.8329 (tp) REVERT: D 467 LEU cc_start: 0.2644 (OUTLIER) cc_final: 0.1977 (mt) REVERT: D 700 TYR cc_start: 0.3357 (t80) cc_final: 0.2499 (t80) REVERT: D 758 LEU cc_start: 0.7269 (mp) cc_final: 0.7010 (tt) outliers start: 113 outliers final: 74 residues processed: 324 average time/residue: 0.1904 time to fit residues: 105.3284 Evaluate side-chains 298 residues out of total 4276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 210 time to evaluate : 1.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 72 GLU Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 106 GLN Chi-restraints excluded: chain A residue 142 ARG Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 349 HIS Chi-restraints excluded: chain A residue 366 GLU Chi-restraints excluded: chain A residue 620 LEU Chi-restraints excluded: chain A residue 714 CYS Chi-restraints excluded: chain A residue 783 LEU Chi-restraints excluded: chain B residue 29 GLN Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 70 PHE Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 87 HIS Chi-restraints excluded: chain B residue 106 GLN Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 133 SER Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 168 ASP Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 372 ASP Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 619 ASN Chi-restraints excluded: chain B residue 758 LEU Chi-restraints excluded: chain B residue 785 SER Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 106 GLN Chi-restraints excluded: chain C residue 142 ARG Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 227 GLU Chi-restraints excluded: chain C residue 332 THR Chi-restraints excluded: chain C residue 349 HIS Chi-restraints excluded: chain C residue 366 GLU Chi-restraints excluded: chain C residue 714 CYS Chi-restraints excluded: chain C residue 781 SER Chi-restraints excluded: chain C residue 783 LEU Chi-restraints excluded: chain D residue 29 GLN Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 70 PHE Chi-restraints excluded: chain D residue 79 ILE Chi-restraints excluded: chain D residue 87 HIS Chi-restraints excluded: chain D residue 89 SER Chi-restraints excluded: chain D residue 106 GLN Chi-restraints excluded: chain D residue 110 ASP Chi-restraints excluded: chain D residue 133 SER Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 168 ASP Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 204 THR Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 257 SER Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 269 THR Chi-restraints excluded: chain D residue 275 THR Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 330 VAL Chi-restraints excluded: chain D residue 353 ASN Chi-restraints excluded: chain D residue 372 ASP Chi-restraints excluded: chain D residue 467 LEU Chi-restraints excluded: chain D residue 792 VAL Chi-restraints excluded: chain E residue 149 TYR Chi-restraints excluded: chain F residue 149 TYR Chi-restraints excluded: chain G residue 150 VAL Chi-restraints excluded: chain G residue 203 TRP Chi-restraints excluded: chain H residue 203 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 16 optimal weight: 3.9990 chunk 234 optimal weight: 0.6980 chunk 260 optimal weight: 0.7980 chunk 256 optimal weight: 0.8980 chunk 407 optimal weight: 20.0000 chunk 69 optimal weight: 30.0000 chunk 201 optimal weight: 8.9990 chunk 488 optimal weight: 10.0000 chunk 165 optimal weight: 0.7980 chunk 447 optimal weight: 30.0000 chunk 243 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 349 HIS B 435 HIS ** C 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 583 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 619 ASN ** E 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** 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 = 0.4867 r_free = 0.4867 target = 0.195029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4544 r_free = 0.4544 target = 0.165723 restraints weight = 72339.064| |-----------------------------------------------------------------------------| r_work (start): 0.4475 rms_B_bonded: 3.53 r_work: 0.4177 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.4177 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4174 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4174 r_free = 0.4174 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4174 r_free = 0.4174 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4174 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6489 moved from start: 0.3899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 35148 Z= 0.135 Angle : 0.608 14.931 47977 Z= 0.299 Chirality : 0.043 0.346 5724 Planarity : 0.003 0.054 6125 Dihedral : 8.063 81.844 5945 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.25 % Allowed : 18.10 % Favored : 79.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.52 (0.12), residues: 4922 helix: 0.69 (0.12), residues: 1904 sheet: -1.74 (0.17), residues: 864 loop : -2.28 (0.12), residues: 2154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 262 TYR 0.018 0.001 TYR D 280 PHE 0.025 0.001 PHE A 527 TRP 0.046 0.001 TRP B 606 HIS 0.003 0.001 HIS C 349 Details of bonding type rmsd covalent geometry : bond 0.00304 (35118) covalent geometry : angle 0.59509 (47903) SS BOND : bond 0.00271 ( 10) SS BOND : angle 1.72059 ( 20) hydrogen bonds : bond 0.03902 ( 1674) hydrogen bonds : angle 4.47485 ( 4752) Misc. bond : bond 0.00007 ( 2) link_BETA1-4 : bond 0.00254 ( 6) link_BETA1-4 : angle 3.46053 ( 18) link_NAG-ASN : bond 0.00393 ( 12) link_NAG-ASN : angle 3.65089 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9844 Ramachandran restraints generated. 4922 Oldfield, 0 Emsley, 4922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9844 Ramachandran restraints generated. 4922 Oldfield, 0 Emsley, 4922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 4276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 214 time to evaluate : 1.116 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 GLN cc_start: 0.8673 (OUTLIER) cc_final: 0.7941 (mm-40) REVERT: A 142 ARG cc_start: 0.8497 (OUTLIER) cc_final: 0.8057 (tpm-80) REVERT: A 195 LEU cc_start: 0.6547 (OUTLIER) cc_final: 0.6015 (mp) REVERT: A 249 MET cc_start: 0.7604 (mmm) cc_final: 0.6929 (ttp) REVERT: A 252 TRP cc_start: 0.5508 (t60) cc_final: 0.4857 (t60) REVERT: A 403 MET cc_start: 0.3306 (mpp) cc_final: 0.3082 (mpp) REVERT: B 407 MET cc_start: 0.2277 (OUTLIER) cc_final: 0.1393 (pmm) REVERT: B 408 MET cc_start: -0.0881 (OUTLIER) cc_final: -0.1145 (mmp) REVERT: B 467 LEU cc_start: 0.2297 (OUTLIER) cc_final: 0.1582 (mt) REVERT: B 700 TYR cc_start: 0.1760 (t80) cc_final: 0.1306 (t80) REVERT: C 106 GLN cc_start: 0.8651 (OUTLIER) cc_final: 0.7903 (mm-40) REVERT: C 142 ARG cc_start: 0.8496 (OUTLIER) cc_final: 0.8074 (tpm-80) REVERT: C 249 MET cc_start: 0.7577 (mmm) cc_final: 0.6922 (ttp) REVERT: C 252 TRP cc_start: 0.5540 (t60) cc_final: 0.4873 (t60) REVERT: C 403 MET cc_start: 0.3478 (mpp) cc_final: 0.3251 (mpp) REVERT: D 407 MET cc_start: 0.2046 (OUTLIER) cc_final: 0.1182 (pmm) REVERT: D 408 MET cc_start: -0.0952 (OUTLIER) cc_final: -0.1186 (mmp) REVERT: D 467 LEU cc_start: 0.2308 (OUTLIER) cc_final: 0.1851 (mt) REVERT: D 700 TYR cc_start: 0.2001 (t80) cc_final: 0.1568 (t80) outliers start: 60 outliers final: 41 residues processed: 258 average time/residue: 0.1882 time to fit residues: 83.4873 Evaluate side-chains 251 residues out of total 4276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 199 time to evaluate : 1.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 106 GLN Chi-restraints excluded: chain A residue 142 ARG Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 349 HIS Chi-restraints excluded: chain A residue 366 GLU Chi-restraints excluded: chain A residue 620 LEU Chi-restraints excluded: chain A residue 714 CYS Chi-restraints excluded: chain A residue 812 TYR Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 168 ASP Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 237 SER Chi-restraints excluded: chain B residue 257 SER Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 106 GLN Chi-restraints excluded: chain C residue 142 ARG Chi-restraints excluded: chain C residue 349 HIS Chi-restraints excluded: chain C residue 366 GLU Chi-restraints excluded: chain C residue 472 VAL Chi-restraints excluded: chain C residue 619 PHE Chi-restraints excluded: chain C residue 714 CYS Chi-restraints excluded: chain C residue 783 LEU Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 168 ASP Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 237 SER Chi-restraints excluded: chain D residue 275 THR Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 407 MET Chi-restraints excluded: chain D residue 408 MET Chi-restraints excluded: chain D residue 467 LEU Chi-restraints excluded: chain D residue 619 ASN Chi-restraints excluded: chain D residue 792 VAL Chi-restraints excluded: chain E residue 149 TYR Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain F residue 149 TYR Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain G residue 203 TRP Chi-restraints excluded: chain H residue 150 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 308 optimal weight: 6.9990 chunk 350 optimal weight: 30.0000 chunk 448 optimal weight: 30.0000 chunk 468 optimal weight: 40.0000 chunk 335 optimal weight: 30.0000 chunk 392 optimal weight: 10.0000 chunk 424 optimal weight: 8.9990 chunk 160 optimal weight: 0.9980 chunk 244 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 237 optimal weight: 0.9980 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 208 HIS B 435 HIS ** C 583 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 619 ASN ** E 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** 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 = 0.5001 r_free = 0.5001 target = 0.201511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4685 r_free = 0.4685 target = 0.171869 restraints weight = 70511.587| |-----------------------------------------------------------------------------| r_work (start): 0.4635 rms_B_bonded: 3.57 r_work: 0.4298 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.4298 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4223 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4223 r_free = 0.4223 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4223 r_free = 0.4223 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4223 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6748 moved from start: 0.4205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.103 35148 Z= 0.289 Angle : 0.714 15.815 47977 Z= 0.355 Chirality : 0.046 0.324 5724 Planarity : 0.004 0.055 6125 Dihedral : 8.258 80.034 5944 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 3.48 % Allowed : 17.83 % Favored : 78.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.50 (0.12), residues: 4922 helix: 0.72 (0.12), residues: 1892 sheet: -1.55 (0.18), residues: 804 loop : -2.36 (0.12), residues: 2226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 258 TYR 0.032 0.002 TYR C 71 PHE 0.026 0.002 PHE A 527 TRP 0.022 0.002 TRP B 605 HIS 0.011 0.002 HIS A 349 Details of bonding type rmsd covalent geometry : bond 0.00698 (35118) covalent geometry : angle 0.70257 (47903) SS BOND : bond 0.00470 ( 10) SS BOND : angle 1.65479 ( 20) hydrogen bonds : bond 0.04590 ( 1674) hydrogen bonds : angle 4.68604 ( 4752) Misc. bond : bond 0.00018 ( 2) link_BETA1-4 : bond 0.00524 ( 6) link_BETA1-4 : angle 3.31992 ( 18) link_NAG-ASN : bond 0.00355 ( 12) link_NAG-ASN : angle 3.85779 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9844 Ramachandran restraints generated. 4922 Oldfield, 0 Emsley, 4922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9844 Ramachandran restraints generated. 4922 Oldfield, 0 Emsley, 4922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 4276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 213 time to evaluate : 1.069 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: A 106 GLN cc_start: 0.8785 (OUTLIER) cc_final: 0.8004 (mm-40) REVERT: A 142 ARG cc_start: 0.8560 (OUTLIER) cc_final: 0.8159 (tpm-80) REVERT: A 195 LEU cc_start: 0.6365 (OUTLIER) cc_final: 0.5804 (mp) REVERT: A 249 MET cc_start: 0.7730 (mmm) cc_final: 0.7034 (ttp) REVERT: B 29 GLN cc_start: 0.8705 (OUTLIER) cc_final: 0.7230 (tp40) REVERT: B 407 MET cc_start: 0.2408 (OUTLIER) cc_final: 0.1350 (pmm) REVERT: B 408 MET cc_start: -0.0754 (mmp) cc_final: -0.1014 (mmp) REVERT: B 700 TYR cc_start: 0.2503 (t80) cc_final: 0.1735 (t80) REVERT: C 106 GLN cc_start: 0.8768 (OUTLIER) cc_final: 0.7989 (mm-40) REVERT: C 142 ARG cc_start: 0.8528 (OUTLIER) cc_final: 0.8137 (tpm-80) REVERT: C 195 LEU cc_start: 0.6309 (OUTLIER) cc_final: 0.5747 (mp) REVERT: C 249 MET cc_start: 0.7781 (mmm) cc_final: 0.7436 (ttp) REVERT: C 619 PHE cc_start: 0.7190 (OUTLIER) cc_final: 0.6303 (t80) REVERT: C 666 MET cc_start: 0.5827 (mpp) cc_final: 0.5442 (mpp) REVERT: D 29 GLN cc_start: 0.8684 (OUTLIER) cc_final: 0.7201 (tp40) REVERT: D 178 LEU cc_start: 0.9122 (OUTLIER) cc_final: 0.8697 (mp) REVERT: D 407 MET cc_start: 0.2458 (OUTLIER) cc_final: 0.1277 (pmm) REVERT: D 408 MET cc_start: -0.0530 (mmp) cc_final: -0.0822 (mmp) REVERT: D 467 LEU cc_start: 0.2359 (OUTLIER) cc_final: 0.1810 (mt) REVERT: D 503 MET cc_start: 0.3235 (mtp) cc_final: 0.2723 (mtt) REVERT: D 700 TYR cc_start: 0.2494 (t80) cc_final: 0.1896 (t80) outliers start: 93 outliers final: 72 residues processed: 297 average time/residue: 0.1843 time to fit residues: 94.6101 Evaluate side-chains 286 residues out of total 4276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 201 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 72 GLU Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 89 CYS Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 106 GLN Chi-restraints excluded: chain A residue 142 ARG Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 349 HIS Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 366 GLU Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 620 LEU Chi-restraints excluded: chain A residue 714 CYS Chi-restraints excluded: chain A residue 812 TYR Chi-restraints excluded: chain B residue 29 GLN Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 87 HIS Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 133 SER Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 168 ASP Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 237 SER Chi-restraints excluded: chain B residue 257 SER Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 331 GLN Chi-restraints excluded: chain B residue 372 ASP Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain B residue 785 SER Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 89 CYS Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 106 GLN Chi-restraints excluded: chain C residue 142 ARG Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 349 HIS Chi-restraints excluded: chain C residue 351 ILE Chi-restraints excluded: chain C residue 366 GLU Chi-restraints excluded: chain C residue 472 VAL Chi-restraints excluded: chain C residue 619 PHE Chi-restraints excluded: chain C residue 714 CYS Chi-restraints excluded: chain C residue 783 LEU Chi-restraints excluded: chain D residue 29 GLN Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 79 ILE Chi-restraints excluded: chain D residue 87 HIS Chi-restraints excluded: chain D residue 133 SER Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 168 ASP Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 237 SER Chi-restraints excluded: chain D residue 269 THR Chi-restraints excluded: chain D residue 275 THR Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 330 VAL Chi-restraints excluded: chain D residue 372 ASP Chi-restraints excluded: chain D residue 407 MET Chi-restraints excluded: chain D residue 467 LEU Chi-restraints excluded: chain D residue 619 ASN Chi-restraints excluded: chain D residue 792 VAL Chi-restraints excluded: chain E residue 149 TYR Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain F residue 149 TYR Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain G residue 29 PHE Chi-restraints excluded: chain G residue 150 VAL Chi-restraints excluded: chain G residue 203 TRP Chi-restraints excluded: chain H residue 150 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 274 optimal weight: 50.0000 chunk 122 optimal weight: 7.9990 chunk 372 optimal weight: 50.0000 chunk 221 optimal weight: 1.9990 chunk 440 optimal weight: 30.0000 chunk 139 optimal weight: 10.0000 chunk 458 optimal weight: 20.0000 chunk 210 optimal weight: 10.0000 chunk 293 optimal weight: 4.9990 chunk 88 optimal weight: 0.8980 chunk 290 optimal weight: 6.9990 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 349 HIS A 787 ASN ** C 583 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 83 HIS ** 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 = 0.4982 r_free = 0.4982 target = 0.200951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4664 r_free = 0.4664 target = 0.170814 restraints weight = 71042.838| |-----------------------------------------------------------------------------| r_work (start): 0.4610 rms_B_bonded: 3.70 r_work: 0.4314 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work: 0.4264 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.4264 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4208 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4208 r_free = 0.4208 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4208 r_free = 0.4208 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4208 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6695 moved from start: 0.4842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.154 35148 Z= 0.456 Angle : 0.885 16.037 47977 Z= 0.449 Chirality : 0.053 0.307 5724 Planarity : 0.005 0.115 6125 Dihedral : 9.150 84.417 5944 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 4.05 % Allowed : 18.25 % Favored : 77.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.84 (0.12), residues: 4922 helix: 0.39 (0.12), residues: 1886 sheet: -1.73 (0.17), residues: 824 loop : -2.48 (0.12), residues: 2212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.001 ARG A 168 TYR 0.040 0.002 TYR A 71 PHE 0.026 0.003 PHE C 603 TRP 0.029 0.003 TRP C 602 HIS 0.012 0.003 HIS C 21 Details of bonding type rmsd covalent geometry : bond 0.01103 (35118) covalent geometry : angle 0.87404 (47903) SS BOND : bond 0.00649 ( 10) SS BOND : angle 1.72393 ( 20) hydrogen bonds : bond 0.05590 ( 1674) hydrogen bonds : angle 5.28767 ( 4752) Misc. bond : bond 0.00027 ( 2) link_BETA1-4 : bond 0.00740 ( 6) link_BETA1-4 : angle 3.79237 ( 18) link_NAG-ASN : bond 0.00379 ( 12) link_NAG-ASN : angle 4.18716 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9844 Ramachandran restraints generated. 4922 Oldfield, 0 Emsley, 4922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9844 Ramachandran restraints generated. 4922 Oldfield, 0 Emsley, 4922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 4276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 210 time to evaluate : 1.282 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 31 LEU cc_start: 0.7032 (OUTLIER) cc_final: 0.5920 (pt) REVERT: A 106 GLN cc_start: 0.8979 (OUTLIER) cc_final: 0.8285 (mm-40) REVERT: A 142 ARG cc_start: 0.8667 (OUTLIER) cc_final: 0.8237 (tpm-80) REVERT: A 249 MET cc_start: 0.7866 (mmm) cc_final: 0.7165 (tmm) REVERT: A 325 GLN cc_start: 0.8172 (OUTLIER) cc_final: 0.7829 (mp10) REVERT: A 620 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8458 (tp) REVERT: A 666 MET cc_start: 0.5797 (mpp) cc_final: 0.5508 (mpp) REVERT: B 29 GLN cc_start: 0.9002 (OUTLIER) cc_final: 0.7595 (tp40) REVERT: B 106 GLN cc_start: 0.8705 (OUTLIER) cc_final: 0.7440 (mp10) REVERT: B 407 MET cc_start: 0.2371 (OUTLIER) cc_final: 0.1202 (pmm) REVERT: B 408 MET cc_start: -0.0742 (mmp) cc_final: -0.1014 (mmp) REVERT: B 700 TYR cc_start: 0.1982 (t80) cc_final: 0.1467 (t80) REVERT: C 31 LEU cc_start: 0.7085 (OUTLIER) cc_final: 0.5967 (pt) REVERT: C 106 GLN cc_start: 0.8965 (OUTLIER) cc_final: 0.8265 (mm-40) REVERT: C 142 ARG cc_start: 0.8610 (OUTLIER) cc_final: 0.8251 (tpm-80) REVERT: C 249 MET cc_start: 0.7849 (mmm) cc_final: 0.7166 (tmm) REVERT: C 325 GLN cc_start: 0.8166 (OUTLIER) cc_final: 0.7821 (mp10) REVERT: D 29 GLN cc_start: 0.8995 (OUTLIER) cc_final: 0.7564 (tp40) REVERT: D 106 GLN cc_start: 0.8718 (OUTLIER) cc_final: 0.7360 (mp10) REVERT: D 407 MET cc_start: 0.2239 (OUTLIER) cc_final: 0.0997 (pmm) REVERT: D 408 MET cc_start: -0.0557 (mmp) cc_final: -0.0822 (mmp) REVERT: D 503 MET cc_start: 0.3474 (mtp) cc_final: 0.2941 (mtt) REVERT: D 700 TYR cc_start: 0.2101 (t80) cc_final: 0.1579 (t80) outliers start: 108 outliers final: 80 residues processed: 305 average time/residue: 0.1758 time to fit residues: 93.9201 Evaluate side-chains 295 residues out of total 4276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 200 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 72 GLU Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 89 CYS Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 106 GLN Chi-restraints excluded: chain A residue 142 ARG Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain A residue 325 GLN Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 366 GLU Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 620 LEU Chi-restraints excluded: chain A residue 714 CYS Chi-restraints excluded: chain B residue 29 GLN Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 70 PHE Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 87 HIS Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 106 GLN Chi-restraints excluded: chain B residue 133 SER Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 168 ASP Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 237 SER Chi-restraints excluded: chain B residue 257 SER Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 331 GLN Chi-restraints excluded: chain B residue 372 ASP Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain B residue 785 SER Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 89 CYS Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 106 GLN Chi-restraints excluded: chain C residue 142 ARG Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 295 ASP Chi-restraints excluded: chain C residue 325 GLN Chi-restraints excluded: chain C residue 349 HIS Chi-restraints excluded: chain C residue 351 ILE Chi-restraints excluded: chain C residue 366 GLU Chi-restraints excluded: chain C residue 472 VAL Chi-restraints excluded: chain C residue 714 CYS Chi-restraints excluded: chain D residue 29 GLN Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 70 PHE Chi-restraints excluded: chain D residue 79 ILE Chi-restraints excluded: chain D residue 87 HIS Chi-restraints excluded: chain D residue 106 GLN Chi-restraints excluded: chain D residue 133 SER Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 168 ASP Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 237 SER Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 269 THR Chi-restraints excluded: chain D residue 275 THR Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 330 VAL Chi-restraints excluded: chain D residue 331 GLN Chi-restraints excluded: chain D residue 372 ASP Chi-restraints excluded: chain D residue 407 MET Chi-restraints excluded: chain D residue 496 MET Chi-restraints excluded: chain D residue 540 LEU Chi-restraints excluded: chain D residue 605 TRP Chi-restraints excluded: chain D residue 619 ASN Chi-restraints excluded: chain D residue 792 VAL Chi-restraints excluded: chain E residue 149 TYR Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain F residue 149 TYR Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain G residue 150 VAL Chi-restraints excluded: chain G residue 203 TRP Chi-restraints excluded: chain H residue 150 VAL Chi-restraints excluded: chain H residue 203 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 96 optimal weight: 0.6980 chunk 427 optimal weight: 4.9990 chunk 325 optimal weight: 5.9990 chunk 33 optimal weight: 0.6980 chunk 12 optimal weight: 0.9990 chunk 377 optimal weight: 50.0000 chunk 115 optimal weight: 30.0000 chunk 466 optimal weight: 40.0000 chunk 38 optimal weight: 20.0000 chunk 224 optimal weight: 2.9990 chunk 150 optimal weight: 30.0000 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 349 HIS ** C 583 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 619 ASN ** E 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 105 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5009 r_free = 0.5009 target = 0.202035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4683 r_free = 0.4683 target = 0.171004 restraints weight = 70708.181| |-----------------------------------------------------------------------------| r_work (start): 0.4609 rms_B_bonded: 3.49 r_work: 0.4315 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.4315 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4265 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4265 r_free = 0.4265 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4265 r_free = 0.4265 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4265 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6677 moved from start: 0.4850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 35148 Z= 0.227 Angle : 0.682 15.760 47977 Z= 0.338 Chirality : 0.045 0.293 5724 Planarity : 0.004 0.058 6125 Dihedral : 8.439 79.615 5944 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 3.18 % Allowed : 19.48 % Favored : 77.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.47 (0.12), residues: 4922 helix: 0.78 (0.12), residues: 1890 sheet: -1.66 (0.17), residues: 830 loop : -2.31 (0.12), residues: 2202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 125 TYR 0.024 0.002 TYR C 71 PHE 0.033 0.002 PHE G 205 TRP 0.043 0.002 TRP D 606 HIS 0.006 0.001 HIS C 349 Details of bonding type rmsd covalent geometry : bond 0.00545 (35118) covalent geometry : angle 0.66926 (47903) SS BOND : bond 0.00329 ( 10) SS BOND : angle 1.59094 ( 20) hydrogen bonds : bond 0.04214 ( 1674) hydrogen bonds : angle 4.68941 ( 4752) Misc. bond : bond 0.00012 ( 2) link_BETA1-4 : bond 0.00413 ( 6) link_BETA1-4 : angle 3.55640 ( 18) link_NAG-ASN : bond 0.00397 ( 12) link_NAG-ASN : angle 3.92066 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9844 Ramachandran restraints generated. 4922 Oldfield, 0 Emsley, 4922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9844 Ramachandran restraints generated. 4922 Oldfield, 0 Emsley, 4922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 4276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 211 time to evaluate : 1.170 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 106 GLN cc_start: 0.8753 (OUTLIER) cc_final: 0.7985 (mm-40) REVERT: A 142 ARG cc_start: 0.8514 (OUTLIER) cc_final: 0.8066 (tpm-80) REVERT: A 195 LEU cc_start: 0.6478 (OUTLIER) cc_final: 0.5888 (mp) REVERT: A 249 MET cc_start: 0.7699 (mmm) cc_final: 0.7100 (ttp) REVERT: A 325 GLN cc_start: 0.7924 (OUTLIER) cc_final: 0.7708 (mp10) REVERT: A 666 MET cc_start: 0.5811 (mpp) cc_final: 0.5579 (mpp) REVERT: A 670 MET cc_start: 0.5731 (tpp) cc_final: 0.5477 (tpp) REVERT: B 29 GLN cc_start: 0.8673 (OUTLIER) cc_final: 0.7170 (tp40) REVERT: B 407 MET cc_start: 0.2433 (OUTLIER) cc_final: 0.1181 (pmm) REVERT: B 408 MET cc_start: -0.0318 (mmp) cc_final: -0.0591 (mmp) REVERT: B 700 TYR cc_start: 0.1894 (t80) cc_final: 0.1442 (t80) REVERT: C 106 GLN cc_start: 0.8736 (OUTLIER) cc_final: 0.7961 (mm-40) REVERT: C 142 ARG cc_start: 0.8481 (OUTLIER) cc_final: 0.8055 (tpm-80) REVERT: C 249 MET cc_start: 0.7694 (mmm) cc_final: 0.7105 (ttp) REVERT: C 325 GLN cc_start: 0.7901 (OUTLIER) cc_final: 0.7685 (mp10) REVERT: D 29 GLN cc_start: 0.8656 (OUTLIER) cc_final: 0.7166 (tp40) REVERT: D 407 MET cc_start: 0.2576 (OUTLIER) cc_final: 0.1231 (pmm) REVERT: D 408 MET cc_start: -0.0736 (mmp) cc_final: -0.1006 (mmp) REVERT: D 700 TYR cc_start: 0.1884 (t80) cc_final: 0.1441 (t80) outliers start: 85 outliers final: 71 residues processed: 288 average time/residue: 0.1832 time to fit residues: 91.1609 Evaluate side-chains 282 residues out of total 4276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 200 time to evaluate : 1.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 72 GLU Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 89 CYS Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 106 GLN Chi-restraints excluded: chain A residue 142 ARG Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 325 GLN Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 366 GLU Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 714 CYS Chi-restraints excluded: chain A residue 812 TYR Chi-restraints excluded: chain B residue 29 GLN Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 70 PHE Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 87 HIS Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 133 SER Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 168 ASP Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 237 SER Chi-restraints excluded: chain B residue 257 SER Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 331 GLN Chi-restraints excluded: chain B residue 372 ASP Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain B residue 785 SER Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 106 GLN Chi-restraints excluded: chain C residue 142 ARG Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 325 GLN Chi-restraints excluded: chain C residue 349 HIS Chi-restraints excluded: chain C residue 351 ILE Chi-restraints excluded: chain C residue 366 GLU Chi-restraints excluded: chain C residue 472 VAL Chi-restraints excluded: chain C residue 714 CYS Chi-restraints excluded: chain D residue 29 GLN Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 70 PHE Chi-restraints excluded: chain D residue 79 ILE Chi-restraints excluded: chain D residue 87 HIS Chi-restraints excluded: chain D residue 89 SER Chi-restraints excluded: chain D residue 133 SER Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 168 ASP Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 237 SER Chi-restraints excluded: chain D residue 269 THR Chi-restraints excluded: chain D residue 275 THR Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 330 VAL Chi-restraints excluded: chain D residue 331 GLN Chi-restraints excluded: chain D residue 372 ASP Chi-restraints excluded: chain D residue 407 MET Chi-restraints excluded: chain D residue 496 MET Chi-restraints excluded: chain D residue 540 LEU Chi-restraints excluded: chain D residue 792 VAL Chi-restraints excluded: chain F residue 149 TYR Chi-restraints excluded: chain G residue 29 PHE Chi-restraints excluded: chain G residue 41 THR Chi-restraints excluded: chain G residue 150 VAL Chi-restraints excluded: chain G residue 203 TRP Chi-restraints excluded: chain H residue 150 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 16 optimal weight: 0.9990 chunk 143 optimal weight: 10.0000 chunk 189 optimal weight: 5.9990 chunk 107 optimal weight: 0.9980 chunk 254 optimal weight: 1.9990 chunk 438 optimal weight: 10.0000 chunk 311 optimal weight: 7.9990 chunk 201 optimal weight: 0.0980 chunk 316 optimal weight: 4.9990 chunk 13 optimal weight: 0.7980 chunk 31 optimal weight: 0.0870 overall best weight: 0.5960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 18 GLN C 582 GLN ** C 583 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 18 GLN ** E 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** 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 = 0.4874 r_free = 0.4874 target = 0.195722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4549 r_free = 0.4549 target = 0.165958 restraints weight = 70474.261| |-----------------------------------------------------------------------------| r_work (start): 0.4471 rms_B_bonded: 3.43 r_work: 0.4159 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.4159 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4141 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4141 r_free = 0.4141 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4141 r_free = 0.4141 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4141 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6536 moved from start: 0.4796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 35148 Z= 0.118 Angle : 0.610 14.792 47977 Z= 0.296 Chirality : 0.043 0.298 5724 Planarity : 0.003 0.058 6125 Dihedral : 7.783 77.108 5944 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.36 % Allowed : 20.46 % Favored : 77.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.05 (0.12), residues: 4922 helix: 1.15 (0.12), residues: 1896 sheet: -1.47 (0.18), residues: 818 loop : -2.09 (0.13), residues: 2208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 168 TYR 0.017 0.001 TYR D 280 PHE 0.031 0.001 PHE G 205 TRP 0.050 0.002 TRP A 601 HIS 0.015 0.001 HIS C 349 Details of bonding type rmsd covalent geometry : bond 0.00266 (35118) covalent geometry : angle 0.59612 (47903) SS BOND : bond 0.00214 ( 10) SS BOND : angle 1.44105 ( 20) hydrogen bonds : bond 0.03545 ( 1674) hydrogen bonds : angle 4.30951 ( 4752) Misc. bond : bond 0.00008 ( 2) link_BETA1-4 : bond 0.00386 ( 6) link_BETA1-4 : angle 3.39922 ( 18) link_NAG-ASN : bond 0.00421 ( 12) link_NAG-ASN : angle 3.94786 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9844 Ramachandran restraints generated. 4922 Oldfield, 0 Emsley, 4922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9844 Ramachandran restraints generated. 4922 Oldfield, 0 Emsley, 4922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 4276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 210 time to evaluate : 1.209 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: A 106 GLN cc_start: 0.8637 (OUTLIER) cc_final: 0.7888 (mm-40) REVERT: A 195 LEU cc_start: 0.6386 (OUTLIER) cc_final: 0.5811 (mp) REVERT: A 249 MET cc_start: 0.7698 (mmm) cc_final: 0.7024 (ttp) REVERT: A 325 GLN cc_start: 0.7927 (OUTLIER) cc_final: 0.7688 (mp10) REVERT: A 403 MET cc_start: 0.1559 (mmt) cc_final: 0.1135 (mmt) REVERT: A 670 MET cc_start: 0.5856 (tpp) cc_final: 0.5573 (tpp) REVERT: B 408 MET cc_start: -0.0566 (mmp) cc_final: -0.0817 (mmp) REVERT: B 700 TYR cc_start: 0.1874 (t80) cc_final: 0.1422 (t80) REVERT: C 106 GLN cc_start: 0.8626 (OUTLIER) cc_final: 0.7863 (mm-40) REVERT: C 195 LEU cc_start: 0.6337 (OUTLIER) cc_final: 0.5770 (mp) REVERT: C 249 MET cc_start: 0.7698 (mmm) cc_final: 0.7016 (ttp) REVERT: C 325 GLN cc_start: 0.7937 (OUTLIER) cc_final: 0.7689 (mp10) REVERT: C 403 MET cc_start: 0.1564 (mmt) cc_final: 0.1080 (mmt) REVERT: D 408 MET cc_start: -0.0517 (mmp) cc_final: -0.0775 (mmp) REVERT: D 700 TYR cc_start: 0.1611 (t80) cc_final: 0.1300 (t80) outliers start: 63 outliers final: 53 residues processed: 266 average time/residue: 0.1806 time to fit residues: 83.8121 Evaluate side-chains 258 residues out of total 4276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 199 time to evaluate : 1.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 72 GLU Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 106 GLN Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 325 GLN Chi-restraints excluded: chain A residue 366 GLU Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 714 CYS Chi-restraints excluded: chain A residue 812 TYR Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 87 HIS Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 168 ASP Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 237 SER Chi-restraints excluded: chain B residue 257 SER Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 619 ASN Chi-restraints excluded: chain B residue 758 LEU Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 89 CYS Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 106 GLN Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 325 GLN Chi-restraints excluded: chain C residue 349 HIS Chi-restraints excluded: chain C residue 351 ILE Chi-restraints excluded: chain C residue 366 GLU Chi-restraints excluded: chain C residue 472 VAL Chi-restraints excluded: chain C residue 714 CYS Chi-restraints excluded: chain C residue 783 LEU Chi-restraints excluded: chain D residue 87 HIS Chi-restraints excluded: chain D residue 89 SER Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 237 SER Chi-restraints excluded: chain D residue 269 THR Chi-restraints excluded: chain D residue 275 THR Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 496 MET Chi-restraints excluded: chain D residue 540 LEU Chi-restraints excluded: chain D residue 792 VAL Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain G residue 29 PHE Chi-restraints excluded: chain G residue 150 VAL Chi-restraints excluded: chain G residue 203 TRP Chi-restraints excluded: chain H residue 150 VAL Chi-restraints excluded: chain H residue 203 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 272 optimal weight: 40.0000 chunk 331 optimal weight: 30.0000 chunk 278 optimal weight: 8.9990 chunk 212 optimal weight: 9.9990 chunk 491 optimal weight: 30.0000 chunk 347 optimal weight: 8.9990 chunk 28 optimal weight: 0.6980 chunk 490 optimal weight: 20.0000 chunk 298 optimal weight: 5.9990 chunk 182 optimal weight: 0.9990 chunk 9 optimal weight: 0.7980 overall best weight: 3.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 349 HIS ** C 583 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4984 r_free = 0.4984 target = 0.201276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4669 r_free = 0.4669 target = 0.171368 restraints weight = 71125.554| |-----------------------------------------------------------------------------| r_work (start): 0.4608 rms_B_bonded: 3.61 r_work: 0.4276 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.4276 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4220 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4220 r_free = 0.4220 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4220 r_free = 0.4220 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4220 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6732 moved from start: 0.5108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.115 35148 Z= 0.348 Angle : 0.784 12.601 47977 Z= 0.391 Chirality : 0.049 0.306 5724 Planarity : 0.004 0.079 6125 Dihedral : 8.268 76.224 5944 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 2.62 % Allowed : 20.23 % Favored : 77.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.35 (0.12), residues: 4922 helix: 0.85 (0.12), residues: 1890 sheet: -1.54 (0.18), residues: 828 loop : -2.24 (0.13), residues: 2204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 258 TYR 0.036 0.002 TYR C 71 PHE 0.034 0.002 PHE C 603 TRP 0.045 0.002 TRP C 601 HIS 0.010 0.002 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00841 (35118) covalent geometry : angle 0.77330 (47903) SS BOND : bond 0.00460 ( 10) SS BOND : angle 1.54424 ( 20) hydrogen bonds : bond 0.04810 ( 1674) hydrogen bonds : angle 4.83054 ( 4752) Misc. bond : bond 0.00014 ( 2) link_BETA1-4 : bond 0.00614 ( 6) link_BETA1-4 : angle 3.39796 ( 18) link_NAG-ASN : bond 0.00407 ( 12) link_NAG-ASN : angle 4.15456 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9844 Ramachandran restraints generated. 4922 Oldfield, 0 Emsley, 4922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9844 Ramachandran restraints generated. 4922 Oldfield, 0 Emsley, 4922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 4276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 203 time to evaluate : 1.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 LEU cc_start: 0.6812 (OUTLIER) cc_final: 0.5752 (pt) REVERT: A 106 GLN cc_start: 0.8896 (OUTLIER) cc_final: 0.8165 (mm-40) REVERT: A 325 GLN cc_start: 0.7999 (OUTLIER) cc_final: 0.7757 (mp10) REVERT: A 403 MET cc_start: 0.1423 (mmt) cc_final: 0.0933 (mmt) REVERT: A 666 MET cc_start: 0.6807 (mpp) cc_final: 0.6481 (mpp) REVERT: A 670 MET cc_start: 0.5831 (tpp) cc_final: 0.5577 (tpp) REVERT: B 248 LEU cc_start: 0.8482 (OUTLIER) cc_final: 0.8189 (tp) REVERT: B 407 MET cc_start: 0.2849 (OUTLIER) cc_final: 0.1369 (pmm) REVERT: B 408 MET cc_start: -0.0408 (mmp) cc_final: -0.0684 (mmp) REVERT: B 629 MET cc_start: 0.3987 (ppp) cc_final: 0.3371 (ptt) REVERT: C 31 LEU cc_start: 0.6781 (OUTLIER) cc_final: 0.5744 (pt) REVERT: C 106 GLN cc_start: 0.8872 (OUTLIER) cc_final: 0.8131 (mm-40) REVERT: C 195 LEU cc_start: 0.6448 (OUTLIER) cc_final: 0.5846 (mp) REVERT: C 249 MET cc_start: 0.7608 (mmm) cc_final: 0.7081 (tmm) REVERT: C 325 GLN cc_start: 0.7977 (OUTLIER) cc_final: 0.7735 (mp10) REVERT: C 403 MET cc_start: 0.1751 (mmt) cc_final: 0.1257 (mmt) REVERT: D 408 MET cc_start: -0.0582 (mmp) cc_final: -0.0854 (mmp) REVERT: D 498 LEU cc_start: 0.3701 (pp) cc_final: 0.3460 (tp) REVERT: D 700 TYR cc_start: 0.2013 (t80) cc_final: 0.1482 (t80) REVERT: F 21 ILE cc_start: 0.7562 (mm) cc_final: 0.7361 (mm) outliers start: 70 outliers final: 58 residues processed: 267 average time/residue: 0.1717 time to fit residues: 80.4476 Evaluate side-chains 267 residues out of total 4276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 200 time to evaluate : 1.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 72 GLU Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 89 CYS Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 106 GLN Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 325 GLN Chi-restraints excluded: chain A residue 366 GLU Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 714 CYS Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 87 HIS Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 168 ASP Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 237 SER Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 257 SER Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 331 GLN Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain B residue 758 LEU Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 89 CYS Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 106 GLN Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 325 GLN Chi-restraints excluded: chain C residue 351 ILE Chi-restraints excluded: chain C residue 366 GLU Chi-restraints excluded: chain C residue 472 VAL Chi-restraints excluded: chain C residue 714 CYS Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 87 HIS Chi-restraints excluded: chain D residue 89 SER Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 168 ASP Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 237 SER Chi-restraints excluded: chain D residue 269 THR Chi-restraints excluded: chain D residue 275 THR Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 331 GLN Chi-restraints excluded: chain D residue 496 MET Chi-restraints excluded: chain D residue 540 LEU Chi-restraints excluded: chain D residue 751 LEU Chi-restraints excluded: chain D residue 792 VAL Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain G residue 41 THR Chi-restraints excluded: chain G residue 150 VAL Chi-restraints excluded: chain G residue 203 TRP Chi-restraints excluded: chain H residue 150 VAL Chi-restraints excluded: chain H residue 203 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 442 optimal weight: 10.0000 chunk 355 optimal weight: 5.9990 chunk 354 optimal weight: 6.9990 chunk 435 optimal weight: 0.3980 chunk 333 optimal weight: 30.0000 chunk 451 optimal weight: 30.0000 chunk 489 optimal weight: 30.0000 chunk 281 optimal weight: 4.9990 chunk 454 optimal weight: 20.0000 chunk 301 optimal weight: 0.9990 chunk 314 optimal weight: 7.9990 overall best weight: 3.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 583 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4967 r_free = 0.4967 target = 0.198610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4635 r_free = 0.4635 target = 0.167885 restraints weight = 69504.793| |-----------------------------------------------------------------------------| r_work (start): 0.4587 rms_B_bonded: 3.50 r_work: 0.4246 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.4246 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4223 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4223 r_free = 0.4223 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4223 r_free = 0.4223 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4223 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6725 moved from start: 0.5503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.137 35148 Z= 0.381 Angle : 0.831 23.401 47977 Z= 0.416 Chirality : 0.050 0.301 5724 Planarity : 0.005 0.087 6125 Dihedral : 8.605 77.478 5944 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 3.03 % Allowed : 20.01 % Favored : 76.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.59 (0.12), residues: 4922 helix: 0.64 (0.12), residues: 1896 sheet: -1.68 (0.17), residues: 852 loop : -2.37 (0.12), residues: 2174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 624 TYR 0.036 0.002 TYR C 71 PHE 0.027 0.002 PHE A 603 TRP 0.042 0.003 TRP C 601 HIS 0.011 0.002 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00922 (35118) covalent geometry : angle 0.81903 (47903) SS BOND : bond 0.00568 ( 10) SS BOND : angle 1.60598 ( 20) hydrogen bonds : bond 0.05035 ( 1674) hydrogen bonds : angle 5.05012 ( 4752) Misc. bond : bond 0.00013 ( 2) link_BETA1-4 : bond 0.00742 ( 6) link_BETA1-4 : angle 3.80020 ( 18) link_NAG-ASN : bond 0.00492 ( 12) link_NAG-ASN : angle 4.39994 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9093.39 seconds wall clock time: 155 minutes 34.56 seconds (9334.56 seconds total)