Starting phenix.real_space_refine on Fri Mar 6 22:40:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7lde_23284/03_2026/7lde_23284_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lde_23284/03_2026/7lde_23284.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7lde_23284/03_2026/7lde_23284_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lde_23284/03_2026/7lde_23284_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7lde_23284/03_2026/7lde_23284.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lde_23284/03_2026/7lde_23284.map" } resolution = 3.9 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= 0.014 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 22102 2.51 5 N 5791 2.21 5 O 6359 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 87 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 34424 Number of models: 1 Model: "" Number of chains: 27 Chain: "A" Number of atoms: 5858 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 776, 5857 Classifications: {'peptide': 776} Incomplete info: {'truncation_to_alanine': 92} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 749} Chain breaks: 2 Unresolved non-hydrogen bonds: 328 Unresolved non-hydrogen angles: 399 Unresolved non-hydrogen dihedrals: 261 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'ASN:plan1': 7, 'PHE:plan': 2, 'GLN:plan1': 3, 'GLU:plan': 16, 'ARG:plan': 11, 'ASP:plan': 9} Unresolved non-hydrogen planarities: 191 Conformer: "B" Number of residues, atoms: 776, 5857 Classifications: {'peptide': 776} Incomplete info: {'truncation_to_alanine': 92} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 749} Chain breaks: 2 Unresolved non-hydrogen bonds: 328 Unresolved non-hydrogen angles: 399 Unresolved non-hydrogen dihedrals: 261 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'ASN:plan1': 7, 'PHE:plan': 2, 'GLN:plan1': 3, 'GLU:plan': 16, 'ARG:plan': 11, 'ASP:plan': 9} Unresolved non-hydrogen planarities: 191 bond proxies already assigned to first conformer: 5989 Chain: "B" Number of atoms: 5652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 778, 5652 Classifications: {'peptide': 778} Incomplete info: {'truncation_to_alanine': 124} Link IDs: {'PCIS': 3, 'PTRANS': 18, 'TRANS': 756} Chain breaks: 2 Unresolved non-hydrogen bonds: 489 Unresolved non-hydrogen angles: 572 Unresolved non-hydrogen dihedrals: 415 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 8, 'ARG:plan': 19, 'GLU:plan': 20, 'ASN:plan1': 4, 'ASP:plan': 8, 'PHE:plan': 2, 'HIS:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 267 Chain: "C" Number of atoms: 5858 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 776, 5857 Classifications: {'peptide': 776} Incomplete info: {'truncation_to_alanine': 92} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 749} Chain breaks: 2 Unresolved non-hydrogen bonds: 328 Unresolved non-hydrogen angles: 399 Unresolved non-hydrogen dihedrals: 261 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'ASN:plan1': 7, 'PHE:plan': 2, 'GLN:plan1': 3, 'GLU:plan': 16, 'ARG:plan': 11, 'ASP:plan': 9} Unresolved non-hydrogen planarities: 191 Conformer: "B" Number of residues, atoms: 776, 5857 Classifications: {'peptide': 776} Incomplete info: {'truncation_to_alanine': 92} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 749} Chain breaks: 2 Unresolved non-hydrogen bonds: 328 Unresolved non-hydrogen angles: 399 Unresolved non-hydrogen dihedrals: 261 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'ASN:plan1': 7, 'PHE:plan': 2, 'GLN:plan1': 3, 'GLU:plan': 16, 'ARG:plan': 11, 'ASP:plan': 9} Unresolved non-hydrogen planarities: 191 bond proxies already assigned to first conformer: 5989 Chain: "D" Number of atoms: 5652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 778, 5652 Classifications: {'peptide': 778} Incomplete info: {'truncation_to_alanine': 124} Link IDs: {'PCIS': 3, 'PTRANS': 18, 'TRANS': 756} Chain breaks: 2 Unresolved non-hydrogen bonds: 489 Unresolved non-hydrogen angles: 572 Unresolved non-hydrogen dihedrals: 415 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 8, 'ARG:plan': 19, 'GLU:plan': 20, 'ASN:plan1': 4, 'ASP:plan': 8, 'PHE:plan': 2, 'HIS:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 267 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: "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: 114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 114 Unusual residues: {'D10': 1, 'HP6': 2, 'NAG': 3, 'OCT': 1, 'R16': 1, 'ZK1': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 3 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: 10.53, per 1000 atoms: 0.31 Number of scatterers: 34424 At special positions: 0 Unit cell: (133.914, 228.559, 276.889, 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 6359 8.00 N 5791 7.00 C 22102 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-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 C 908 " - " ASN C 345 " " 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 D 235 " Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.77 Conformation dependent library (CDL) restraints added in 2.1 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: 142 helices and 65 sheets defined 39.8% alpha, 13.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.33 Creating SS restraints... Processing helix chain 'A' and resid 20 through 31 removed outlier: 3.938A pdb=" N LEU A 31 " --> pdb=" O ALA A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 63 Processing helix chain 'A' and resid 76 through 87 removed outlier: 4.196A pdb=" N THR A 80 " --> pdb=" O VAL A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 123 Processing helix chain 'A' and resid 138 through 151 removed outlier: 3.836A pdb=" N ARG A 142 " --> pdb=" O SER A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 176 Processing helix chain 'A' and resid 187 through 199 removed outlier: 3.868A pdb=" N GLN A 197 " --> pdb=" O ALA A 193 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL A 199 " --> pdb=" O LEU A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 220 removed outlier: 3.518A pdb=" N ILE A 220 " --> pdb=" O PHE A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 259 removed outlier: 3.598A pdb=" N ALA A 246 " --> pdb=" O ASP A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 292 removed outlier: 4.270A pdb=" N ALA A 273 " --> pdb=" O LYS A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 325 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: 3.874A 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: 3.546A 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 Processing helix chain 'B' and resid 49 through 62 removed outlier: 3.873A pdb=" N ARG B 62 " --> pdb=" O SER B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 86 removed outlier: 3.813A pdb=" N ILE B 79 " --> pdb=" O SER B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 123 Processing helix chain 'B' and resid 137 through 151 Processing helix chain 'B' and resid 166 through 179 Processing helix chain 'B' and resid 180 through 182 No H-bonds generated for 'chain 'B' and resid 180 through 182' Processing helix chain 'B' and resid 193 through 206 removed outlier: 3.529A pdb=" N ASP B 197 " --> pdb=" O ASP B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 258 removed outlier: 3.910A pdb=" N THR B 258 " --> pdb=" O GLU B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 296 Processing helix chain 'B' and resid 317 through 329 removed outlier: 4.100A pdb=" N VAL B 321 " --> pdb=" O TRP B 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 436 Processing helix chain 'B' and resid 461 through 469 removed outlier: 3.614A pdb=" N TYR B 469 " --> pdb=" O GLY B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 487 removed outlier: 3.650A 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: 4.349A 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: 5.881A pdb=" N VAL B 795 " --> pdb=" O ASN B 791 " (cutoff:3.500A) removed outlier: 3.770A 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 20 through 29 Processing helix chain 'C' and resid 48 through 63 removed outlier: 3.511A pdb=" N GLY C 63 " --> pdb=" O GLN C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 87 removed outlier: 3.859A pdb=" N LEU C 79 " --> pdb=" O THR C 75 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N THR C 80 " --> pdb=" O VAL C 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 123 Processing helix chain 'C' and resid 137 through 150 removed outlier: 3.858A pdb=" N GLN C 141 " --> pdb=" O LEU C 137 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ARG C 142 " --> pdb=" O SER C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 163 through 176 Processing helix chain 'C' and resid 187 through 199 removed outlier: 3.981A pdb=" N GLN C 197 " --> pdb=" O ALA C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 258 removed outlier: 3.577A pdb=" N ALA C 246 " --> pdb=" O ASP C 242 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA C 257 " --> pdb=" O ARG C 253 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ARG C 258 " --> pdb=" O THR C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 292 removed outlier: 3.794A pdb=" N ALA C 273 " --> pdb=" O LYS C 269 " (cutoff:3.500A) Processing helix chain 'C' and resid 313 through 325 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: 3.570A pdb=" N SER C 572 " --> pdb=" O GLY C 568 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LEU C 573 " --> pdb=" O ILE C 569 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N TRP C 574 " --> pdb=" O PHE C 570 " (cutoff:3.500A) Processing helix chain 'C' and resid 591 through 625 removed outlier: 3.666A 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: 4.040A 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: 3.528A 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: 3.525A 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: 3.806A pdb=" N PHE C 792 " --> pdb=" O VAL C 788 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N LYS C 813 " --> pdb=" O GLU C 809 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 30 Processing helix chain 'D' and resid 48 through 62 removed outlier: 3.762A pdb=" N ARG D 62 " --> pdb=" O SER D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 86 removed outlier: 3.867A pdb=" N ILE D 79 " --> pdb=" O SER D 75 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 123 Processing helix chain 'D' and resid 137 through 151 Processing helix chain 'D' and resid 166 through 179 removed outlier: 3.573A pdb=" N ARG D 172 " --> pdb=" O ASP D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 206 removed outlier: 3.636A pdb=" N ASP D 197 " --> pdb=" O ASP D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 246 through 258 removed outlier: 4.019A pdb=" N THR D 258 " --> pdb=" O GLU D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 273 through 296 removed outlier: 3.508A pdb=" N ALA D 277 " --> pdb=" O LYS D 273 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 329 removed outlier: 4.177A pdb=" N VAL D 321 " --> pdb=" O TRP D 317 " (cutoff:3.500A) 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: 3.675A 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: 3.653A 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: 3.687A 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: 3.520A 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: 3.833A pdb=" N VAL D 792 " --> pdb=" O SER D 788 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N GLY D 794 " --> pdb=" O SER D 790 " (cutoff:3.500A) removed outlier: 5.807A 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: 3.811A 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: 3.999A pdb=" N SER E 19 " --> pdb=" O VAL E 15 " (cutoff:3.500A) removed outlier: 3.566A 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: 3.501A 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: 3.505A 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: 3.584A pdb=" N GLY E 92 " --> pdb=" O TRP E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 94 through 108 removed outlier: 3.604A 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: 3.901A 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: 3.662A 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: 3.573A pdb=" N TYR E 149 " --> pdb=" O SER E 145 " (cutoff:3.500A) Processing helix chain 'E' and resid 153 through 158 removed outlier: 3.571A 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: 3.980A 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: 3.631A pdb=" N PHE F 82 " --> pdb=" O PHE F 78 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LEU F 83 " --> pdb=" O CYS F 79 " (cutoff:3.500A) Processing helix chain 'F' and resid 87 through 92 removed outlier: 3.569A 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: 3.746A 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: 3.847A 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: 3.574A 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: 4.118A pdb=" N LEU G 34 " --> pdb=" O SER G 30 " (cutoff:3.500A) removed outlier: 4.092A 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: 3.800A pdb=" N ARG G 122 " --> pdb=" O GLU G 118 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL G 124 " --> pdb=" O LEU G 120 " (cutoff:3.500A) Processing helix chain 'G' and resid 129 through 145 removed outlier: 4.312A pdb=" N ALA G 135 " --> pdb=" O PRO G 131 " (cutoff:3.500A) Processing helix chain 'G' and resid 146 through 149 removed outlier: 4.018A 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: 3.709A 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: 3.554A 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: 3.642A pdb=" N TYR G 226 " --> pdb=" O ALA G 222 " (cutoff:3.500A) Processing helix chain 'H' and resid 21 through 39 removed outlier: 4.383A 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: 4.119A pdb=" N LEU H 34 " --> pdb=" O SER H 30 " (cutoff:3.500A) removed outlier: 4.092A 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: 3.801A 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: 4.312A 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: 3.845A pdb=" N GLY H 160 " --> pdb=" O ASN H 156 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA H 161 " --> pdb=" O ILE H 157 " (cutoff:3.500A) removed outlier: 3.771A 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: 3.665A pdb=" N TYR H 179 " --> pdb=" O GLY H 175 " (cutoff:3.500A) removed outlier: 3.665A 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: 4.091A pdb=" N GLY H 208 " --> pdb=" O SER H 204 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLY H 209 " --> pdb=" O PHE H 205 " (cutoff:3.500A) removed outlier: 3.640A 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: 4.052A 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: 3.641A pdb=" N TYR H 226 " --> pdb=" O ALA H 222 " (cutoff:3.500A) Processing helix chain 'I' and resid 87 through 91 removed outlier: 3.744A pdb=" N ASP I 90 " --> pdb=" O ARG I 87 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N THR I 91 " --> pdb=" O SER I 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 87 through 91' Processing helix chain 'J' and resid 122 through 129 Processing helix chain 'J' and resid 184 through 190 removed outlier: 3.519A pdb=" N HIS J 190 " --> pdb=" O GLU J 186 " (cutoff:3.500A) Processing helix chain 'K' and resid 160 through 165 removed outlier: 3.828A pdb=" N SER K 163 " --> pdb=" O THR K 160 " (cutoff:3.500A) Processing helix chain 'L' and resid 64 through 68 removed outlier: 3.507A pdb=" N LYS L 67 " --> pdb=" O LEU L 64 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ILE L 68 " --> pdb=" O LYS L 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 64 through 68' Processing helix chain 'L' and resid 87 through 91 Processing helix chain 'L' and resid 217 through 221 removed outlier: 3.693A pdb=" N ALA L 221 " --> pdb=" O ALA L 218 " (cutoff:3.500A) Processing helix chain 'M' and resid 122 through 129 removed outlier: 3.692A pdb=" N GLY M 129 " --> pdb=" O GLN M 125 " (cutoff:3.500A) Processing helix chain 'M' and resid 184 through 190 Processing helix chain 'N' and resid 163 through 165 No H-bonds generated for 'chain 'N' and resid 163 through 165' Processing sheet with id=AA1, first strand: chain 'A' and resid 36 through 43 removed outlier: 6.088A pdb=" N ILE A 7 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N GLN A 40 " --> pdb=" O ILE A 7 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N ILE A 9 " --> pdb=" O GLN A 40 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N ASP A 42 " --> pdb=" O ILE A 9 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N GLY A 11 " --> pdb=" O ASP A 42 " (cutoff:3.500A) removed outlier: 10.294A pdb=" N ALA A 66 " --> pdb=" O ASN A 6 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N GLN A 8 " --> pdb=" O ALA A 66 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N PHE A 68 " --> pdb=" O GLN A 8 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N GLY A 10 " --> pdb=" O PHE A 68 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N ILE A 67 " --> pdb=" O ILE A 91 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N PHE A 90 " --> pdb=" O LEU A 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 153 through 158 removed outlier: 3.794A pdb=" N THR A 155 " --> pdb=" O PHE A 127 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N LEU A 181 " --> pdb=" O THR A 126 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N ARG A 180 " --> pdb=" O HIS A 209 " (cutoff:3.500A) removed outlier: 8.390A pdb=" N ILE A 211 " --> pdb=" O ARG A 180 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N VAL A 182 " --> pdb=" O ILE A 211 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N PHE A 235 " --> pdb=" O LEU A 212 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL A 232 " --> pdb=" O MET A 353 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N LEU A 348 " --> pdb=" O TYR A 363 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N TYR A 363 " --> pdb=" O LEU A 348 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N VAL A 350 " --> pdb=" O ILE A 361 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N TYR A 363 " --> pdb=" O VAL A 371 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N VAL A 371 " --> pdb=" O TYR A 363 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 327 through 329 removed outlier: 3.671A pdb=" N PHE A 328 " --> pdb=" O VAL A 335 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLN A 336 " --> pdb=" O THR A 344 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 437 through 440 removed outlier: 5.736A 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: 9.035A 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: 8.547A 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 5 through 7 removed outlier: 6.585A pdb=" N ILE B 6 " --> pdb=" O THR B 38 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 41 through 43 removed outlier: 6.695A pdb=" N GLY B 10 " --> pdb=" O ASP B 42 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ILE B 67 " --> pdb=" O ILE B 91 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N PHE B 90 " --> pdb=" O ILE B 105 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 153 through 158 removed outlier: 7.139A pdb=" N PHE B 127 " --> pdb=" O THR B 155 " (cutoff:3.500A) removed outlier: 8.504A pdb=" N ILE B 157 " --> pdb=" O PHE B 127 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N TYR B 129 " --> pdb=" O ILE B 157 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N ARG B 185 " --> pdb=" O LYS B 126 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N TYR B 214 " --> pdb=" O SER B 237 " (cutoff:3.500A) removed outlier: 8.411A pdb=" N PHE B 239 " --> pdb=" O TYR B 214 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N ILE B 216 " --> pdb=" O PHE B 239 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ILE B 352 " --> pdb=" O TYR B 367 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N TYR B 367 " --> pdb=" O ILE B 352 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N ILE B 354 " --> pdb=" O ILE B 365 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 397 through 398 removed outlier: 3.506A 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: 4.202A pdb=" N LEU B 479 " --> pdb=" O GLY B 733 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 646 through 648 removed outlier: 3.634A pdb=" N ALA B 701 " --> pdb=" O ALA B 646 " (cutoff:3.500A) removed outlier: 8.779A pdb=" N TYR B 700 " --> pdb=" O LYS B 505 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N LYS B 505 " --> pdb=" O TYR B 700 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE B 502 " --> pdb=" O VAL B 723 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 36 through 43 removed outlier: 6.135A pdb=" N ILE C 7 " --> pdb=" O LEU C 38 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N GLN C 40 " --> pdb=" O ILE C 7 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ILE C 9 " --> pdb=" O GLN C 40 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N ASP C 42 " --> pdb=" O ILE C 9 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N GLY C 11 " --> pdb=" O ASP C 42 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ALA C 66 " --> pdb=" O GLN C 8 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N ILE C 67 " --> pdb=" O ILE C 91 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N PHE C 90 " --> pdb=" O LEU C 105 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 153 through 158 removed outlier: 3.733A pdb=" N THR C 155 " --> pdb=" O PHE C 127 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N LEU C 181 " --> pdb=" O THR C 126 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N ARG C 180 " --> pdb=" O HIS C 209 " (cutoff:3.500A) removed outlier: 8.148A pdb=" N ILE C 211 " --> pdb=" O ARG C 180 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N VAL C 182 " --> pdb=" O ILE C 211 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL C 232 " --> pdb=" O MET C 353 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLY C 362 " --> pdb=" O VAL C 350 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N GLU C 352 " --> pdb=" O LYS C 360 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N LYS C 360 " --> pdb=" O GLU C 352 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N VAL C 371 " --> pdb=" O TYR C 363 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 328 through 329 removed outlier: 3.755A pdb=" N PHE C 328 " --> pdb=" O VAL C 335 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 437 through 440 removed outlier: 5.737A pdb=" N VAL C 393 " --> pdb=" O GLU C 439 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 403 through 404 Processing sheet with id=AC1, first strand: chain 'C' and resid 486 through 487 Processing sheet with id=AC2, 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=AC3, 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: 6.733A pdb=" N THR C 645 " --> pdb=" O VAL C 679 " (cutoff:3.500A) removed outlier: 6.918A 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: 8.564A 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=AC4, first strand: chain 'D' and resid 6 through 7 removed outlier: 6.675A pdb=" N ILE D 6 " --> pdb=" O THR D 38 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'D' and resid 41 through 43 removed outlier: 6.986A pdb=" N GLY D 10 " --> pdb=" O ASP D 42 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ILE D 67 " --> pdb=" O ILE D 91 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N PHE D 90 " --> pdb=" O ILE D 105 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 153 through 158 removed outlier: 3.506A pdb=" N PHE D 127 " --> pdb=" O GLN D 153 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N THR D 155 " --> pdb=" O PHE D 127 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N TYR D 131 " --> pdb=" O ILE D 157 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N ARG D 185 " --> pdb=" O LYS D 126 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N TYR D 214 " --> pdb=" O SER D 237 " (cutoff:3.500A) removed outlier: 8.584A pdb=" N PHE D 239 " --> pdb=" O TYR D 214 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N ILE D 216 " --> pdb=" O PHE D 239 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N VAL D 236 " --> pdb=" O LEU D 357 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N ILE D 352 " --> pdb=" O TYR D 367 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N TYR D 367 " --> pdb=" O ILE D 352 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N ILE D 354 " --> pdb=" O ILE D 365 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 333 through 334 Processing sheet with id=AC8, 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: 7.551A 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: 4.198A pdb=" N LEU D 479 " --> pdb=" O GLY D 733 " (cutoff:3.500A) Processing sheet with id=AC9, 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=AD1, 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=AD2, first strand: chain 'G' and resid 88 through 89 removed outlier: 3.607A pdb=" N ILE G 89 " --> pdb=" O VAL G 101 " (cutoff:3.500A) Processing sheet with id=AD3, 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=AD4, 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=AD5, first strand: chain 'I' and resid 3 through 7 removed outlier: 3.626A pdb=" N LYS I 3 " --> pdb=" O SER I 25 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N SER I 21 " --> pdb=" O SER I 7 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 35 through 39 removed outlier: 7.083A pdb=" N TRP I 36 " --> pdb=" O ILE I 48 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ILE I 48 " --> pdb=" O TRP I 36 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 139 through 141 Processing sheet with id=AD8, first strand: chain 'I' and resid 144 through 147 removed outlier: 6.348A pdb=" N LEU I 145 " --> pdb=" O GLU I 243 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'J' and resid 12 through 14 removed outlier: 3.739A pdb=" N TYR J 87 " --> pdb=" O THR J 103 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N THR J 86 " --> pdb=" O GLN J 39 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N GLN J 39 " --> pdb=" O THR J 86 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 21 through 24 removed outlier: 3.602A pdb=" N LEU J 74 " --> pdb=" O ILE J 22 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N SER J 73 " --> pdb=" O SER J 66 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 49 through 50 Processing sheet with id=AE3, first strand: chain 'J' and resid 118 through 119 removed outlier: 3.828A pdb=" N VAL J 134 " --> pdb=" O PHE J 119 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 137 through 140 removed outlier: 4.691A pdb=" N ASN J 138 " --> pdb=" O MET J 176 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N MET J 176 " --> pdb=" O ASN J 138 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'J' and resid 154 through 156 removed outlier: 3.587A pdb=" N TRP J 149 " --> pdb=" O ARG J 156 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N TYR J 193 " --> pdb=" O PHE J 210 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'K' and resid 4 through 8 removed outlier: 3.858A pdb=" N LYS K 6 " --> pdb=" O THR K 24 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'K' and resid 12 through 13 removed outlier: 3.864A pdb=" N VAL K 13 " --> pdb=" O THR K 117 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'K' and resid 58 through 60 removed outlier: 3.706A pdb=" N ASN K 59 " --> pdb=" O VAL K 51 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N VAL K 51 " --> pdb=" O ASN K 59 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N TRP K 48 " --> pdb=" O ARG K 39 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ARG K 39 " --> pdb=" O TRP K 48 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N MET K 93 " --> pdb=" O GLN K 40 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'K' and resid 143 through 144 Processing sheet with id=AF1, first strand: chain 'K' and resid 147 through 149 Processing sheet with id=AF2, first strand: chain 'K' and resid 204 through 205 Processing sheet with id=AF3, first strand: chain 'L' and resid 3 through 7 removed outlier: 3.944A pdb=" N SER L 21 " --> pdb=" O SER L 7 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR L 78 " --> pdb=" O ASP L 73 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'L' and resid 10 through 11 removed outlier: 7.206A pdb=" N GLY L 10 " --> pdb=" O THR L 116 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF4 Processing sheet with id=AF5, first strand: chain 'L' and resid 35 through 39 removed outlier: 7.754A pdb=" N TRP L 36 " --> pdb=" O ILE L 48 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ILE L 48 " --> pdb=" O TRP L 36 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'L' and resid 139 through 141 Processing sheet with id=AF7, first strand: chain 'L' and resid 144 through 147 removed outlier: 6.163A pdb=" N LEU L 145 " --> pdb=" O GLU L 243 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'M' and resid 21 through 24 Processing sheet with id=AF9, first strand: chain 'M' and resid 45 through 47 removed outlier: 3.822A pdb=" N THR M 103 " --> pdb=" O TYR M 87 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'M' and resid 49 through 50 Processing sheet with id=AG2, first strand: chain 'M' and resid 118 through 119 removed outlier: 4.004A pdb=" N VAL M 134 " --> pdb=" O PHE M 119 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'M' and resid 130 through 131 Processing sheet with id=AG4, first strand: chain 'M' and resid 154 through 156 removed outlier: 3.909A pdb=" N TRP M 149 " --> pdb=" O ARG M 156 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'M' and resid 160 through 162 removed outlier: 3.947A pdb=" N LEU M 161 " --> pdb=" O THR M 179 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N THR M 179 " --> pdb=" O LEU M 161 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG5 Processing sheet with id=AG6, first strand: chain 'N' and resid 4 through 8 removed outlier: 3.593A pdb=" N SER N 26 " --> pdb=" O GLN N 4 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LYS N 6 " --> pdb=" O THR N 24 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'N' and resid 12 through 13 removed outlier: 3.581A pdb=" N VAL N 13 " --> pdb=" O THR N 117 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG7 Processing sheet with id=AG8, first strand: chain 'N' and resid 47 through 52 removed outlier: 5.138A pdb=" N TRP N 48 " --> pdb=" O ARG N 39 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N ARG N 39 " --> pdb=" O TRP N 48 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'N' and resid 127 through 130 removed outlier: 3.690A pdb=" N SER N 127 " --> pdb=" O LYS N 150 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'N' and resid 142 through 144 Processing sheet with id=AH2, first strand: chain 'N' and resid 158 through 161 removed outlier: 3.516A pdb=" N THR N 160 " --> pdb=" O ASN N 203 " (cutoff:3.500A) 1594 hydrogen bonds defined for protein. 4542 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.62 Time building geometry restraints manager: 3.72 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: 11340 1.36 - 1.49: 8967 1.49 - 1.62: 14473 1.62 - 1.75: 0 1.75 - 1.88: 234 Bond restraints: 35014 Sorted by residual: bond pdb=" CAU ZK1 A 901 " pdb=" OAB ZK1 A 901 " ideal model delta sigma weight residual 1.215 1.404 -0.189 2.00e-02 2.50e+03 8.89e+01 bond pdb=" CAU ZK1 C 901 " pdb=" OAB ZK1 C 901 " ideal model delta sigma weight residual 1.215 1.404 -0.189 2.00e-02 2.50e+03 8.89e+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 D 906 " pdb=" OAB ZK1 D 906 " ideal model delta sigma weight residual 1.215 1.403 -0.188 2.00e-02 2.50e+03 8.85e+01 bond pdb=" CAT ZK1 D 906 " pdb=" OAA ZK1 D 906 " ideal model delta sigma weight residual 1.214 1.395 -0.181 2.00e-02 2.50e+03 8.16e+01 ... (remaining 35009 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.77: 47222 1.77 - 3.55: 422 3.55 - 5.32: 75 5.32 - 7.10: 26 7.10 - 8.87: 9 Bond angle restraints: 47754 Sorted by residual: angle pdb=" CAM ZK1 D 906 " pdb=" NAX ZK1 D 906 " pdb=" CAN ZK1 D 906 " ideal model delta sigma weight residual 111.06 119.93 -8.87 3.00e+00 1.11e-01 8.74e+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 8.65e+00 angle pdb=" CAM ZK1 B 901 " pdb=" NAX ZK1 B 901 " pdb=" CAN ZK1 B 901 " ideal model delta sigma weight residual 111.06 119.86 -8.80 3.00e+00 1.11e-01 8.61e+00 angle pdb=" CAM ZK1 C 901 " pdb=" NAX ZK1 C 901 " pdb=" CAN ZK1 C 901 " ideal model delta sigma weight residual 111.06 119.84 -8.78 3.00e+00 1.11e-01 8.57e+00 angle pdb=" CAN ZK1 B 901 " pdb=" NAX ZK1 B 901 " pdb=" CAR ZK1 B 901 " ideal model delta sigma weight residual 112.98 120.16 -7.18 3.00e+00 1.11e-01 5.73e+00 ... (remaining 47749 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.74: 19898 23.74 - 47.48: 513 47.48 - 71.23: 48 71.23 - 94.97: 26 94.97 - 118.71: 21 Dihedral angle restraints: 20506 sinusoidal: 6172 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 93.00 131.75 -38.75 1 1.00e+01 1.00e-02 2.11e+01 ... (remaining 20503 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.326: 5684 0.326 - 0.652: 2 0.652 - 0.978: 1 0.978 - 1.305: 0 1.305 - 1.631: 2 Chirality restraints: 5689 Sorted by residual: chirality pdb=" C1 NAG R 2 " pdb=" O4 NAG R 1 " pdb=" C2 NAG R 2 " pdb=" O5 NAG R 2 " both_signs ideal model delta sigma weight residual False -2.40 -0.77 -1.63 2.00e-02 2.50e+03 6.65e+03 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 -1.08 -1.32 2.00e-02 2.50e+03 4.39e+03 chirality pdb=" C1 NAG O 2 " pdb=" O4 NAG O 1 " pdb=" C2 NAG O 2 " pdb=" O5 NAG O 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.45 -0.95 2.00e-02 2.50e+03 2.26e+03 ... (remaining 5686 not shown) Planarity restraints: 6126 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 244 " 0.022 5.00e-02 4.00e+02 3.26e-02 1.71e+00 pdb=" N PRO A 245 " -0.056 5.00e-02 4.00e+02 pdb=" CA PRO A 245 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 245 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 244 " -0.021 5.00e-02 4.00e+02 3.16e-02 1.59e+00 pdb=" N PRO C 245 " 0.055 5.00e-02 4.00e+02 pdb=" CA PRO C 245 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO C 245 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 92 " -0.020 5.00e-02 4.00e+02 2.98e-02 1.42e+00 pdb=" N PRO A 93 " 0.052 5.00e-02 4.00e+02 pdb=" CA PRO A 93 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 93 " -0.016 5.00e-02 4.00e+02 ... (remaining 6123 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.22: 2 2.22 - 2.89: 13168 2.89 - 3.56: 45946 3.56 - 4.23: 72493 4.23 - 4.90: 121444 Nonbonded interactions: 253053 Sorted by model distance: nonbonded pdb=" NZ LYS C 178 " pdb=" O TYR C 465 " model vdw 1.548 3.120 nonbonded pdb=" NZ LYS C 178 " pdb=" C TYR C 465 " model vdw 2.188 3.350 nonbonded pdb=" OE2 GLU D 179 " pdb=" NZ LYS D 207 " model vdw 2.229 3.120 nonbonded pdb=" O4 NAG P 1 " pdb=" O7 NAG P 1 " model vdw 2.231 3.040 nonbonded pdb=" O4 NAG S 1 " pdb=" O7 NAG S 1 " model vdw 2.241 3.040 ... (remaining 253048 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 907)) selection = (chain 'C' and (resid 1 through 649 or resid 651 through 907)) } 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' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 11.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 0.560 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 36.630 Find NCS groups from input model: 0.860 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5557 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.189 35043 Z= 0.221 Angle : 0.577 34.839 47825 Z= 0.265 Chirality : 0.050 1.631 5689 Planarity : 0.002 0.033 6114 Dihedral : 11.880 118.710 11260 Min Nonbonded Distance : 1.548 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % 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: -3.63 (0.10), residues: 4922 helix: -1.50 (0.10), residues: 1850 sheet: -2.99 (0.16), residues: 849 loop : -2.92 (0.11), residues: 2223 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 599 TYR 0.008 0.000 TYR D 533 PHE 0.015 0.001 PHE A 24 TRP 0.013 0.000 TRP A 252 HIS 0.001 0.000 HIS B 101 Details of bonding type rmsd covalent geometry : bond 0.00428 (35014) covalent geometry : angle 0.47266 (47754) SS BOND : bond 0.00410 ( 10) SS BOND : angle 1.03940 ( 20) hydrogen bonds : bond 0.23513 ( 1594) hydrogen bonds : angle 7.85769 ( 4542) Misc. bond : bond 0.00052 ( 2) link_BETA1-4 : bond 0.06485 ( 5) link_BETA1-4 : angle 18.57591 ( 15) link_NAG-ASN : bond 0.00347 ( 12) link_NAG-ASN : angle 1.40672 ( 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 279 residues out of total 4276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 279 time to evaluate : 1.275 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 43 ILE cc_start: 0.8690 (mm) cc_final: 0.8480 (mm) REVERT: A 249 MET cc_start: 0.5436 (mmm) cc_final: 0.5062 (ttp) REVERT: C 249 MET cc_start: 0.4511 (mmm) cc_final: 0.3618 (ttp) REVERT: C 265 TRP cc_start: 0.1798 (m100) cc_final: 0.0646 (m100) outliers start: 0 outliers final: 0 residues processed: 279 average time/residue: 0.2214 time to fit residues: 100.8906 Evaluate side-chains 148 residues out of total 4276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 148 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 432 optimal weight: 20.0000 chunk 197 optimal weight: 5.9990 chunk 388 optimal weight: 20.0000 chunk 455 optimal weight: 9.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 0.0170 chunk 207 optimal weight: 0.7980 chunk 470 optimal weight: 20.0000 overall best weight: 1.5020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 87 HIS A 125 GLN A 250 GLN A 571 ASN A 583 GLN A 722 ASN B 714 GLN B 764 ASN C 571 ASN C 722 ASN ** D 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 268 HIS D 714 GLN ** E 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 132 GLN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.086212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.070171 restraints weight = 217611.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.068415 restraints weight = 177891.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.068162 restraints weight = 157716.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.067824 restraints weight = 121634.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.067887 restraints weight = 104951.760| |-----------------------------------------------------------------------------| r_work (final): 0.3807 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3808 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3808 r_free = 0.3808 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3808 r_free = 0.3808 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3808 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6575 moved from start: 0.1852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 35043 Z= 0.144 Angle : 0.574 14.037 47825 Z= 0.289 Chirality : 0.043 0.295 5689 Planarity : 0.003 0.042 6114 Dihedral : 7.413 82.980 5921 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 0.61 % Allowed : 8.42 % Favored : 90.97 % 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: -2.23 (0.11), residues: 4922 helix: 0.17 (0.12), residues: 1882 sheet: -2.58 (0.16), residues: 877 loop : -2.50 (0.12), residues: 2163 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 293 TYR 0.018 0.001 TYR B 797 PHE 0.025 0.002 PHE B 667 TRP 0.026 0.002 TRP B 606 HIS 0.010 0.001 HIS B 435 Details of bonding type rmsd covalent geometry : bond 0.00303 (35014) covalent geometry : angle 0.57022 (47754) SS BOND : bond 0.00415 ( 10) SS BOND : angle 1.05398 ( 20) hydrogen bonds : bond 0.04471 ( 1594) hydrogen bonds : angle 4.85876 ( 4542) Misc. bond : bond 0.00012 ( 2) link_BETA1-4 : bond 0.00417 ( 5) link_BETA1-4 : angle 1.89433 ( 15) link_NAG-ASN : bond 0.00384 ( 12) link_NAG-ASN : angle 1.89341 ( 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 178 residues out of total 4276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 162 time to evaluate : 1.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 704 MET cc_start: 0.7699 (mmm) cc_final: 0.7268 (mmm) REVERT: C 249 MET cc_start: 0.5144 (mmm) cc_final: 0.4485 (ttp) REVERT: C 499 MET cc_start: 0.7308 (ppp) cc_final: 0.6168 (ttt) REVERT: C 514 LEU cc_start: 0.8200 (mt) cc_final: 0.7597 (mt) REVERT: C 577 LEU cc_start: 0.8767 (tp) cc_final: 0.8499 (tp) REVERT: D 616 TYR cc_start: 0.9133 (t80) cc_final: 0.8840 (t80) outliers start: 16 outliers final: 9 residues processed: 173 average time/residue: 0.2048 time to fit residues: 60.6302 Evaluate side-chains 145 residues out of total 4276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 136 time to evaluate : 1.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 374 MET Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain C residue 363 TYR Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 768 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 179 optimal weight: 0.1980 chunk 165 optimal weight: 0.9980 chunk 462 optimal weight: 0.9990 chunk 174 optimal weight: 10.0000 chunk 312 optimal weight: 30.0000 chunk 336 optimal weight: 0.9980 chunk 220 optimal weight: 5.9990 chunk 404 optimal weight: 8.9990 chunk 324 optimal weight: 8.9990 chunk 73 optimal weight: 0.0070 chunk 172 optimal weight: 1.9990 overall best weight: 0.6400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 ASN B 587 GLN C 19 GLN ** C 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 87 HIS ** D 208 HIS ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.086912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.068978 restraints weight = 215546.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.065335 restraints weight = 169788.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.064991 restraints weight = 152791.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.064971 restraints weight = 130045.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.065323 restraints weight = 121728.807| |-----------------------------------------------------------------------------| r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3681 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3681 r_free = 0.3681 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3681 r_free = 0.3681 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3681 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6927 moved from start: 0.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 35043 Z= 0.101 Angle : 0.490 14.553 47825 Z= 0.245 Chirality : 0.041 0.276 5689 Planarity : 0.003 0.037 6114 Dihedral : 6.533 78.533 5921 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 0.53 % Allowed : 10.17 % Favored : 89.30 % 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: 0.90 (0.12), residues: 1890 sheet: -2.31 (0.16), residues: 858 loop : -2.21 (0.12), residues: 2174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 258 TYR 0.020 0.001 TYR B 533 PHE 0.027 0.001 PHE B 796 TRP 0.036 0.001 TRP C 522 HIS 0.004 0.000 HIS B 435 Details of bonding type rmsd covalent geometry : bond 0.00209 (35014) covalent geometry : angle 0.48678 (47754) SS BOND : bond 0.00318 ( 10) SS BOND : angle 0.98501 ( 20) hydrogen bonds : bond 0.03828 ( 1594) hydrogen bonds : angle 4.29156 ( 4542) Misc. bond : bond 0.00005 ( 2) link_BETA1-4 : bond 0.00375 ( 5) link_BETA1-4 : angle 1.69562 ( 15) link_NAG-ASN : bond 0.00308 ( 12) link_NAG-ASN : angle 1.79806 ( 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 155 residues out of total 4276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 141 time to evaluate : 1.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 MET cc_start: 0.7903 (tmm) cc_final: 0.7653 (tmm) REVERT: A 403 MET cc_start: 0.3636 (mpp) cc_final: 0.3427 (mpp) REVERT: A 604 PHE cc_start: 0.8451 (t80) cc_final: 0.8196 (m-80) REVERT: A 704 MET cc_start: 0.8246 (mmm) cc_final: 0.7780 (mmm) REVERT: A 717 MET cc_start: 0.9232 (ppp) cc_final: 0.8591 (ppp) REVERT: B 107 MET cc_start: 0.8174 (mmm) cc_final: 0.7962 (mtp) REVERT: B 503 MET cc_start: 0.5227 (tpp) cc_final: 0.4905 (mtt) REVERT: C 249 MET cc_start: 0.4909 (mmm) cc_final: 0.4215 (ttp) REVERT: C 581 MET cc_start: 0.8213 (mmm) cc_final: 0.7867 (mmp) REVERT: D 463 MET cc_start: 0.5714 (mmp) cc_final: 0.5250 (mmp) REVERT: D 585 MET cc_start: 0.6360 (tpp) cc_final: 0.6000 (tpp) REVERT: D 670 MET cc_start: 0.8199 (ppp) cc_final: 0.7825 (ppp) REVERT: E 11 MET cc_start: 0.8236 (mtt) cc_final: 0.7675 (mmm) REVERT: E 153 MET cc_start: 0.5233 (mmm) cc_final: 0.4735 (tmm) REVERT: H 35 MET cc_start: 0.6879 (ttm) cc_final: 0.6402 (ptp) outliers start: 14 outliers final: 9 residues processed: 151 average time/residue: 0.2067 time to fit residues: 53.9851 Evaluate side-chains 142 residues out of total 4276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 133 time to evaluate : 1.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 603 PHE Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 374 MET Chi-restraints excluded: chain C residue 252 TRP Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 367 TYR Chi-restraints excluded: chain D residue 768 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 22 optimal weight: 3.9990 chunk 86 optimal weight: 0.9980 chunk 481 optimal weight: 8.9990 chunk 148 optimal weight: 9.9990 chunk 371 optimal weight: 20.0000 chunk 254 optimal weight: 0.0020 chunk 90 optimal weight: 6.9990 chunk 123 optimal weight: 9.9990 chunk 338 optimal weight: 40.0000 chunk 378 optimal weight: 30.0000 chunk 296 optimal weight: 30.0000 overall best weight: 4.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 HIS ** C 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 250 GLN ** C 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 230 GLN ** E 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 = 0.4273 r_free = 0.4273 target = 0.085223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.070569 restraints weight = 211810.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.068926 restraints weight = 224660.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.068965 restraints weight = 196428.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.068200 restraints weight = 164314.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.068346 restraints weight = 140767.263| |-----------------------------------------------------------------------------| r_work (final): 0.3851 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3851 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3851 r_free = 0.3851 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3851 r_free = 0.3851 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3851 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6720 moved from start: 0.3640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 35043 Z= 0.274 Angle : 0.698 15.557 47825 Z= 0.361 Chirality : 0.045 0.313 5689 Planarity : 0.004 0.075 6114 Dihedral : 7.098 78.061 5921 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.08 % Favored : 94.90 % Rotamer: Outliers : 1.30 % Allowed : 11.89 % Favored : 86.82 % 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: -1.53 (0.12), residues: 4922 helix: 0.85 (0.12), residues: 1897 sheet: -2.43 (0.16), residues: 886 loop : -2.09 (0.13), residues: 2139 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 24 TYR 0.036 0.002 TYR C 346 PHE 0.032 0.003 PHE A 26 TRP 0.038 0.002 TRP A 602 HIS 0.010 0.002 HIS C 349 Details of bonding type rmsd covalent geometry : bond 0.00606 (35014) covalent geometry : angle 0.69284 (47754) SS BOND : bond 0.00704 ( 10) SS BOND : angle 1.32676 ( 20) hydrogen bonds : bond 0.04379 ( 1594) hydrogen bonds : angle 4.78134 ( 4542) Misc. bond : bond 0.00031 ( 2) link_BETA1-4 : bond 0.00512 ( 5) link_BETA1-4 : angle 1.55173 ( 15) link_NAG-ASN : bond 0.00743 ( 12) link_NAG-ASN : angle 3.02957 ( 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 186 residues out of total 4276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 152 time to evaluate : 1.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 403 MET cc_start: 0.3779 (mpp) cc_final: 0.3419 (mpp) REVERT: A 499 MET cc_start: 0.7545 (tmm) cc_final: 0.7215 (tpt) REVERT: B 503 MET cc_start: 0.5077 (tpp) cc_final: 0.4625 (mtp) REVERT: B 584 PHE cc_start: 0.7349 (t80) cc_final: 0.7135 (t80) REVERT: C 346 TYR cc_start: 0.8300 (OUTLIER) cc_final: 0.7756 (m-10) REVERT: C 363 TYR cc_start: 0.7763 (OUTLIER) cc_final: 0.7056 (p90) REVERT: C 499 MET cc_start: 0.6461 (ppp) cc_final: 0.5521 (ttm) REVERT: D 367 TYR cc_start: 0.7590 (OUTLIER) cc_final: 0.7378 (p90) REVERT: D 463 MET cc_start: 0.4531 (mmp) cc_final: 0.3948 (mmp) REVERT: D 585 MET cc_start: 0.7465 (tpp) cc_final: 0.7066 (tpp) REVERT: D 616 TYR cc_start: 0.8810 (t80) cc_final: 0.8426 (t80) REVERT: D 670 MET cc_start: 0.8339 (ppp) cc_final: 0.7888 (ppp) outliers start: 34 outliers final: 17 residues processed: 178 average time/residue: 0.1925 time to fit residues: 59.9927 Evaluate side-chains 160 residues out of total 4276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 140 time to evaluate : 1.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 602 TRP Chi-restraints excluded: chain B residue 70 PHE Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain B residue 797 TYR Chi-restraints excluded: chain C residue 252 TRP Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 346 TYR Chi-restraints excluded: chain C residue 363 TYR Chi-restraints excluded: chain D residue 70 PHE Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain D residue 187 ILE Chi-restraints excluded: chain D residue 367 TYR Chi-restraints excluded: chain D residue 768 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 436 optimal weight: 30.0000 chunk 172 optimal weight: 0.9980 chunk 397 optimal weight: 10.0000 chunk 220 optimal weight: 4.9990 chunk 12 optimal weight: 4.9990 chunk 422 optimal weight: 20.0000 chunk 83 optimal weight: 0.8980 chunk 43 optimal weight: 50.0000 chunk 369 optimal weight: 8.9990 chunk 2 optimal weight: 0.6980 chunk 318 optimal weight: 5.9990 overall best weight: 2.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 59 GLN C 583 GLN ** E 75 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 = 0.4284 r_free = 0.4284 target = 0.085794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.071070 restraints weight = 210574.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.069588 restraints weight = 217152.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.069210 restraints weight = 180931.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.069222 restraints weight = 125089.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.069453 restraints weight = 119020.171| |-----------------------------------------------------------------------------| r_work (final): 0.3884 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3884 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3884 r_free = 0.3884 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3884 r_free = 0.3884 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3884 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6662 moved from start: 0.3868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 35043 Z= 0.166 Angle : 0.550 10.957 47825 Z= 0.282 Chirality : 0.043 0.289 5689 Planarity : 0.003 0.042 6114 Dihedral : 6.544 74.248 5921 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.22 % Allowed : 12.95 % Favored : 85.83 % 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: -1.12 (0.12), residues: 4922 helix: 1.29 (0.12), residues: 1883 sheet: -2.27 (0.17), residues: 857 loop : -1.95 (0.13), residues: 2182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 327 TYR 0.020 0.001 TYR C 346 PHE 0.028 0.002 PHE A 604 TRP 0.029 0.002 TRP C 601 HIS 0.005 0.001 HIS C 349 Details of bonding type rmsd covalent geometry : bond 0.00363 (35014) covalent geometry : angle 0.54449 (47754) SS BOND : bond 0.00395 ( 10) SS BOND : angle 1.03955 ( 20) hydrogen bonds : bond 0.03604 ( 1594) hydrogen bonds : angle 4.34827 ( 4542) Misc. bond : bond 0.00017 ( 2) link_BETA1-4 : bond 0.00497 ( 5) link_BETA1-4 : angle 1.80114 ( 15) link_NAG-ASN : bond 0.00305 ( 12) link_NAG-ASN : angle 2.57723 ( 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 176 residues out of total 4276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 144 time to evaluate : 1.025 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 403 MET cc_start: 0.3777 (mpp) cc_final: 0.3468 (mpp) REVERT: B 496 MET cc_start: 0.5210 (ptp) cc_final: 0.4737 (ptp) REVERT: B 584 PHE cc_start: 0.7359 (t80) cc_final: 0.7062 (t80) REVERT: C 363 TYR cc_start: 0.7694 (OUTLIER) cc_final: 0.6901 (p90) REVERT: C 459 MET cc_start: 0.6552 (mmt) cc_final: 0.6345 (mmt) REVERT: C 704 MET cc_start: 0.7763 (mmp) cc_final: 0.7538 (mmp) REVERT: D 355 MET cc_start: 0.8635 (mmm) cc_final: 0.8033 (mmm) REVERT: D 367 TYR cc_start: 0.7647 (OUTLIER) cc_final: 0.7384 (p90) REVERT: D 463 MET cc_start: 0.4457 (mmp) cc_final: 0.3858 (mmp) REVERT: D 585 MET cc_start: 0.7507 (tpp) cc_final: 0.6537 (tpp) REVERT: D 670 MET cc_start: 0.8323 (ppp) cc_final: 0.7879 (ppp) REVERT: G 35 MET cc_start: 0.5399 (ppp) cc_final: 0.5159 (ppp) outliers start: 32 outliers final: 19 residues processed: 172 average time/residue: 0.1920 time to fit residues: 57.5991 Evaluate side-chains 154 residues out of total 4276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 133 time to evaluate : 1.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 252 TRP Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 374 MET Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 252 TRP Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 363 TYR Chi-restraints excluded: chain D residue 44 LEU Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain D residue 286 MET Chi-restraints excluded: chain D residue 367 TYR Chi-restraints excluded: chain D residue 768 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 13 optimal weight: 3.9990 chunk 451 optimal weight: 8.9990 chunk 182 optimal weight: 0.9980 chunk 139 optimal weight: 0.9980 chunk 83 optimal weight: 0.9980 chunk 269 optimal weight: 0.1980 chunk 196 optimal weight: 20.0000 chunk 398 optimal weight: 3.9990 chunk 89 optimal weight: 0.6980 chunk 267 optimal weight: 7.9990 chunk 303 optimal weight: 10.0000 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 101 ASN ** E 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 = 0.4301 r_free = 0.4301 target = 0.086543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.071720 restraints weight = 208859.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.069982 restraints weight = 208383.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.069947 restraints weight = 196088.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.069685 restraints weight = 138104.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.069855 restraints weight = 122435.181| |-----------------------------------------------------------------------------| r_work (final): 0.3891 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3891 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3891 r_free = 0.3891 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3891 r_free = 0.3891 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3891 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6632 moved from start: 0.3934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 35043 Z= 0.102 Angle : 0.517 17.901 47825 Z= 0.260 Chirality : 0.041 0.265 5689 Planarity : 0.003 0.045 6114 Dihedral : 6.046 68.682 5921 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 0.84 % Allowed : 13.68 % Favored : 85.49 % 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: -0.83 (0.12), residues: 4922 helix: 1.56 (0.12), residues: 1890 sheet: -2.19 (0.17), residues: 896 loop : -1.77 (0.13), residues: 2136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 586 TYR 0.020 0.001 TYR B 533 PHE 0.021 0.001 PHE B 667 TRP 0.070 0.002 TRP C 602 HIS 0.003 0.001 HIS D 268 Details of bonding type rmsd covalent geometry : bond 0.00219 (35014) covalent geometry : angle 0.51160 (47754) SS BOND : bond 0.00235 ( 10) SS BOND : angle 0.88155 ( 20) hydrogen bonds : bond 0.03264 ( 1594) hydrogen bonds : angle 4.03922 ( 4542) Misc. bond : bond 0.00005 ( 2) link_BETA1-4 : bond 0.00378 ( 5) link_BETA1-4 : angle 2.14650 ( 15) link_NAG-ASN : bond 0.00324 ( 12) link_NAG-ASN : angle 2.46763 ( 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 162 residues out of total 4276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 140 time to evaluate : 1.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 403 MET cc_start: 0.3655 (mpp) cc_final: 0.3388 (mpp) REVERT: A 604 PHE cc_start: 0.8699 (OUTLIER) cc_final: 0.8121 (m-80) REVERT: A 704 MET cc_start: 0.7615 (mmt) cc_final: 0.7340 (mmt) REVERT: C 346 TYR cc_start: 0.7956 (OUTLIER) cc_final: 0.7681 (m-10) REVERT: C 459 MET cc_start: 0.6428 (mmt) cc_final: 0.6195 (mmt) REVERT: C 704 MET cc_start: 0.7813 (mmp) cc_final: 0.7486 (mmp) REVERT: D 355 MET cc_start: 0.8826 (mmm) cc_final: 0.8544 (mmt) REVERT: D 367 TYR cc_start: 0.7762 (OUTLIER) cc_final: 0.7487 (p90) REVERT: D 463 MET cc_start: 0.4656 (mmp) cc_final: 0.4029 (mmp) REVERT: D 585 MET cc_start: 0.7238 (tpp) cc_final: 0.6905 (tpp) REVERT: D 670 MET cc_start: 0.8429 (ppp) cc_final: 0.7972 (ppp) REVERT: E 81 MET cc_start: 0.7397 (pmm) cc_final: 0.7158 (pmm) REVERT: H 35 MET cc_start: 0.5963 (ppp) cc_final: 0.5235 (ptm) outliers start: 22 outliers final: 13 residues processed: 156 average time/residue: 0.1863 time to fit residues: 51.5063 Evaluate side-chains 150 residues out of total 4276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 134 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 252 TRP Chi-restraints excluded: chain A residue 604 PHE Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 374 MET Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 252 TRP Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 346 TYR Chi-restraints excluded: chain C residue 603 PHE Chi-restraints excluded: chain D residue 44 LEU Chi-restraints excluded: chain D residue 367 TYR Chi-restraints excluded: chain D residue 768 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 326 optimal weight: 30.0000 chunk 191 optimal weight: 0.0870 chunk 15 optimal weight: 6.9990 chunk 183 optimal weight: 5.9990 chunk 221 optimal weight: 7.9990 chunk 333 optimal weight: 20.0000 chunk 239 optimal weight: 1.9990 chunk 66 optimal weight: 5.9990 chunk 345 optimal weight: 10.0000 chunk 141 optimal weight: 0.6980 chunk 280 optimal weight: 0.8980 overall best weight: 1.9362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 223 ASN ** E 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 = 0.4287 r_free = 0.4287 target = 0.086011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.071047 restraints weight = 207795.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.069418 restraints weight = 205208.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.069432 restraints weight = 181960.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.068770 restraints weight = 147327.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.068854 restraints weight = 126328.284| |-----------------------------------------------------------------------------| r_work (final): 0.3864 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3865 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3865 r_free = 0.3865 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3865 r_free = 0.3865 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3865 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6700 moved from start: 0.4219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 35043 Z= 0.142 Angle : 0.535 15.905 47825 Z= 0.271 Chirality : 0.042 0.268 5689 Planarity : 0.003 0.042 6114 Dihedral : 5.965 66.594 5921 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.14 % Allowed : 14.06 % Favored : 84.80 % 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: -0.71 (0.12), residues: 4922 helix: 1.68 (0.12), residues: 1891 sheet: -2.13 (0.17), residues: 896 loop : -1.72 (0.13), residues: 2135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 327 TYR 0.018 0.001 TYR C 346 PHE 0.022 0.001 PHE A 26 TRP 0.064 0.002 TRP A 602 HIS 0.004 0.001 HIS C 349 Details of bonding type rmsd covalent geometry : bond 0.00314 (35014) covalent geometry : angle 0.52910 (47754) SS BOND : bond 0.00303 ( 10) SS BOND : angle 0.82395 ( 20) hydrogen bonds : bond 0.03328 ( 1594) hydrogen bonds : angle 4.05530 ( 4542) Misc. bond : bond 0.00011 ( 2) link_BETA1-4 : bond 0.00354 ( 5) link_BETA1-4 : angle 2.04878 ( 15) link_NAG-ASN : bond 0.00319 ( 12) link_NAG-ASN : angle 2.62254 ( 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 174 residues out of total 4276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 144 time to evaluate : 1.186 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: A 403 MET cc_start: 0.3612 (mpp) cc_final: 0.3337 (mpp) REVERT: A 604 PHE cc_start: 0.8770 (OUTLIER) cc_final: 0.7974 (m-80) REVERT: A 704 MET cc_start: 0.7453 (mmt) cc_final: 0.7248 (mmt) REVERT: C 346 TYR cc_start: 0.8023 (OUTLIER) cc_final: 0.7631 (m-10) REVERT: C 459 MET cc_start: 0.6530 (mmt) cc_final: 0.6243 (mmt) REVERT: C 601 TRP cc_start: 0.7533 (t-100) cc_final: 0.7103 (t-100) REVERT: C 704 MET cc_start: 0.7894 (mmp) cc_final: 0.7598 (mmp) REVERT: D 355 MET cc_start: 0.8718 (mmm) cc_final: 0.8386 (mmm) REVERT: D 367 TYR cc_start: 0.7701 (OUTLIER) cc_final: 0.7438 (p90) REVERT: D 463 MET cc_start: 0.4559 (mmp) cc_final: 0.3935 (mmp) REVERT: D 585 MET cc_start: 0.7282 (tpp) cc_final: 0.6965 (tpp) REVERT: D 670 MET cc_start: 0.8528 (ppp) cc_final: 0.8063 (ppp) REVERT: E 81 MET cc_start: 0.7382 (pmm) cc_final: 0.7050 (pmm) REVERT: H 35 MET cc_start: 0.5981 (ppp) cc_final: 0.5601 (ppp) outliers start: 30 outliers final: 22 residues processed: 166 average time/residue: 0.1943 time to fit residues: 56.1761 Evaluate side-chains 164 residues out of total 4276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 139 time to evaluate : 1.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 252 TRP Chi-restraints excluded: chain A residue 499 MET Chi-restraints excluded: chain A residue 604 PHE Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 374 MET Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain B residue 574 PHE Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 252 TRP Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 346 TYR Chi-restraints excluded: chain C residue 603 PHE Chi-restraints excluded: chain D residue 44 LEU Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 286 MET Chi-restraints excluded: chain D residue 367 TYR Chi-restraints excluded: chain D residue 768 TYR Chi-restraints excluded: chain D residue 785 SER Chi-restraints excluded: chain G residue 150 VAL Chi-restraints excluded: chain G residue 176 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 294 optimal weight: 9.9990 chunk 60 optimal weight: 10.0000 chunk 315 optimal weight: 7.9990 chunk 191 optimal weight: 0.5980 chunk 224 optimal weight: 7.9990 chunk 412 optimal weight: 20.0000 chunk 400 optimal weight: 30.0000 chunk 383 optimal weight: 40.0000 chunk 354 optimal weight: 20.0000 chunk 456 optimal weight: 30.0000 chunk 263 optimal weight: 0.9990 overall best weight: 5.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 15 ASN ** C 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 153 GLN ** C 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 355 HIS ** C 638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 77 ASN D 284 GLN ** D 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.084454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.070408 restraints weight = 212993.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.068525 restraints weight = 241635.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.068061 restraints weight = 195472.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.068036 restraints weight = 132495.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.068325 restraints weight = 125143.913| |-----------------------------------------------------------------------------| r_work (final): 0.3847 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3847 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3847 r_free = 0.3847 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3847 r_free = 0.3847 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3847 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6772 moved from start: 0.5242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.102 35043 Z= 0.348 Angle : 0.780 16.140 47825 Z= 0.404 Chirality : 0.047 0.274 5689 Planarity : 0.005 0.099 6114 Dihedral : 7.248 78.634 5921 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 13.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 1.79 % Allowed : 13.83 % Favored : 84.38 % 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: -1.36 (0.12), residues: 4922 helix: 1.03 (0.12), residues: 1920 sheet: -2.36 (0.16), residues: 892 loop : -2.06 (0.13), residues: 2110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 25 TYR 0.043 0.002 TYR C 346 PHE 0.044 0.003 PHE A 26 TRP 0.060 0.003 TRP A 602 HIS 0.014 0.002 HIS C 349 Details of bonding type rmsd covalent geometry : bond 0.00769 (35014) covalent geometry : angle 0.77359 (47754) SS BOND : bond 0.00734 ( 10) SS BOND : angle 1.07513 ( 20) hydrogen bonds : bond 0.04534 ( 1594) hydrogen bonds : angle 4.95409 ( 4542) Misc. bond : bond 0.00040 ( 2) link_BETA1-4 : bond 0.00587 ( 5) link_BETA1-4 : angle 1.94517 ( 15) link_NAG-ASN : bond 0.00837 ( 12) link_NAG-ASN : angle 3.48031 ( 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 191 residues out of total 4276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 144 time to evaluate : 1.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 MET cc_start: 0.7632 (tmm) cc_final: 0.6882 (tmm) REVERT: A 403 MET cc_start: 0.3635 (mpp) cc_final: 0.3346 (mpp) REVERT: A 604 PHE cc_start: 0.8749 (OUTLIER) cc_final: 0.8215 (m-80) REVERT: A 625 MET cc_start: 0.9284 (ppp) cc_final: 0.8827 (ppp) REVERT: A 704 MET cc_start: 0.7641 (mmt) cc_final: 0.7327 (mmt) REVERT: B 496 MET cc_start: 0.6091 (ptp) cc_final: 0.5783 (ptp) REVERT: C 15 ASN cc_start: 0.8876 (OUTLIER) cc_final: 0.8466 (p0) REVERT: C 346 TYR cc_start: 0.8163 (OUTLIER) cc_final: 0.7729 (m-10) REVERT: C 363 TYR cc_start: 0.7921 (OUTLIER) cc_final: 0.7444 (p90) REVERT: C 459 MET cc_start: 0.7088 (mmt) cc_final: 0.6735 (mmt) REVERT: C 601 TRP cc_start: 0.7752 (t-100) cc_final: 0.7491 (t-100) REVERT: C 704 MET cc_start: 0.8254 (mmp) cc_final: 0.7911 (mmp) REVERT: D 367 TYR cc_start: 0.7735 (OUTLIER) cc_final: 0.7475 (p90) REVERT: D 463 MET cc_start: 0.4672 (mmp) cc_final: 0.4119 (mmp) REVERT: D 503 MET cc_start: 0.3910 (tpt) cc_final: 0.3668 (tpt) REVERT: D 585 MET cc_start: 0.7496 (tpp) cc_final: 0.7162 (tpp) REVERT: D 670 MET cc_start: 0.8568 (ppp) cc_final: 0.8133 (ppp) REVERT: E 81 MET cc_start: 0.7731 (pmm) cc_final: 0.7256 (pmm) REVERT: H 35 MET cc_start: 0.6130 (ppp) cc_final: 0.5707 (ppp) outliers start: 47 outliers final: 34 residues processed: 181 average time/residue: 0.1921 time to fit residues: 60.6573 Evaluate side-chains 179 residues out of total 4276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 140 time to evaluate : 1.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 252 TRP Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 499 MET Chi-restraints excluded: chain A residue 602 TRP Chi-restraints excluded: chain A residue 604 PHE Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 70 PHE Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain B residue 574 PHE Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain C residue 15 ASN Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 252 TRP Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 346 TYR Chi-restraints excluded: chain C residue 363 TYR Chi-restraints excluded: chain D residue 44 LEU Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 187 ILE Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 286 MET Chi-restraints excluded: chain D residue 367 TYR Chi-restraints excluded: chain D residue 608 PHE Chi-restraints excluded: chain D residue 768 TYR Chi-restraints excluded: chain D residue 785 SER Chi-restraints excluded: chain E residue 4 THR Chi-restraints excluded: chain G residue 150 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 302 optimal weight: 7.9990 chunk 98 optimal weight: 1.9990 chunk 411 optimal weight: 20.0000 chunk 283 optimal weight: 6.9990 chunk 24 optimal weight: 0.7980 chunk 305 optimal weight: 20.0000 chunk 107 optimal weight: 5.9990 chunk 114 optimal weight: 0.5980 chunk 437 optimal weight: 6.9990 chunk 138 optimal weight: 3.9990 chunk 148 optimal weight: 7.9990 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 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 = 0.4264 r_free = 0.4264 target = 0.084896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.070887 restraints weight = 211234.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.070290 restraints weight = 260844.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.069925 restraints weight = 170930.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.069821 restraints weight = 122755.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.069749 restraints weight = 125039.947| |-----------------------------------------------------------------------------| r_work (final): 0.3881 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3881 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3881 r_free = 0.3881 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3881 r_free = 0.3881 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3881 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6677 moved from start: 0.5266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.286 35043 Z= 0.301 Angle : 0.855 59.197 47825 Z= 0.461 Chirality : 0.047 0.752 5689 Planarity : 0.005 0.098 6114 Dihedral : 7.253 79.108 5921 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 14.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer: Outliers : 1.68 % Allowed : 14.02 % Favored : 84.30 % 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: -1.41 (0.12), residues: 4922 helix: 0.98 (0.12), residues: 1919 sheet: -2.39 (0.16), residues: 891 loop : -2.08 (0.13), residues: 2112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.042 0.001 ARG A 293 TYR 0.040 0.002 TYR C 346 PHE 0.062 0.002 PHE E 78 TRP 0.070 0.003 TRP A 602 HIS 0.011 0.002 HIS C 349 Details of bonding type rmsd covalent geometry : bond 0.00656 (35014) covalent geometry : angle 0.84918 (47754) SS BOND : bond 0.00412 ( 10) SS BOND : angle 1.07267 ( 20) hydrogen bonds : bond 0.04443 ( 1594) hydrogen bonds : angle 4.92392 ( 4542) Misc. bond : bond 0.00012 ( 2) link_BETA1-4 : bond 0.00308 ( 5) link_BETA1-4 : angle 2.14337 ( 15) link_NAG-ASN : bond 0.00851 ( 12) link_NAG-ASN : angle 3.46394 ( 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 184 residues out of total 4276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 140 time to evaluate : 1.476 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: A 78 MET cc_start: 0.7577 (tmm) cc_final: 0.6880 (tmm) REVERT: A 403 MET cc_start: 0.3590 (mpp) cc_final: 0.3301 (mpp) REVERT: A 603 PHE cc_start: 0.7660 (m-80) cc_final: 0.7211 (m-80) REVERT: A 604 PHE cc_start: 0.8604 (OUTLIER) cc_final: 0.8107 (m-80) REVERT: A 625 MET cc_start: 0.9232 (ppp) cc_final: 0.8680 (ppp) REVERT: A 704 MET cc_start: 0.7453 (mmt) cc_final: 0.7162 (mmt) REVERT: B 496 MET cc_start: 0.5834 (ptp) cc_final: 0.5486 (ptp) REVERT: C 346 TYR cc_start: 0.8163 (OUTLIER) cc_final: 0.7733 (m-10) REVERT: C 363 TYR cc_start: 0.7979 (OUTLIER) cc_final: 0.7505 (p90) REVERT: C 459 MET cc_start: 0.6947 (mmt) cc_final: 0.6536 (mmt) REVERT: C 581 MET cc_start: 0.8802 (ttm) cc_final: 0.8483 (ttm) REVERT: C 601 TRP cc_start: 0.7627 (t-100) cc_final: 0.7385 (t-100) REVERT: C 704 MET cc_start: 0.8117 (mmp) cc_final: 0.7798 (mmp) REVERT: D 367 TYR cc_start: 0.7811 (OUTLIER) cc_final: 0.7525 (p90) REVERT: D 463 MET cc_start: 0.4544 (mmp) cc_final: 0.4011 (mmp) REVERT: D 503 MET cc_start: 0.3909 (tpt) cc_final: 0.3631 (tpt) REVERT: D 585 MET cc_start: 0.7578 (tpp) cc_final: 0.7248 (tpp) REVERT: D 670 MET cc_start: 0.8519 (ppp) cc_final: 0.8100 (ppp) REVERT: E 153 MET cc_start: 0.8001 (tmm) cc_final: 0.7519 (tpp) REVERT: H 35 MET cc_start: 0.6047 (ppp) cc_final: 0.5665 (ppp) outliers start: 44 outliers final: 38 residues processed: 176 average time/residue: 0.1924 time to fit residues: 59.9240 Evaluate side-chains 181 residues out of total 4276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 139 time to evaluate : 1.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 252 TRP Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 499 MET Chi-restraints excluded: chain A residue 602 TRP Chi-restraints excluded: chain A residue 604 PHE Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 70 PHE Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain B residue 574 PHE Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain C residue 70 PHE Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 252 TRP Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 346 TYR Chi-restraints excluded: chain C residue 363 TYR Chi-restraints excluded: chain C residue 714 CYS Chi-restraints excluded: chain D residue 44 LEU Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 187 ILE Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 286 MET Chi-restraints excluded: chain D residue 367 TYR Chi-restraints excluded: chain D residue 768 TYR Chi-restraints excluded: chain D residue 785 SER Chi-restraints excluded: chain E residue 4 THR Chi-restraints excluded: chain G residue 150 VAL Chi-restraints excluded: chain G residue 176 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 69 optimal weight: 0.7980 chunk 138 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 21 optimal weight: 0.4980 chunk 150 optimal weight: 30.0000 chunk 282 optimal weight: 5.9990 chunk 111 optimal weight: 0.5980 chunk 261 optimal weight: 4.9990 chunk 2 optimal weight: 0.6980 chunk 439 optimal weight: 20.0000 chunk 171 optimal weight: 4.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 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 = 0.4264 r_free = 0.4264 target = 0.084945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.068650 restraints weight = 212246.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.066419 restraints weight = 179203.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.065269 restraints weight = 232964.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.065016 restraints weight = 212974.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.065480 restraints weight = 145875.067| |-----------------------------------------------------------------------------| r_work (final): 0.3732 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3732 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3732 r_free = 0.3732 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3732 r_free = 0.3732 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3732 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7138 moved from start: 0.5268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.286 35043 Z= 0.301 Angle : 0.855 59.197 47825 Z= 0.461 Chirality : 0.047 0.752 5689 Planarity : 0.005 0.098 6114 Dihedral : 7.253 79.108 5921 Min Nonbonded Distance : 1.522 Molprobity Statistics. All-atom Clashscore : 15.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer: Outliers : 1.60 % Allowed : 14.10 % Favored : 84.30 % 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: -1.41 (0.12), residues: 4922 helix: 0.98 (0.12), residues: 1919 sheet: -2.39 (0.16), residues: 891 loop : -2.08 (0.13), residues: 2112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.042 0.001 ARG A 293 TYR 0.040 0.002 TYR C 346 PHE 0.062 0.002 PHE E 78 TRP 0.070 0.003 TRP A 602 HIS 0.011 0.002 HIS C 349 Details of bonding type rmsd covalent geometry : bond 0.00656 (35014) covalent geometry : angle 0.84918 (47754) SS BOND : bond 0.00412 ( 10) SS BOND : angle 1.07267 ( 20) hydrogen bonds : bond 0.04443 ( 1594) hydrogen bonds : angle 4.92392 ( 4542) Misc. bond : bond 0.00012 ( 2) link_BETA1-4 : bond 0.00308 ( 5) link_BETA1-4 : angle 2.14337 ( 15) link_NAG-ASN : bond 0.00851 ( 12) link_NAG-ASN : angle 3.46394 ( 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 181 residues out of total 4276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 139 time to evaluate : 1.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 MET cc_start: 0.7506 (tmm) cc_final: 0.6903 (tmm) REVERT: A 603 PHE cc_start: 0.8440 (m-80) cc_final: 0.8143 (m-80) REVERT: A 604 PHE cc_start: 0.8658 (OUTLIER) cc_final: 0.8284 (m-80) REVERT: A 704 MET cc_start: 0.8356 (mmt) cc_final: 0.7977 (mmt) REVERT: B 496 MET cc_start: 0.7853 (ptp) cc_final: 0.7490 (ptp) REVERT: C 346 TYR cc_start: 0.8122 (OUTLIER) cc_final: 0.7724 (m-10) REVERT: C 363 TYR cc_start: 0.7822 (OUTLIER) cc_final: 0.7360 (p90) REVERT: C 601 TRP cc_start: 0.7926 (t-100) cc_final: 0.7595 (t-100) REVERT: C 704 MET cc_start: 0.8360 (mmp) cc_final: 0.8074 (mmp) REVERT: D 367 TYR cc_start: 0.7760 (OUTLIER) cc_final: 0.7507 (p90) REVERT: D 463 MET cc_start: 0.6120 (mmp) cc_final: 0.5757 (mmp) REVERT: D 585 MET cc_start: 0.6312 (tpp) cc_final: 0.6027 (tpp) REVERT: D 670 MET cc_start: 0.8665 (ppp) cc_final: 0.8252 (ppp) REVERT: E 153 MET cc_start: 0.7644 (tmm) cc_final: 0.7404 (tpp) REVERT: H 35 MET cc_start: 0.6730 (ppp) cc_final: 0.6088 (ppp) outliers start: 42 outliers final: 38 residues processed: 173 average time/residue: 0.1893 time to fit residues: 58.2498 Evaluate side-chains 181 residues out of total 4276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 139 time to evaluate : 1.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 252 TRP Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 499 MET Chi-restraints excluded: chain A residue 602 TRP Chi-restraints excluded: chain A residue 604 PHE Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 70 PHE Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain B residue 574 PHE Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain C residue 70 PHE Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 252 TRP Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 346 TYR Chi-restraints excluded: chain C residue 363 TYR Chi-restraints excluded: chain C residue 714 CYS Chi-restraints excluded: chain D residue 44 LEU Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 187 ILE Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 286 MET Chi-restraints excluded: chain D residue 367 TYR Chi-restraints excluded: chain D residue 768 TYR Chi-restraints excluded: chain D residue 785 SER Chi-restraints excluded: chain E residue 4 THR Chi-restraints excluded: chain G residue 150 VAL Chi-restraints excluded: chain G residue 176 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 229 optimal weight: 2.9990 chunk 231 optimal weight: 0.9980 chunk 463 optimal weight: 50.0000 chunk 301 optimal weight: 8.9990 chunk 141 optimal weight: 20.0000 chunk 341 optimal weight: 7.9990 chunk 70 optimal weight: 0.9990 chunk 217 optimal weight: 0.1980 chunk 429 optimal weight: 50.0000 chunk 131 optimal weight: 9.9990 chunk 184 optimal weight: 9.9990 overall best weight: 2.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 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 = 0.4263 r_free = 0.4263 target = 0.084966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.070673 restraints weight = 211446.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.068784 restraints weight = 234885.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.068373 restraints weight = 192349.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.068327 restraints weight = 131926.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.068651 restraints weight = 123941.392| |-----------------------------------------------------------------------------| r_work (final): 0.3851 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3853 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3853 r_free = 0.3853 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3853 r_free = 0.3853 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3853 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6781 moved from start: 0.5269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.286 35043 Z= 0.301 Angle : 0.855 59.197 47825 Z= 0.461 Chirality : 0.047 0.752 5689 Planarity : 0.005 0.098 6114 Dihedral : 7.253 79.108 5921 Min Nonbonded Distance : 1.522 Molprobity Statistics. All-atom Clashscore : 15.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer: Outliers : 1.60 % Allowed : 14.10 % Favored : 84.30 % 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: -1.41 (0.12), residues: 4922 helix: 0.98 (0.12), residues: 1919 sheet: -2.39 (0.16), residues: 891 loop : -2.08 (0.13), residues: 2112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.042 0.001 ARG A 293 TYR 0.040 0.002 TYR C 346 PHE 0.062 0.002 PHE E 78 TRP 0.070 0.003 TRP A 602 HIS 0.011 0.002 HIS C 349 Details of bonding type rmsd covalent geometry : bond 0.00656 (35014) covalent geometry : angle 0.84918 (47754) SS BOND : bond 0.00412 ( 10) SS BOND : angle 1.07267 ( 20) hydrogen bonds : bond 0.04443 ( 1594) hydrogen bonds : angle 4.92392 ( 4542) Misc. bond : bond 0.00012 ( 2) link_BETA1-4 : bond 0.00308 ( 5) link_BETA1-4 : angle 2.14337 ( 15) link_NAG-ASN : bond 0.00851 ( 12) link_NAG-ASN : angle 3.46394 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7209.92 seconds wall clock time: 124 minutes 30.00 seconds (7470.00 seconds total)