Starting phenix.real_space_refine on Sat Mar 7 07:10:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7x01_32914/03_2026/7x01_32914.cif Found real_map, /net/cci-nas-00/data/ceres_data/7x01_32914/03_2026/7x01_32914.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7x01_32914/03_2026/7x01_32914.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7x01_32914/03_2026/7x01_32914.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7x01_32914/03_2026/7x01_32914.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7x01_32914/03_2026/7x01_32914.map" } resolution = 2.62 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= 0.004 sd= 0.085 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 12 6.06 5 S 324 5.16 5 C 24996 2.51 5 N 6924 2.21 5 O 7464 1.98 5 F 12 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 34 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: 39732 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 3289 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 421, 3283 Classifications: {'peptide': 421} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 21, 'TRANS': 399} Chain breaks: 3 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 6 Conformer: "B" Number of residues, atoms: 421, 3283 Classifications: {'peptide': 421} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 21, 'TRANS': 399} Chain breaks: 3 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 6 bond proxies already assigned to first conformer: 3344 Chain: "B" Number of atoms: 3289 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 421, 3283 Classifications: {'peptide': 421} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 21, 'TRANS': 399} Chain breaks: 3 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 6 Conformer: "B" Number of residues, atoms: 421, 3283 Classifications: {'peptide': 421} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 21, 'TRANS': 399} Chain breaks: 3 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 6 bond proxies already assigned to first conformer: 3344 Chain: "C" Number of atoms: 3289 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 421, 3283 Classifications: {'peptide': 421} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 21, 'TRANS': 399} Chain breaks: 3 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 6 Conformer: "B" Number of residues, atoms: 421, 3283 Classifications: {'peptide': 421} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 21, 'TRANS': 399} Chain breaks: 3 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 6 bond proxies already assigned to first conformer: 3344 Chain: "D" Number of atoms: 3289 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 421, 3283 Classifications: {'peptide': 421} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 21, 'TRANS': 399} Chain breaks: 3 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 6 Conformer: "B" Number of residues, atoms: 421, 3283 Classifications: {'peptide': 421} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 21, 'TRANS': 399} Chain breaks: 3 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 6 bond proxies already assigned to first conformer: 3344 Chain: "E" Number of atoms: 3289 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 421, 3283 Classifications: {'peptide': 421} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 21, 'TRANS': 399} Chain breaks: 3 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 6 Conformer: "B" Number of residues, atoms: 421, 3283 Classifications: {'peptide': 421} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 21, 'TRANS': 399} Chain breaks: 3 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 6 bond proxies already assigned to first conformer: 3344 Chain: "F" Number of atoms: 3289 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 421, 3283 Classifications: {'peptide': 421} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 21, 'TRANS': 399} Chain breaks: 3 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 6 Conformer: "B" Number of residues, atoms: 421, 3283 Classifications: {'peptide': 421} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 21, 'TRANS': 399} Chain breaks: 3 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 6 bond proxies already assigned to first conformer: 3344 Chain: "G" Number of atoms: 3289 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 421, 3283 Classifications: {'peptide': 421} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 21, 'TRANS': 399} Chain breaks: 3 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 6 Conformer: "B" Number of residues, atoms: 421, 3283 Classifications: {'peptide': 421} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 21, 'TRANS': 399} Chain breaks: 3 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 6 bond proxies already assigned to first conformer: 3344 Chain: "H" Number of atoms: 3289 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 421, 3283 Classifications: {'peptide': 421} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 21, 'TRANS': 399} Chain breaks: 3 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 6 Conformer: "B" Number of residues, atoms: 421, 3283 Classifications: {'peptide': 421} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 21, 'TRANS': 399} Chain breaks: 3 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 6 bond proxies already assigned to first conformer: 3344 Chain: "I" Number of atoms: 3289 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 421, 3283 Classifications: {'peptide': 421} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 21, 'TRANS': 399} Chain breaks: 3 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 6 Conformer: "B" Number of residues, atoms: 421, 3283 Classifications: {'peptide': 421} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 21, 'TRANS': 399} Chain breaks: 3 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 6 bond proxies already assigned to first conformer: 3344 Chain: "J" Number of atoms: 3289 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 421, 3283 Classifications: {'peptide': 421} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 21, 'TRANS': 399} Chain breaks: 3 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 6 Conformer: "B" Number of residues, atoms: 421, 3283 Classifications: {'peptide': 421} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 21, 'TRANS': 399} Chain breaks: 3 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 6 bond proxies already assigned to first conformer: 3344 Chain: "K" Number of atoms: 3289 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 421, 3283 Classifications: {'peptide': 421} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 21, 'TRANS': 399} Chain breaks: 3 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 6 Conformer: "B" Number of residues, atoms: 421, 3283 Classifications: {'peptide': 421} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 21, 'TRANS': 399} Chain breaks: 3 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 6 bond proxies already assigned to first conformer: 3344 Chain: "L" Number of atoms: 3289 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 421, 3283 Classifications: {'peptide': 421} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 21, 'TRANS': 399} Chain breaks: 3 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 6 Conformer: "B" Number of residues, atoms: 421, 3283 Classifications: {'peptide': 421} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 21, 'TRANS': 399} Chain breaks: 3 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 6 bond proxies already assigned to first conformer: 3344 Chain: "A" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' ZN': 1, '7XQ': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' ZN': 1, '7XQ': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' ZN': 1, '7XQ': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' ZN': 1, '7XQ': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' ZN': 1, '7XQ': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' ZN': 1, '7XQ': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' ZN': 1, '7XQ': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' ZN': 1, '7XQ': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' ZN': 1, '7XQ': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' ZN': 1, '7XQ': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' ZN': 1, '7XQ': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' ZN': 1, '7XQ': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1024 SG CYS A 134 73.126 19.496 59.460 1.00 72.50 S ATOM 1076 SG CYS A 141 69.321 19.950 58.584 1.00 63.16 S ATOM 4313 SG CYS B 134 118.246 16.138 59.431 1.00 70.94 S ATOM 4365 SG CYS B 141 114.724 14.601 58.627 1.00 64.93 S ATOM 7602 SG CYS C 134 159.013 35.783 59.468 1.00 70.38 S ATOM 7654 SG CYS C 141 156.773 32.673 58.593 1.00 66.81 S ATOM 10891 SG CYS D 134 184.506 73.125 59.457 1.00 71.42 S ATOM 10943 SG CYS D 141 184.044 69.322 58.582 1.00 62.34 S ATOM 14180 SG CYS E 134 187.880 118.267 59.413 1.00 70.20 S ATOM 14232 SG CYS E 141 189.407 114.722 58.631 1.00 64.87 S ATOM 17469 SG CYS F 134 168.252 159.044 59.422 1.00 69.59 S ATOM 17521 SG CYS F 141 171.333 156.738 58.607 1.00 65.21 S ATOM 20758 SG CYS G 134 130.867 184.528 59.430 1.00 71.31 S ATOM 20810 SG CYS G 141 134.679 184.075 58.568 1.00 62.60 S ATOM 24047 SG CYS H 134 85.735 187.891 59.405 1.00 70.38 S ATOM 24099 SG CYS H 141 89.279 189.438 58.602 1.00 66.23 S ATOM 27336 SG CYS I 134 44.983 168.220 59.445 1.00 71.14 S ATOM 27388 SG CYS I 141 47.214 171.354 58.544 1.00 66.99 S ATOM 30625 SG CYS J 134 19.496 130.875 59.443 1.00 71.96 S ATOM 30677 SG CYS J 141 19.917 134.678 58.569 1.00 63.38 S ATOM 33914 SG CYS K 134 16.123 85.750 59.417 1.00 70.85 S ATOM 33966 SG CYS K 141 14.587 89.286 58.598 1.00 65.53 S ATOM 37203 SG CYS L 134 35.723 44.931 59.498 1.00 71.32 S ATOM 37255 SG CYS L 141 32.660 47.215 58.574 1.00 66.30 S Residues with excluded nonbonded symmetry interactions: 12 residue: pdb=" N ACYS A 236 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS A 236 " occ=0.50 residue: pdb=" N ACYS B 236 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS B 236 " occ=0.50 residue: pdb=" N ACYS C 236 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS C 236 " occ=0.50 residue: pdb=" N ACYS D 236 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS D 236 " occ=0.50 residue: pdb=" N ACYS E 236 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS E 236 " occ=0.50 residue: pdb=" N ACYS F 236 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS F 236 " occ=0.50 residue: pdb=" N ACYS G 236 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS G 236 " occ=0.50 residue: pdb=" N ACYS H 236 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS H 236 " occ=0.50 residue: pdb=" N ACYS I 236 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS I 236 " occ=0.50 residue: pdb=" N ACYS J 236 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS J 236 " occ=0.50 residue: pdb=" N ACYS K 236 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS K 236 " occ=0.50 residue: pdb=" N ACYS L 236 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS L 236 " occ=0.50 Time building chain proxies: 15.07, per 1000 atoms: 0.38 Number of scatterers: 39732 At special positions: 0 Unit cell: (204.85, 204.85, 88.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 12 29.99 S 324 16.00 F 12 9.00 O 7464 8.00 N 6924 7.00 C 24996 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.05 Conformation dependent library (CDL) restraints added in 3.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" NE2 HIS A 79 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 141 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 134 " pdb=" ZN B1001 " pdb="ZN ZN B1001 " - pdb=" NE2 HIS B 79 " pdb="ZN ZN B1001 " - pdb=" SG CYS B 134 " pdb="ZN ZN B1001 " - pdb=" SG CYS B 141 " pdb=" ZN C1001 " pdb="ZN ZN C1001 " - pdb=" NE2 HIS C 79 " pdb="ZN ZN C1001 " - pdb=" SG CYS C 134 " pdb="ZN ZN C1001 " - pdb=" SG CYS C 141 " pdb=" ZN D1001 " pdb="ZN ZN D1001 " - pdb=" NE2 HIS D 79 " pdb="ZN ZN D1001 " - pdb=" SG CYS D 134 " pdb="ZN ZN D1001 " - pdb=" SG CYS D 141 " pdb=" ZN E1001 " pdb="ZN ZN E1001 " - pdb=" NE2 HIS E 79 " pdb="ZN ZN E1001 " - pdb=" SG CYS E 134 " pdb="ZN ZN E1001 " - pdb=" SG CYS E 141 " pdb=" ZN F1001 " pdb="ZN ZN F1001 " - pdb=" NE2 HIS F 79 " pdb="ZN ZN F1001 " - pdb=" SG CYS F 134 " pdb="ZN ZN F1001 " - pdb=" SG CYS F 141 " pdb=" ZN G1001 " pdb="ZN ZN G1001 " - pdb=" NE2 HIS G 79 " pdb="ZN ZN G1001 " - pdb=" SG CYS G 134 " pdb="ZN ZN G1001 " - pdb=" SG CYS G 141 " pdb=" ZN H1001 " pdb="ZN ZN H1001 " - pdb=" NE2 HIS H 79 " pdb="ZN ZN H1001 " - pdb=" SG CYS H 134 " pdb="ZN ZN H1001 " - pdb=" SG CYS H 141 " pdb=" ZN I1001 " pdb="ZN ZN I1001 " - pdb=" NE2 HIS I 79 " pdb="ZN ZN I1001 " - pdb=" SG CYS I 134 " pdb="ZN ZN I1001 " - pdb=" SG CYS I 141 " pdb=" ZN J1001 " pdb="ZN ZN J1001 " - pdb=" NE2 HIS J 79 " pdb="ZN ZN J1001 " - pdb=" SG CYS J 134 " pdb="ZN ZN J1001 " - pdb=" SG CYS J 141 " pdb=" ZN K1001 " pdb="ZN ZN K1001 " - pdb=" NE2 HIS K 79 " pdb="ZN ZN K1001 " - pdb=" SG CYS K 134 " pdb="ZN ZN K1001 " - pdb=" SG CYS K 141 " pdb=" ZN L1001 " pdb="ZN ZN L1001 " - pdb=" NE2 HIS L 79 " pdb="ZN ZN L1001 " - pdb=" SG CYS L 141 " pdb="ZN ZN L1001 " - pdb=" SG CYS L 134 " 9984 Ramachandran restraints generated. 4992 Oldfield, 0 Emsley, 4992 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9600 Finding SS restraints... Secondary structure from input PDB file: 156 helices and 48 sheets defined 31.6% alpha, 23.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.50 Creating SS restraints... Processing helix chain 'A' and resid 13 through 22 removed outlier: 3.930A pdb=" N ALA A 17 " --> pdb=" O ALA A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 54 removed outlier: 3.722A pdb=" N ALA A 42 " --> pdb=" O ALA A 38 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N PHE A 43 " --> pdb=" O ASN A 39 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ILE A 48 " --> pdb=" O SER A 44 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LYS A 49 " --> pdb=" O HIS A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 102 removed outlier: 3.852A pdb=" N ARG A 92 " --> pdb=" O GLU A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 125 Processing helix chain 'A' and resid 157 through 167 removed outlier: 3.510A pdb=" N ILE A 167 " --> pdb=" O TYR A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 185 Processing helix chain 'A' and resid 203 through 205 No H-bonds generated for 'chain 'A' and resid 203 through 205' Processing helix chain 'A' and resid 252 through 257 Processing helix chain 'A' and resid 335 through 342 Processing helix chain 'A' and resid 344 through 348 Processing helix chain 'A' and resid 351 through 363 Processing helix chain 'A' and resid 380 through 382 No H-bonds generated for 'chain 'A' and resid 380 through 382' Processing helix chain 'A' and resid 383 through 403 Processing helix chain 'B' and resid 13 through 22 removed outlier: 3.919A pdb=" N ALA B 17 " --> pdb=" O ALA B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 54 removed outlier: 3.705A pdb=" N ALA B 42 " --> pdb=" O ALA B 38 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N PHE B 43 " --> pdb=" O ASN B 39 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ILE B 48 " --> pdb=" O SER B 44 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LYS B 49 " --> pdb=" O HIS B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 102 removed outlier: 3.676A pdb=" N ARG B 92 " --> pdb=" O GLU B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 125 Processing helix chain 'B' and resid 157 through 167 removed outlier: 3.515A pdb=" N ILE B 167 " --> pdb=" O TYR B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 185 removed outlier: 3.524A pdb=" N MET B 184 " --> pdb=" O THR B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 205 No H-bonds generated for 'chain 'B' and resid 203 through 205' Processing helix chain 'B' and resid 252 through 257 Processing helix chain 'B' and resid 335 through 342 Processing helix chain 'B' and resid 344 through 348 Processing helix chain 'B' and resid 351 through 363 Processing helix chain 'B' and resid 380 through 382 No H-bonds generated for 'chain 'B' and resid 380 through 382' Processing helix chain 'B' and resid 383 through 403 Processing helix chain 'C' and resid 13 through 22 removed outlier: 3.989A pdb=" N ALA C 17 " --> pdb=" O ALA C 13 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 54 removed outlier: 3.763A pdb=" N ALA C 42 " --> pdb=" O ALA C 38 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE C 43 " --> pdb=" O ASN C 39 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ILE C 48 " --> pdb=" O SER C 44 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS C 49 " --> pdb=" O HIS C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 102 removed outlier: 3.583A pdb=" N ARG C 92 " --> pdb=" O GLU C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 125 Processing helix chain 'C' and resid 157 through 167 removed outlier: 3.527A pdb=" N ILE C 167 " --> pdb=" O TYR C 163 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 185 Processing helix chain 'C' and resid 203 through 205 No H-bonds generated for 'chain 'C' and resid 203 through 205' Processing helix chain 'C' and resid 252 through 257 Processing helix chain 'C' and resid 335 through 342 Processing helix chain 'C' and resid 344 through 348 Processing helix chain 'C' and resid 351 through 363 Processing helix chain 'C' and resid 380 through 382 No H-bonds generated for 'chain 'C' and resid 380 through 382' Processing helix chain 'C' and resid 383 through 403 Processing helix chain 'D' and resid 13 through 22 removed outlier: 3.928A pdb=" N ALA D 17 " --> pdb=" O ALA D 13 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 54 removed outlier: 3.706A pdb=" N ALA D 42 " --> pdb=" O ALA D 38 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N PHE D 43 " --> pdb=" O ASN D 39 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ILE D 48 " --> pdb=" O SER D 44 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LYS D 49 " --> pdb=" O HIS D 45 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 102 removed outlier: 3.853A pdb=" N ARG D 92 " --> pdb=" O GLU D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 125 Processing helix chain 'D' and resid 157 through 167 removed outlier: 3.504A pdb=" N ILE D 167 " --> pdb=" O TYR D 163 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 185 Processing helix chain 'D' and resid 203 through 205 No H-bonds generated for 'chain 'D' and resid 203 through 205' Processing helix chain 'D' and resid 252 through 257 Processing helix chain 'D' and resid 335 through 342 Processing helix chain 'D' and resid 344 through 348 Processing helix chain 'D' and resid 351 through 363 Processing helix chain 'D' and resid 380 through 382 No H-bonds generated for 'chain 'D' and resid 380 through 382' Processing helix chain 'D' and resid 383 through 403 Processing helix chain 'E' and resid 13 through 22 removed outlier: 3.953A pdb=" N ALA E 17 " --> pdb=" O ALA E 13 " (cutoff:3.500A) Processing helix chain 'E' and resid 38 through 54 removed outlier: 3.723A pdb=" N ALA E 42 " --> pdb=" O ALA E 38 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N PHE E 43 " --> pdb=" O ASN E 39 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ILE E 48 " --> pdb=" O SER E 44 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS E 49 " --> pdb=" O HIS E 45 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 102 removed outlier: 3.715A pdb=" N ARG E 92 " --> pdb=" O GLU E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 125 Processing helix chain 'E' and resid 157 through 167 removed outlier: 3.507A pdb=" N ILE E 167 " --> pdb=" O TYR E 163 " (cutoff:3.500A) Processing helix chain 'E' and resid 180 through 185 removed outlier: 3.509A pdb=" N MET E 184 " --> pdb=" O THR E 180 " (cutoff:3.500A) Processing helix chain 'E' and resid 203 through 205 No H-bonds generated for 'chain 'E' and resid 203 through 205' Processing helix chain 'E' and resid 252 through 257 Processing helix chain 'E' and resid 335 through 342 Processing helix chain 'E' and resid 344 through 348 Processing helix chain 'E' and resid 351 through 363 Processing helix chain 'E' and resid 380 through 382 No H-bonds generated for 'chain 'E' and resid 380 through 382' Processing helix chain 'E' and resid 383 through 403 Processing helix chain 'F' and resid 13 through 22 removed outlier: 3.989A pdb=" N ALA F 17 " --> pdb=" O ALA F 13 " (cutoff:3.500A) Processing helix chain 'F' and resid 38 through 54 removed outlier: 3.731A pdb=" N ALA F 42 " --> pdb=" O ALA F 38 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N PHE F 43 " --> pdb=" O ASN F 39 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE F 48 " --> pdb=" O SER F 44 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS F 49 " --> pdb=" O HIS F 45 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 102 removed outlier: 3.580A pdb=" N ARG F 92 " --> pdb=" O GLU F 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 111 through 125 Processing helix chain 'F' and resid 157 through 167 removed outlier: 3.518A pdb=" N ILE F 167 " --> pdb=" O TYR F 163 " (cutoff:3.500A) Processing helix chain 'F' and resid 180 through 185 Processing helix chain 'F' and resid 203 through 205 No H-bonds generated for 'chain 'F' and resid 203 through 205' Processing helix chain 'F' and resid 252 through 257 Processing helix chain 'F' and resid 335 through 342 Processing helix chain 'F' and resid 344 through 348 Processing helix chain 'F' and resid 351 through 363 Processing helix chain 'F' and resid 380 through 382 No H-bonds generated for 'chain 'F' and resid 380 through 382' Processing helix chain 'F' and resid 383 through 403 Processing helix chain 'G' and resid 13 through 22 removed outlier: 3.946A pdb=" N ALA G 17 " --> pdb=" O ALA G 13 " (cutoff:3.500A) Processing helix chain 'G' and resid 38 through 54 removed outlier: 3.695A pdb=" N ALA G 42 " --> pdb=" O ALA G 38 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE G 43 " --> pdb=" O ASN G 39 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE G 48 " --> pdb=" O SER G 44 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LYS G 49 " --> pdb=" O HIS G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 88 through 102 removed outlier: 3.850A pdb=" N ARG G 92 " --> pdb=" O GLU G 88 " (cutoff:3.500A) Processing helix chain 'G' and resid 111 through 125 Processing helix chain 'G' and resid 157 through 167 removed outlier: 3.535A pdb=" N ILE G 167 " --> pdb=" O TYR G 163 " (cutoff:3.500A) Processing helix chain 'G' and resid 180 through 185 Processing helix chain 'G' and resid 203 through 205 No H-bonds generated for 'chain 'G' and resid 203 through 205' Processing helix chain 'G' and resid 252 through 257 Processing helix chain 'G' and resid 335 through 342 Processing helix chain 'G' and resid 344 through 348 Processing helix chain 'G' and resid 351 through 363 Processing helix chain 'G' and resid 380 through 382 No H-bonds generated for 'chain 'G' and resid 380 through 382' Processing helix chain 'G' and resid 383 through 403 Processing helix chain 'H' and resid 13 through 22 removed outlier: 3.903A pdb=" N ALA H 17 " --> pdb=" O ALA H 13 " (cutoff:3.500A) Processing helix chain 'H' and resid 38 through 54 removed outlier: 3.747A pdb=" N ALA H 42 " --> pdb=" O ALA H 38 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N PHE H 43 " --> pdb=" O ASN H 39 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ILE H 48 " --> pdb=" O SER H 44 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LYS H 49 " --> pdb=" O HIS H 45 " (cutoff:3.500A) Processing helix chain 'H' and resid 88 through 102 removed outlier: 3.719A pdb=" N ARG H 92 " --> pdb=" O GLU H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 125 Processing helix chain 'H' and resid 157 through 167 Processing helix chain 'H' and resid 180 through 185 removed outlier: 3.522A pdb=" N MET H 184 " --> pdb=" O THR H 180 " (cutoff:3.500A) Processing helix chain 'H' and resid 203 through 205 No H-bonds generated for 'chain 'H' and resid 203 through 205' Processing helix chain 'H' and resid 252 through 257 Processing helix chain 'H' and resid 335 through 342 Processing helix chain 'H' and resid 344 through 348 Processing helix chain 'H' and resid 351 through 363 Processing helix chain 'H' and resid 380 through 382 No H-bonds generated for 'chain 'H' and resid 380 through 382' Processing helix chain 'H' and resid 383 through 403 Processing helix chain 'I' and resid 13 through 22 removed outlier: 3.956A pdb=" N ALA I 17 " --> pdb=" O ALA I 13 " (cutoff:3.500A) Processing helix chain 'I' and resid 38 through 54 removed outlier: 3.767A pdb=" N ALA I 42 " --> pdb=" O ALA I 38 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE I 43 " --> pdb=" O ASN I 39 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE I 48 " --> pdb=" O SER I 44 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LYS I 49 " --> pdb=" O HIS I 45 " (cutoff:3.500A) Processing helix chain 'I' and resid 88 through 102 removed outlier: 3.578A pdb=" N ARG I 92 " --> pdb=" O GLU I 88 " (cutoff:3.500A) Processing helix chain 'I' and resid 111 through 125 Processing helix chain 'I' and resid 157 through 167 removed outlier: 3.512A pdb=" N ILE I 167 " --> pdb=" O TYR I 163 " (cutoff:3.500A) Processing helix chain 'I' and resid 180 through 185 Processing helix chain 'I' and resid 203 through 205 No H-bonds generated for 'chain 'I' and resid 203 through 205' Processing helix chain 'I' and resid 252 through 257 Processing helix chain 'I' and resid 335 through 342 Processing helix chain 'I' and resid 344 through 348 Processing helix chain 'I' and resid 351 through 363 Processing helix chain 'I' and resid 380 through 382 No H-bonds generated for 'chain 'I' and resid 380 through 382' Processing helix chain 'I' and resid 383 through 403 Processing helix chain 'J' and resid 13 through 22 removed outlier: 3.927A pdb=" N ALA J 17 " --> pdb=" O ALA J 13 " (cutoff:3.500A) Processing helix chain 'J' and resid 38 through 54 removed outlier: 3.711A pdb=" N ALA J 42 " --> pdb=" O ALA J 38 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N PHE J 43 " --> pdb=" O ASN J 39 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ILE J 48 " --> pdb=" O SER J 44 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS J 49 " --> pdb=" O HIS J 45 " (cutoff:3.500A) Processing helix chain 'J' and resid 88 through 102 removed outlier: 3.895A pdb=" N ARG J 92 " --> pdb=" O GLU J 88 " (cutoff:3.500A) Processing helix chain 'J' and resid 111 through 125 Processing helix chain 'J' and resid 157 through 167 removed outlier: 3.521A pdb=" N ILE J 167 " --> pdb=" O TYR J 163 " (cutoff:3.500A) Processing helix chain 'J' and resid 180 through 185 Processing helix chain 'J' and resid 203 through 205 No H-bonds generated for 'chain 'J' and resid 203 through 205' Processing helix chain 'J' and resid 252 through 257 Processing helix chain 'J' and resid 335 through 342 Processing helix chain 'J' and resid 344 through 348 Processing helix chain 'J' and resid 351 through 363 Processing helix chain 'J' and resid 380 through 382 No H-bonds generated for 'chain 'J' and resid 380 through 382' Processing helix chain 'J' and resid 383 through 403 Processing helix chain 'K' and resid 13 through 22 removed outlier: 3.936A pdb=" N ALA K 17 " --> pdb=" O ALA K 13 " (cutoff:3.500A) Processing helix chain 'K' and resid 38 through 54 removed outlier: 3.704A pdb=" N ALA K 42 " --> pdb=" O ALA K 38 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE K 48 " --> pdb=" O SER K 44 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LYS K 49 " --> pdb=" O HIS K 45 " (cutoff:3.500A) Processing helix chain 'K' and resid 88 through 102 removed outlier: 3.605A pdb=" N ARG K 92 " --> pdb=" O GLU K 88 " (cutoff:3.500A) Processing helix chain 'K' and resid 111 through 125 Processing helix chain 'K' and resid 157 through 167 Processing helix chain 'K' and resid 180 through 185 removed outlier: 3.524A pdb=" N MET K 184 " --> pdb=" O THR K 180 " (cutoff:3.500A) Processing helix chain 'K' and resid 203 through 205 No H-bonds generated for 'chain 'K' and resid 203 through 205' Processing helix chain 'K' and resid 252 through 257 Processing helix chain 'K' and resid 335 through 342 Processing helix chain 'K' and resid 344 through 348 Processing helix chain 'K' and resid 351 through 363 Processing helix chain 'K' and resid 380 through 382 No H-bonds generated for 'chain 'K' and resid 380 through 382' Processing helix chain 'K' and resid 383 through 403 Processing helix chain 'L' and resid 13 through 22 removed outlier: 3.975A pdb=" N ALA L 17 " --> pdb=" O ALA L 13 " (cutoff:3.500A) Processing helix chain 'L' and resid 38 through 54 removed outlier: 3.802A pdb=" N ALA L 42 " --> pdb=" O ALA L 38 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N PHE L 43 " --> pdb=" O ASN L 39 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ILE L 48 " --> pdb=" O SER L 44 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LYS L 49 " --> pdb=" O HIS L 45 " (cutoff:3.500A) Processing helix chain 'L' and resid 88 through 102 removed outlier: 3.610A pdb=" N ARG L 92 " --> pdb=" O GLU L 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 111 through 125 Processing helix chain 'L' and resid 157 through 167 removed outlier: 3.519A pdb=" N ILE L 167 " --> pdb=" O TYR L 163 " (cutoff:3.500A) Processing helix chain 'L' and resid 180 through 185 Processing helix chain 'L' and resid 203 through 205 No H-bonds generated for 'chain 'L' and resid 203 through 205' Processing helix chain 'L' and resid 252 through 257 Processing helix chain 'L' and resid 335 through 342 Processing helix chain 'L' and resid 344 through 348 Processing helix chain 'L' and resid 351 through 363 Processing helix chain 'L' and resid 380 through 382 No H-bonds generated for 'chain 'L' and resid 380 through 382' Processing helix chain 'L' and resid 383 through 403 Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 6 Processing sheet with id=AA2, first strand: chain 'A' and resid 133 through 134 removed outlier: 8.777A pdb=" N CYS A 134 " --> pdb=" O TYR A 78 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N CYS A 80 " --> pdb=" O CYS A 134 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ILE A 61 " --> pdb=" O HIS A 79 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N VAL A 81 " --> pdb=" O ILE A 61 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ASP A 63 " --> pdb=" O VAL A 81 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE A 149 " --> pdb=" O LEU A 62 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N GLN A 151 " --> pdb=" O ILE A 64 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N TYR A 285 " --> pdb=" O SER A 281 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N SER A 281 " --> pdb=" O TYR A 285 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N VAL A 287 " --> pdb=" O VAL A 279 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 246 through 251 removed outlier: 3.621A pdb=" N THR A 197 " --> pdb=" O TYR A 192 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ALA A 189 " --> pdb=" O CYS A 331 " (cutoff:3.500A) removed outlier: 9.247A pdb=" N TYR A 333 " --> pdb=" O ALA A 189 " (cutoff:3.500A) removed outlier: 8.446A pdb=" N ALA A 191 " --> pdb=" O TYR A 333 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 303 through 308 removed outlier: 3.906A pdb=" N THR A 437 " --> pdb=" O HIS A 308 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 4 through 6 removed outlier: 5.991A pdb=" N VAL B 4 " --> pdb=" O GLU B 28 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 133 through 134 removed outlier: 8.857A pdb=" N CYS B 134 " --> pdb=" O TYR B 78 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N CYS B 80 " --> pdb=" O CYS B 134 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ILE B 61 " --> pdb=" O HIS B 79 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N VAL B 81 " --> pdb=" O ILE B 61 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ASP B 63 " --> pdb=" O VAL B 81 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N VAL B 147 " --> pdb=" O THR B 60 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE B 64 " --> pdb=" O ILE B 149 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N GLN B 151 " --> pdb=" O ILE B 64 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ALA B 148 " --> pdb=" O TYR B 174 " (cutoff:3.500A) removed outlier: 8.508A pdb=" N VAL B 176 " --> pdb=" O ALA B 148 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N TYR B 150 " --> pdb=" O VAL B 176 " (cutoff:3.500A) removed outlier: 9.050A pdb=" N PHE B 178 " --> pdb=" O TYR B 150 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL B 280 " --> pdb=" O VAL B 287 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ARG B 289 " --> pdb=" O THR B 278 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N THR B 278 " --> pdb=" O ARG B 289 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N THR B 291 " --> pdb=" O CYS B 276 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N CYS B 276 " --> pdb=" O THR B 291 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N SER B 293 " --> pdb=" O CYS B 274 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N CYS B 274 " --> pdb=" O SER B 293 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 246 through 251 removed outlier: 3.615A pdb=" N THR B 197 " --> pdb=" O TYR B 192 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N ALA B 189 " --> pdb=" O CYS B 331 " (cutoff:3.500A) removed outlier: 9.259A pdb=" N TYR B 333 " --> pdb=" O ALA B 189 " (cutoff:3.500A) removed outlier: 8.436A pdb=" N ALA B 191 " --> pdb=" O TYR B 333 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 303 through 308 removed outlier: 3.910A pdb=" N THR B 437 " --> pdb=" O HIS B 308 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 4 through 6 removed outlier: 5.979A pdb=" N VAL C 4 " --> pdb=" O GLU C 28 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'C' and resid 133 through 134 removed outlier: 8.831A pdb=" N CYS C 134 " --> pdb=" O TYR C 78 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N CYS C 80 " --> pdb=" O CYS C 134 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ILE C 61 " --> pdb=" O HIS C 79 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N VAL C 81 " --> pdb=" O ILE C 61 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ASP C 63 " --> pdb=" O VAL C 81 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N GLN C 151 " --> pdb=" O ILE C 64 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N TYR C 285 " --> pdb=" O SER C 281 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N SER C 281 " --> pdb=" O TYR C 285 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N VAL C 287 " --> pdb=" O VAL C 279 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 246 through 251 removed outlier: 3.594A pdb=" N THR C 197 " --> pdb=" O TYR C 192 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N ALA C 189 " --> pdb=" O CYS C 331 " (cutoff:3.500A) removed outlier: 9.251A pdb=" N TYR C 333 " --> pdb=" O ALA C 189 " (cutoff:3.500A) removed outlier: 8.435A pdb=" N ALA C 191 " --> pdb=" O TYR C 333 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 303 through 308 removed outlier: 3.866A pdb=" N THR C 437 " --> pdb=" O HIS C 308 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 3 through 6 Processing sheet with id=AB5, first strand: chain 'D' and resid 133 through 134 removed outlier: 8.798A pdb=" N CYS D 134 " --> pdb=" O TYR D 78 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N CYS D 80 " --> pdb=" O CYS D 134 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ILE D 61 " --> pdb=" O HIS D 79 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N VAL D 81 " --> pdb=" O ILE D 61 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ASP D 63 " --> pdb=" O VAL D 81 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE D 149 " --> pdb=" O LEU D 62 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N GLN D 151 " --> pdb=" O ILE D 64 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N TYR D 285 " --> pdb=" O SER D 281 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N SER D 281 " --> pdb=" O TYR D 285 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N VAL D 287 " --> pdb=" O VAL D 279 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 246 through 251 removed outlier: 3.625A pdb=" N THR D 197 " --> pdb=" O TYR D 192 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N ALA D 189 " --> pdb=" O CYS D 331 " (cutoff:3.500A) removed outlier: 9.249A pdb=" N TYR D 333 " --> pdb=" O ALA D 189 " (cutoff:3.500A) removed outlier: 8.452A pdb=" N ALA D 191 " --> pdb=" O TYR D 333 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 303 through 308 removed outlier: 3.905A pdb=" N THR D 437 " --> pdb=" O HIS D 308 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 4 through 6 removed outlier: 6.055A pdb=" N VAL E 4 " --> pdb=" O GLU E 28 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'E' and resid 133 through 134 removed outlier: 8.827A pdb=" N CYS E 134 " --> pdb=" O TYR E 78 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N CYS E 80 " --> pdb=" O CYS E 134 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ILE E 61 " --> pdb=" O HIS E 79 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N VAL E 81 " --> pdb=" O ILE E 61 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ASP E 63 " --> pdb=" O VAL E 81 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL E 147 " --> pdb=" O THR E 60 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE E 64 " --> pdb=" O ILE E 149 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N GLN E 151 " --> pdb=" O ILE E 64 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VAL E 280 " --> pdb=" O VAL E 287 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ARG E 289 " --> pdb=" O THR E 278 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N THR E 278 " --> pdb=" O ARG E 289 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N THR E 291 " --> pdb=" O CYS E 276 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N CYS E 276 " --> pdb=" O THR E 291 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N SER E 293 " --> pdb=" O CYS E 274 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N CYS E 274 " --> pdb=" O SER E 293 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 246 through 251 removed outlier: 3.621A pdb=" N THR E 197 " --> pdb=" O TYR E 192 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ALA E 189 " --> pdb=" O CYS E 331 " (cutoff:3.500A) removed outlier: 9.258A pdb=" N TYR E 333 " --> pdb=" O ALA E 189 " (cutoff:3.500A) removed outlier: 8.435A pdb=" N ALA E 191 " --> pdb=" O TYR E 333 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 303 through 308 removed outlier: 3.916A pdb=" N THR E 437 " --> pdb=" O HIS E 308 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 3 through 6 Processing sheet with id=AC4, first strand: chain 'F' and resid 133 through 134 removed outlier: 8.807A pdb=" N CYS F 134 " --> pdb=" O TYR F 78 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N CYS F 80 " --> pdb=" O CYS F 134 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ILE F 61 " --> pdb=" O HIS F 79 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N VAL F 81 " --> pdb=" O ILE F 61 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ASP F 63 " --> pdb=" O VAL F 81 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE F 149 " --> pdb=" O LEU F 62 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N GLN F 151 " --> pdb=" O ILE F 64 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ALA F 148 " --> pdb=" O TYR F 174 " (cutoff:3.500A) removed outlier: 8.581A pdb=" N VAL F 176 " --> pdb=" O ALA F 148 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N TYR F 150 " --> pdb=" O VAL F 176 " (cutoff:3.500A) removed outlier: 9.056A pdb=" N PHE F 178 " --> pdb=" O TYR F 150 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N TYR F 285 " --> pdb=" O SER F 281 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N SER F 281 " --> pdb=" O TYR F 285 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N VAL F 287 " --> pdb=" O VAL F 279 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 246 through 251 removed outlier: 3.591A pdb=" N THR F 197 " --> pdb=" O TYR F 192 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ALA F 189 " --> pdb=" O CYS F 331 " (cutoff:3.500A) removed outlier: 9.256A pdb=" N TYR F 333 " --> pdb=" O ALA F 189 " (cutoff:3.500A) removed outlier: 8.447A pdb=" N ALA F 191 " --> pdb=" O TYR F 333 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 303 through 308 removed outlier: 3.870A pdb=" N THR F 437 " --> pdb=" O HIS F 308 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 4 through 6 removed outlier: 5.970A pdb=" N VAL G 4 " --> pdb=" O GLU G 28 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'G' and resid 133 through 134 removed outlier: 8.788A pdb=" N CYS G 134 " --> pdb=" O TYR G 78 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N CYS G 80 " --> pdb=" O CYS G 134 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ILE G 61 " --> pdb=" O HIS G 79 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N VAL G 81 " --> pdb=" O ILE G 61 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ASP G 63 " --> pdb=" O VAL G 81 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE G 149 " --> pdb=" O LEU G 62 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N GLN G 151 " --> pdb=" O ILE G 64 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL G 280 " --> pdb=" O VAL G 287 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ARG G 289 " --> pdb=" O THR G 278 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N THR G 278 " --> pdb=" O ARG G 289 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N THR G 291 " --> pdb=" O CYS G 276 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N CYS G 276 " --> pdb=" O THR G 291 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N SER G 293 " --> pdb=" O CYS G 274 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N CYS G 274 " --> pdb=" O SER G 293 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 246 through 251 removed outlier: 3.621A pdb=" N THR G 197 " --> pdb=" O TYR G 192 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ALA G 189 " --> pdb=" O CYS G 331 " (cutoff:3.500A) removed outlier: 9.250A pdb=" N TYR G 333 " --> pdb=" O ALA G 189 " (cutoff:3.500A) removed outlier: 8.452A pdb=" N ALA G 191 " --> pdb=" O TYR G 333 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 303 through 308 removed outlier: 3.904A pdb=" N THR G 437 " --> pdb=" O HIS G 308 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AD3, first strand: chain 'H' and resid 133 through 134 removed outlier: 8.770A pdb=" N CYS H 134 " --> pdb=" O TYR H 78 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N CYS H 80 " --> pdb=" O CYS H 134 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ILE H 61 " --> pdb=" O HIS H 79 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N VAL H 81 " --> pdb=" O ILE H 61 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ASP H 63 " --> pdb=" O VAL H 81 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL H 147 " --> pdb=" O THR H 60 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE H 64 " --> pdb=" O ILE H 149 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N GLN H 151 " --> pdb=" O ILE H 64 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL H 280 " --> pdb=" O VAL H 287 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ARG H 289 " --> pdb=" O THR H 278 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N THR H 278 " --> pdb=" O ARG H 289 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N THR H 291 " --> pdb=" O CYS H 276 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N CYS H 276 " --> pdb=" O THR H 291 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N SER H 293 " --> pdb=" O CYS H 274 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N CYS H 274 " --> pdb=" O SER H 293 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 246 through 251 removed outlier: 3.623A pdb=" N THR H 197 " --> pdb=" O TYR H 192 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N ALA H 189 " --> pdb=" O CYS H 331 " (cutoff:3.500A) removed outlier: 9.267A pdb=" N TYR H 333 " --> pdb=" O ALA H 189 " (cutoff:3.500A) removed outlier: 8.448A pdb=" N ALA H 191 " --> pdb=" O TYR H 333 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 303 through 308 removed outlier: 3.911A pdb=" N THR H 437 " --> pdb=" O HIS H 308 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 3 through 6 Processing sheet with id=AD7, first strand: chain 'I' and resid 133 through 134 removed outlier: 8.774A pdb=" N CYS I 134 " --> pdb=" O TYR I 78 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N CYS I 80 " --> pdb=" O CYS I 134 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ILE I 61 " --> pdb=" O HIS I 79 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N VAL I 81 " --> pdb=" O ILE I 61 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ASP I 63 " --> pdb=" O VAL I 81 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N GLN I 151 " --> pdb=" O ILE I 64 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N TYR I 285 " --> pdb=" O SER I 281 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N SER I 281 " --> pdb=" O TYR I 285 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N VAL I 287 " --> pdb=" O VAL I 279 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 246 through 251 removed outlier: 3.594A pdb=" N THR I 197 " --> pdb=" O TYR I 192 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ALA I 189 " --> pdb=" O CYS I 331 " (cutoff:3.500A) removed outlier: 9.251A pdb=" N TYR I 333 " --> pdb=" O ALA I 189 " (cutoff:3.500A) removed outlier: 8.438A pdb=" N ALA I 191 " --> pdb=" O TYR I 333 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 303 through 308 removed outlier: 3.866A pdb=" N THR I 437 " --> pdb=" O HIS I 308 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 3 through 6 Processing sheet with id=AE2, first strand: chain 'J' and resid 133 through 134 removed outlier: 8.751A pdb=" N CYS J 134 " --> pdb=" O TYR J 78 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N CYS J 80 " --> pdb=" O CYS J 134 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ILE J 61 " --> pdb=" O HIS J 79 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N VAL J 81 " --> pdb=" O ILE J 61 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ASP J 63 " --> pdb=" O VAL J 81 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N GLN J 151 " --> pdb=" O ILE J 64 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N VAL J 280 " --> pdb=" O VAL J 287 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ARG J 289 " --> pdb=" O THR J 278 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N THR J 278 " --> pdb=" O ARG J 289 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N THR J 291 " --> pdb=" O CYS J 276 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N CYS J 276 " --> pdb=" O THR J 291 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N SER J 293 " --> pdb=" O CYS J 274 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N CYS J 274 " --> pdb=" O SER J 293 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 246 through 251 removed outlier: 3.618A pdb=" N THR J 197 " --> pdb=" O TYR J 192 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ALA J 189 " --> pdb=" O CYS J 331 " (cutoff:3.500A) removed outlier: 9.247A pdb=" N TYR J 333 " --> pdb=" O ALA J 189 " (cutoff:3.500A) removed outlier: 8.446A pdb=" N ALA J 191 " --> pdb=" O TYR J 333 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 303 through 308 removed outlier: 3.904A pdb=" N THR J 437 " --> pdb=" O HIS J 308 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'K' and resid 4 through 6 removed outlier: 5.997A pdb=" N VAL K 4 " --> pdb=" O GLU K 28 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'K' and resid 133 through 134 removed outlier: 8.787A pdb=" N CYS K 134 " --> pdb=" O TYR K 78 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N CYS K 80 " --> pdb=" O CYS K 134 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ILE K 61 " --> pdb=" O HIS K 79 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N VAL K 81 " --> pdb=" O ILE K 61 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ASP K 63 " --> pdb=" O VAL K 81 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VAL K 147 " --> pdb=" O THR K 60 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE K 64 " --> pdb=" O ILE K 149 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N GLN K 151 " --> pdb=" O ILE K 64 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ALA K 148 " --> pdb=" O TYR K 174 " (cutoff:3.500A) removed outlier: 8.509A pdb=" N VAL K 176 " --> pdb=" O ALA K 148 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N TYR K 150 " --> pdb=" O VAL K 176 " (cutoff:3.500A) removed outlier: 9.047A pdb=" N PHE K 178 " --> pdb=" O TYR K 150 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N TYR K 285 " --> pdb=" O SER K 281 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N SER K 281 " --> pdb=" O TYR K 285 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N VAL K 287 " --> pdb=" O VAL K 279 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'K' and resid 246 through 251 removed outlier: 3.615A pdb=" N THR K 197 " --> pdb=" O TYR K 192 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ALA K 189 " --> pdb=" O CYS K 331 " (cutoff:3.500A) removed outlier: 9.248A pdb=" N TYR K 333 " --> pdb=" O ALA K 189 " (cutoff:3.500A) removed outlier: 8.425A pdb=" N ALA K 191 " --> pdb=" O TYR K 333 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'K' and resid 303 through 308 removed outlier: 3.906A pdb=" N THR K 437 " --> pdb=" O HIS K 308 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'L' and resid 3 through 6 Processing sheet with id=AF1, first strand: chain 'L' and resid 133 through 134 removed outlier: 8.788A pdb=" N CYS L 134 " --> pdb=" O TYR L 78 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N CYS L 80 " --> pdb=" O CYS L 134 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ILE L 61 " --> pdb=" O HIS L 79 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N VAL L 81 " --> pdb=" O ILE L 61 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ASP L 63 " --> pdb=" O VAL L 81 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N GLN L 151 " --> pdb=" O ILE L 64 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N TYR L 285 " --> pdb=" O SER L 281 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N SER L 281 " --> pdb=" O TYR L 285 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N VAL L 287 " --> pdb=" O VAL L 279 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'L' and resid 246 through 251 removed outlier: 3.593A pdb=" N THR L 197 " --> pdb=" O TYR L 192 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ALA L 189 " --> pdb=" O CYS L 331 " (cutoff:3.500A) removed outlier: 9.250A pdb=" N TYR L 333 " --> pdb=" O ALA L 189 " (cutoff:3.500A) removed outlier: 8.438A pdb=" N ALA L 191 " --> pdb=" O TYR L 333 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'L' and resid 303 through 308 removed outlier: 3.867A pdb=" N THR L 437 " --> pdb=" O HIS L 308 " (cutoff:3.500A) 1624 hydrogen bonds defined for protein. 4677 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: 8.38 Time building geometry restraints manager: 4.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 10608 1.33 - 1.45: 6901 1.45 - 1.57: 22523 1.57 - 1.69: 60 1.69 - 1.81: 480 Bond restraints: 40572 Sorted by residual: bond pdb=" C10 7XQ B1002 " pdb=" C11 7XQ B1002 " ideal model delta sigma weight residual 1.536 1.338 0.198 2.00e-02 2.50e+03 9.80e+01 bond pdb=" C10 7XQ C1002 " pdb=" C11 7XQ C1002 " ideal model delta sigma weight residual 1.536 1.338 0.198 2.00e-02 2.50e+03 9.80e+01 bond pdb=" C10 7XQ I1002 " pdb=" C11 7XQ I1002 " ideal model delta sigma weight residual 1.536 1.338 0.198 2.00e-02 2.50e+03 9.80e+01 bond pdb=" C10 7XQ D1002 " pdb=" C11 7XQ D1002 " ideal model delta sigma weight residual 1.536 1.338 0.198 2.00e-02 2.50e+03 9.77e+01 bond pdb=" C10 7XQ F1002 " pdb=" C11 7XQ F1002 " ideal model delta sigma weight residual 1.536 1.338 0.198 2.00e-02 2.50e+03 9.77e+01 ... (remaining 40567 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.60: 52929 1.60 - 3.19: 1713 3.19 - 4.79: 239 4.79 - 6.39: 88 6.39 - 7.98: 27 Bond angle restraints: 54996 Sorted by residual: angle pdb=" C MET D 383 " pdb=" N ILE D 384 " pdb=" CA ILE D 384 " ideal model delta sigma weight residual 120.33 123.75 -3.42 8.00e-01 1.56e+00 1.83e+01 angle pdb=" C MET G 383 " pdb=" N ILE G 384 " pdb=" CA ILE G 384 " ideal model delta sigma weight residual 120.33 123.71 -3.38 8.00e-01 1.56e+00 1.79e+01 angle pdb=" C MET J 383 " pdb=" N ILE J 384 " pdb=" CA ILE J 384 " ideal model delta sigma weight residual 120.33 123.65 -3.32 8.00e-01 1.56e+00 1.72e+01 angle pdb=" C MET A 383 " pdb=" N ILE A 384 " pdb=" CA ILE A 384 " ideal model delta sigma weight residual 120.33 123.44 -3.11 8.00e-01 1.56e+00 1.52e+01 angle pdb=" C MET B 383 " pdb=" N ILE B 384 " pdb=" CA ILE B 384 " ideal model delta sigma weight residual 120.33 123.35 -3.02 8.00e-01 1.56e+00 1.42e+01 ... (remaining 54991 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.68: 22256 17.68 - 35.37: 2090 35.37 - 53.05: 423 53.05 - 70.73: 42 70.73 - 88.42: 29 Dihedral angle restraints: 24840 sinusoidal: 9996 harmonic: 14844 Sorted by residual: dihedral pdb=" CA GLY I 298 " pdb=" C GLY I 298 " pdb=" N LYS I 299 " pdb=" CA LYS I 299 " ideal model delta harmonic sigma weight residual 180.00 -161.37 -18.63 0 5.00e+00 4.00e-02 1.39e+01 dihedral pdb=" CA GLY J 298 " pdb=" C GLY J 298 " pdb=" N LYS J 299 " pdb=" CA LYS J 299 " ideal model delta harmonic sigma weight residual 180.00 -161.75 -18.25 0 5.00e+00 4.00e-02 1.33e+01 dihedral pdb=" CA GLY C 298 " pdb=" C GLY C 298 " pdb=" N LYS C 299 " pdb=" CA LYS C 299 " ideal model delta harmonic sigma weight residual 180.00 -162.05 -17.95 0 5.00e+00 4.00e-02 1.29e+01 ... (remaining 24837 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 4909 0.053 - 0.106: 1054 0.106 - 0.160: 193 0.160 - 0.213: 12 0.213 - 0.266: 24 Chirality restraints: 6192 Sorted by residual: chirality pdb=" C15 7XQ B1002 " pdb=" C13 7XQ B1002 " pdb=" C16 7XQ B1002 " pdb=" C19 7XQ B1002 " both_signs ideal model delta sigma weight residual False -2.47 -2.73 0.27 2.00e-01 2.50e+01 1.77e+00 chirality pdb=" C15 7XQ K1002 " pdb=" C13 7XQ K1002 " pdb=" C16 7XQ K1002 " pdb=" C19 7XQ K1002 " both_signs ideal model delta sigma weight residual False -2.47 -2.73 0.27 2.00e-01 2.50e+01 1.77e+00 chirality pdb=" C15 7XQ D1002 " pdb=" C13 7XQ D1002 " pdb=" C16 7XQ D1002 " pdb=" C19 7XQ D1002 " both_signs ideal model delta sigma weight residual False -2.47 -2.73 0.27 2.00e-01 2.50e+01 1.76e+00 ... (remaining 6189 not shown) Planarity restraints: 7032 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 130 " -0.046 5.00e-02 4.00e+02 6.95e-02 7.72e+00 pdb=" N PRO A 131 " 0.120 5.00e-02 4.00e+02 pdb=" CA PRO A 131 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 131 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR D 130 " -0.046 5.00e-02 4.00e+02 6.94e-02 7.70e+00 pdb=" N PRO D 131 " 0.120 5.00e-02 4.00e+02 pdb=" CA PRO D 131 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO D 131 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR F 130 " 0.045 5.00e-02 4.00e+02 6.89e-02 7.59e+00 pdb=" N PRO F 131 " -0.119 5.00e-02 4.00e+02 pdb=" CA PRO F 131 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO F 131 " 0.038 5.00e-02 4.00e+02 ... (remaining 7029 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 6048 2.77 - 3.31: 34133 3.31 - 3.84: 61780 3.84 - 4.37: 73312 4.37 - 4.90: 129599 Nonbonded interactions: 304872 Sorted by model distance: nonbonded pdb=" OE2 GLU L 52 " pdb=" OH TYR L 78 " model vdw 2.242 3.040 nonbonded pdb=" OE2 GLU E 353 " pdb=" NH1 ARG F 399 " model vdw 2.245 3.120 nonbonded pdb=" OD1 ASN C 95 " pdb=" NZ LYS C 99 " model vdw 2.250 3.120 nonbonded pdb=" OE2 GLU I 52 " pdb=" OH TYR I 78 " model vdw 2.253 3.040 nonbonded pdb=" OE2 GLU F 52 " pdb=" OH TYR F 78 " model vdw 2.255 3.040 ... (remaining 304867 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: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 235 or resid 237 through 1002)) selection = (chain 'B' and (resid 2 through 235 or resid 237 through 1002)) selection = (chain 'C' and (resid 2 through 235 or resid 237 through 1002)) selection = (chain 'D' and (resid 2 through 235 or resid 237 through 1002)) selection = (chain 'E' and (resid 2 through 235 or resid 237 through 1002)) selection = (chain 'F' and (resid 2 through 235 or resid 237 through 1002)) selection = (chain 'G' and (resid 2 through 235 or resid 237 through 1002)) selection = (chain 'H' and (resid 2 through 235 or resid 237 through 1002)) selection = (chain 'I' and (resid 2 through 235 or resid 237 through 1002)) selection = (chain 'J' and (resid 2 through 235 or resid 237 through 1002)) selection = (chain 'K' and (resid 2 through 235 or resid 237 through 1002)) selection = (chain 'L' and (resid 2 through 235 or resid 237 through 1002)) } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.460 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: 0.670 Check model and map are aligned: 0.100 Set scattering table: 0.110 Process input model: 48.450 Find NCS groups from input model: 1.180 Set up NCS constraints: 0.150 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:9.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 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 : 0.007 0.198 40608 Z= 0.359 Angle : 0.692 7.982 54996 Z= 0.387 Chirality : 0.047 0.266 6192 Planarity : 0.005 0.069 7032 Dihedral : 14.007 88.418 15240 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 0.00 % Allowed : 0.05 % Favored : 99.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.67 (0.12), residues: 4992 helix: 1.23 (0.15), residues: 1416 sheet: 0.20 (0.14), residues: 1272 loop : -1.97 (0.11), residues: 2304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 20 TYR 0.017 0.001 TYR D 297 PHE 0.016 0.002 PHE B 25 TRP 0.010 0.001 TRP H 394 HIS 0.010 0.001 HIS F 45 Details of bonding type rmsd covalent geometry : bond 0.00710 (40572) covalent geometry : angle 0.69214 (54996) hydrogen bonds : bond 0.18460 ( 1624) hydrogen bonds : angle 5.42893 ( 4677) metal coordination : bond 0.00154 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9984 Ramachandran restraints generated. 4992 Oldfield, 0 Emsley, 4992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9984 Ramachandran restraints generated. 4992 Oldfield, 0 Emsley, 4992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 556 residues out of total 4308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 556 time to evaluate : 1.268 Fit side-chains REVERT: A 123 MET cc_start: 0.6304 (mmp) cc_final: 0.5849 (mpm) REVERT: B 30 ARG cc_start: 0.5903 (ttp80) cc_final: 0.5616 (ttp80) REVERT: B 123 MET cc_start: 0.6181 (mmp) cc_final: 0.5689 (mpm) REVERT: C 30 ARG cc_start: 0.5885 (tmm-80) cc_final: 0.5290 (ttp80) REVERT: C 73 MET cc_start: 0.6942 (mmm) cc_final: 0.6681 (mmm) REVERT: D 123 MET cc_start: 0.6248 (mmp) cc_final: 0.5785 (mpm) REVERT: E 30 ARG cc_start: 0.5704 (ttp80) cc_final: 0.5428 (tmm-80) REVERT: E 123 MET cc_start: 0.6191 (mmp) cc_final: 0.5690 (mpm) REVERT: F 91 GLU cc_start: 0.7360 (mp0) cc_final: 0.7072 (mp0) REVERT: G 123 MET cc_start: 0.6308 (mmp) cc_final: 0.5821 (mpm) REVERT: H 30 ARG cc_start: 0.5914 (ttp80) cc_final: 0.5548 (ttp80) REVERT: H 123 MET cc_start: 0.6236 (mmp) cc_final: 0.5700 (mpm) REVERT: I 30 ARG cc_start: 0.5892 (tmm-80) cc_final: 0.5149 (tmm-80) REVERT: I 91 GLU cc_start: 0.7322 (mp0) cc_final: 0.7067 (mp0) REVERT: K 123 MET cc_start: 0.6220 (mmp) cc_final: 0.5728 (mpm) REVERT: L 30 ARG cc_start: 0.5818 (tmm-80) cc_final: 0.5211 (tmm-80) REVERT: L 91 GLU cc_start: 0.7458 (mp0) cc_final: 0.7247 (mp0) outliers start: 0 outliers final: 0 residues processed: 556 average time/residue: 0.8614 time to fit residues: 559.7476 Evaluate side-chains 385 residues out of total 4308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 385 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 432 optimal weight: 8.9990 chunk 197 optimal weight: 4.9990 chunk 388 optimal weight: 0.7980 chunk 455 optimal weight: 0.5980 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 0.6980 chunk 132 optimal weight: 3.9990 chunk 494 optimal weight: 0.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 3.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 HIS C 45 HIS D 37 HIS D 45 HIS G 37 HIS G 45 HIS G 389 GLN H 95 ASN J 37 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.163886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.120509 restraints weight = 136869.014| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 3.35 r_work: 0.3038 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3022 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3022 r_free = 0.3022 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3022 r_free = 0.3022 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3022 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.1136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 40608 Z= 0.143 Angle : 0.622 7.189 54996 Z= 0.331 Chirality : 0.046 0.139 6192 Planarity : 0.005 0.066 7032 Dihedral : 5.586 53.997 5856 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 1.17 % Allowed : 7.63 % Favored : 91.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.64 (0.12), residues: 4992 helix: 1.50 (0.15), residues: 1452 sheet: 0.16 (0.15), residues: 1080 loop : -1.99 (0.11), residues: 2460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG K 222 TYR 0.015 0.001 TYR A 297 PHE 0.017 0.002 PHE L 183 TRP 0.009 0.001 TRP A 175 HIS 0.009 0.001 HIS D 37 Details of bonding type rmsd covalent geometry : bond 0.00309 (40572) covalent geometry : angle 0.62234 (54996) hydrogen bonds : bond 0.06026 ( 1624) hydrogen bonds : angle 4.67651 ( 4677) metal coordination : bond 0.00345 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9984 Ramachandran restraints generated. 4992 Oldfield, 0 Emsley, 4992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9984 Ramachandran restraints generated. 4992 Oldfield, 0 Emsley, 4992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 4308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 387 time to evaluate : 1.067 Fit side-chains REVERT: A 123 MET cc_start: 0.6310 (mmp) cc_final: 0.5883 (mpm) REVERT: B 91 GLU cc_start: 0.7199 (mp0) cc_final: 0.6915 (mp0) REVERT: B 123 MET cc_start: 0.6189 (mmp) cc_final: 0.5690 (mpm) REVERT: C 30 ARG cc_start: 0.5695 (tmm-80) cc_final: 0.4923 (ttp80) REVERT: C 78 TYR cc_start: 0.8224 (m-80) cc_final: 0.7929 (m-80) REVERT: C 95 ASN cc_start: 0.8167 (t0) cc_final: 0.7493 (t0) REVERT: C 99 LYS cc_start: 0.7264 (mptp) cc_final: 0.6655 (mptp) REVERT: C 165 GLN cc_start: 0.7876 (OUTLIER) cc_final: 0.7362 (tp40) REVERT: D 26 GLU cc_start: 0.6174 (mt-10) cc_final: 0.5475 (pt0) REVERT: D 53 GLN cc_start: 0.7735 (tm-30) cc_final: 0.7527 (tm-30) REVERT: D 95 ASN cc_start: 0.8190 (t0) cc_final: 0.7893 (t0) REVERT: D 99 LYS cc_start: 0.7367 (OUTLIER) cc_final: 0.6817 (mptp) REVERT: D 123 MET cc_start: 0.6261 (mmp) cc_final: 0.5830 (mpm) REVERT: E 30 ARG cc_start: 0.5627 (ttp80) cc_final: 0.5018 (tmm-80) REVERT: E 95 ASN cc_start: 0.8167 (t0) cc_final: 0.7527 (t0) REVERT: E 123 MET cc_start: 0.6215 (mmp) cc_final: 0.5702 (mpm) REVERT: F 91 GLU cc_start: 0.7224 (mp0) cc_final: 0.6878 (mp0) REVERT: F 165 GLN cc_start: 0.7856 (OUTLIER) cc_final: 0.7316 (tp40) REVERT: G 73 MET cc_start: 0.7394 (tpp) cc_final: 0.6922 (mmm) REVERT: G 99 LYS cc_start: 0.7033 (mptp) cc_final: 0.6693 (mptp) REVERT: G 123 MET cc_start: 0.6374 (mmp) cc_final: 0.5924 (mpm) REVERT: H 95 ASN cc_start: 0.8108 (t0) cc_final: 0.7862 (t0) REVERT: H 123 MET cc_start: 0.6258 (mmp) cc_final: 0.5791 (mpm) REVERT: I 30 ARG cc_start: 0.5634 (tmm-80) cc_final: 0.4801 (tmm-80) REVERT: I 91 GLU cc_start: 0.7227 (mp0) cc_final: 0.6925 (mp0) REVERT: I 165 GLN cc_start: 0.7850 (OUTLIER) cc_final: 0.7399 (tp40) REVERT: J 99 LYS cc_start: 0.7066 (mptp) cc_final: 0.6686 (mptp) REVERT: K 15 LEU cc_start: 0.7520 (tt) cc_final: 0.7208 (tm) REVERT: K 123 MET cc_start: 0.6199 (mmp) cc_final: 0.5748 (mpm) REVERT: L 30 ARG cc_start: 0.5650 (tmm-80) cc_final: 0.4842 (tmm-80) REVERT: L 99 LYS cc_start: 0.7280 (mptp) cc_final: 0.6888 (mttp) REVERT: L 165 GLN cc_start: 0.7867 (OUTLIER) cc_final: 0.7420 (tp40) outliers start: 50 outliers final: 7 residues processed: 414 average time/residue: 0.7384 time to fit residues: 365.0037 Evaluate side-chains 374 residues out of total 4308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 362 time to evaluate : 1.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain C residue 165 GLN Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 99 LYS Chi-restraints excluded: chain F residue 165 GLN Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain I residue 165 GLN Chi-restraints excluded: chain J residue 15 LEU Chi-restraints excluded: chain J residue 45 HIS Chi-restraints excluded: chain L residue 165 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 299 optimal weight: 10.0000 chunk 153 optimal weight: 4.9990 chunk 50 optimal weight: 10.0000 chunk 79 optimal weight: 0.6980 chunk 185 optimal weight: 4.9990 chunk 44 optimal weight: 0.0980 chunk 22 optimal weight: 10.0000 chunk 275 optimal weight: 6.9990 chunk 400 optimal weight: 9.9990 chunk 162 optimal weight: 0.0980 chunk 357 optimal weight: 5.9990 overall best weight: 2.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 45 HIS D 45 HIS G 45 HIS I 37 HIS K 45 HIS L 37 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.162286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.117087 restraints weight = 121532.999| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 3.20 r_work: 0.3014 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3000 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3000 r_free = 0.3000 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3000 r_free = 0.3000 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3000 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.1400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 40608 Z= 0.173 Angle : 0.659 8.321 54996 Z= 0.353 Chirality : 0.048 0.150 6192 Planarity : 0.005 0.065 7032 Dihedral : 5.726 59.921 5856 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 1.43 % Allowed : 8.59 % Favored : 89.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.58 (0.12), residues: 4992 helix: 1.55 (0.15), residues: 1452 sheet: 0.26 (0.16), residues: 1080 loop : -1.98 (0.11), residues: 2460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG K 222 TYR 0.017 0.002 TYR B 297 PHE 0.019 0.002 PHE I 183 TRP 0.010 0.002 TRP H 175 HIS 0.010 0.001 HIS I 37 Details of bonding type rmsd covalent geometry : bond 0.00389 (40572) covalent geometry : angle 0.65875 (54996) hydrogen bonds : bond 0.06663 ( 1624) hydrogen bonds : angle 4.65760 ( 4677) metal coordination : bond 0.00497 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9984 Ramachandran restraints generated. 4992 Oldfield, 0 Emsley, 4992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9984 Ramachandran restraints generated. 4992 Oldfield, 0 Emsley, 4992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 4308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 378 time to evaluate : 1.527 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 99 LYS cc_start: 0.7166 (mptp) cc_final: 0.6842 (mptp) REVERT: A 123 MET cc_start: 0.6346 (mmp) cc_final: 0.5828 (mpm) REVERT: B 30 ARG cc_start: 0.6026 (ttp80) cc_final: 0.5431 (ttp80) REVERT: B 91 GLU cc_start: 0.7204 (mp0) cc_final: 0.6863 (mp0) REVERT: B 95 ASN cc_start: 0.8012 (t0) cc_final: 0.7428 (t0) REVERT: B 99 LYS cc_start: 0.7348 (mmmm) cc_final: 0.6851 (mptp) REVERT: B 123 MET cc_start: 0.6212 (mmp) cc_final: 0.5683 (mpm) REVERT: B 285 TYR cc_start: 0.9016 (OUTLIER) cc_final: 0.7648 (m-80) REVERT: C 30 ARG cc_start: 0.5712 (tmm-80) cc_final: 0.4904 (tmm-80) REVERT: C 95 ASN cc_start: 0.8127 (t0) cc_final: 0.7851 (t0) REVERT: C 99 LYS cc_start: 0.7096 (mptp) cc_final: 0.6661 (mttp) REVERT: C 165 GLN cc_start: 0.7961 (OUTLIER) cc_final: 0.7492 (tp40) REVERT: C 285 TYR cc_start: 0.9011 (OUTLIER) cc_final: 0.7430 (m-80) REVERT: D 53 GLN cc_start: 0.7727 (tm-30) cc_final: 0.7524 (tm-30) REVERT: D 95 ASN cc_start: 0.8159 (t0) cc_final: 0.7883 (t0) REVERT: D 99 LYS cc_start: 0.7268 (OUTLIER) cc_final: 0.6794 (mptp) REVERT: D 123 MET cc_start: 0.6382 (mmp) cc_final: 0.5862 (mpm) REVERT: E 30 ARG cc_start: 0.5829 (ttp80) cc_final: 0.5316 (ttp80) REVERT: E 123 MET cc_start: 0.6220 (mmp) cc_final: 0.5661 (mpm) REVERT: F 91 GLU cc_start: 0.7206 (mp0) cc_final: 0.6804 (mp0) REVERT: F 99 LYS cc_start: 0.7226 (mptp) cc_final: 0.6904 (mttp) REVERT: F 165 GLN cc_start: 0.7902 (OUTLIER) cc_final: 0.7427 (tp40) REVERT: F 285 TYR cc_start: 0.9014 (OUTLIER) cc_final: 0.7441 (m-80) REVERT: G 95 ASN cc_start: 0.8192 (t0) cc_final: 0.7892 (t0) REVERT: G 99 LYS cc_start: 0.6996 (mptp) cc_final: 0.6575 (mptp) REVERT: G 123 MET cc_start: 0.6380 (mmp) cc_final: 0.5843 (mpm) REVERT: H 123 MET cc_start: 0.6184 (mmp) cc_final: 0.5676 (mpm) REVERT: H 232 LYS cc_start: 0.8496 (OUTLIER) cc_final: 0.8223 (mptm) REVERT: I 30 ARG cc_start: 0.5671 (tmm-80) cc_final: 0.4848 (tmm-80) REVERT: I 91 GLU cc_start: 0.7216 (mp0) cc_final: 0.6798 (mp0) REVERT: I 165 GLN cc_start: 0.7908 (OUTLIER) cc_final: 0.7436 (tp40) REVERT: I 221 ARG cc_start: 0.6597 (OUTLIER) cc_final: 0.4838 (ttt180) REVERT: I 285 TYR cc_start: 0.9014 (OUTLIER) cc_final: 0.7504 (m-80) REVERT: K 46 LEU cc_start: 0.8090 (mt) cc_final: 0.7885 (mp) REVERT: K 123 MET cc_start: 0.6100 (mmp) cc_final: 0.5601 (mpm) REVERT: K 285 TYR cc_start: 0.8991 (OUTLIER) cc_final: 0.7732 (m-80) REVERT: L 30 ARG cc_start: 0.5699 (tmm-80) cc_final: 0.4905 (tmm-80) REVERT: L 99 LYS cc_start: 0.7351 (mptp) cc_final: 0.6914 (mttp) REVERT: L 165 GLN cc_start: 0.7913 (OUTLIER) cc_final: 0.7448 (tp40) REVERT: L 221 ARG cc_start: 0.6584 (OUTLIER) cc_final: 0.4788 (ttt180) REVERT: L 285 TYR cc_start: 0.9020 (OUTLIER) cc_final: 0.7497 (m-80) outliers start: 61 outliers final: 15 residues processed: 413 average time/residue: 0.7336 time to fit residues: 362.1087 Evaluate side-chains 398 residues out of total 4308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 369 time to evaluate : 1.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 402 MET Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 285 TYR Chi-restraints excluded: chain C residue 165 GLN Chi-restraints excluded: chain C residue 202 GLU Chi-restraints excluded: chain C residue 285 TYR Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 99 LYS Chi-restraints excluded: chain D residue 402 MET Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 389 GLN Chi-restraints excluded: chain F residue 165 GLN Chi-restraints excluded: chain F residue 285 TYR Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain G residue 402 MET Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain H residue 50 LEU Chi-restraints excluded: chain H residue 232 LYS Chi-restraints excluded: chain I residue 165 GLN Chi-restraints excluded: chain I residue 221 ARG Chi-restraints excluded: chain I residue 285 TYR Chi-restraints excluded: chain J residue 15 LEU Chi-restraints excluded: chain J residue 45 HIS Chi-restraints excluded: chain K residue 285 TYR Chi-restraints excluded: chain L residue 165 GLN Chi-restraints excluded: chain L residue 221 ARG Chi-restraints excluded: chain L residue 285 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 49 optimal weight: 3.9990 chunk 166 optimal weight: 0.0970 chunk 323 optimal weight: 0.7980 chunk 419 optimal weight: 3.9990 chunk 339 optimal weight: 1.9990 chunk 198 optimal weight: 0.9980 chunk 117 optimal weight: 0.6980 chunk 202 optimal weight: 0.0040 chunk 237 optimal weight: 3.9990 chunk 473 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 overall best weight: 0.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 HIS D 45 HIS F 95 ASN F 389 GLN G 45 HIS ** I 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 389 GLN J 95 ASN K 45 HIS L 95 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.166705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.123484 restraints weight = 136498.325| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 3.30 r_work: 0.3093 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3080 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3080 r_free = 0.3080 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3080 r_free = 0.3080 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3080 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.1425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 40608 Z= 0.104 Angle : 0.530 7.593 54996 Z= 0.278 Chirality : 0.043 0.133 6192 Planarity : 0.005 0.061 7032 Dihedral : 5.129 58.264 5856 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.57 % Allowed : 8.99 % Favored : 89.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.28 (0.12), residues: 4992 helix: 1.88 (0.15), residues: 1464 sheet: 0.71 (0.16), residues: 960 loop : -1.91 (0.10), residues: 2568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 222 TYR 0.014 0.001 TYR D 297 PHE 0.015 0.002 PHE D 423 TRP 0.007 0.001 TRP A 175 HIS 0.002 0.001 HIS F 45 Details of bonding type rmsd covalent geometry : bond 0.00219 (40572) covalent geometry : angle 0.52983 (54996) hydrogen bonds : bond 0.04041 ( 1624) hydrogen bonds : angle 4.28096 ( 4677) metal coordination : bond 0.00138 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9984 Ramachandran restraints generated. 4992 Oldfield, 0 Emsley, 4992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9984 Ramachandran restraints generated. 4992 Oldfield, 0 Emsley, 4992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 4308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 392 time to evaluate : 1.631 Fit side-chains REVERT: A 99 LYS cc_start: 0.7149 (OUTLIER) cc_final: 0.6729 (mptp) REVERT: A 123 MET cc_start: 0.6353 (mmp) cc_final: 0.5809 (mpm) REVERT: A 285 TYR cc_start: 0.8882 (OUTLIER) cc_final: 0.7493 (m-80) REVERT: B 30 ARG cc_start: 0.5955 (ttp80) cc_final: 0.5413 (ttp80) REVERT: B 91 GLU cc_start: 0.7160 (mp0) cc_final: 0.6834 (mp0) REVERT: B 95 ASN cc_start: 0.8009 (t0) cc_final: 0.7440 (t0) REVERT: B 99 LYS cc_start: 0.7362 (mmmm) cc_final: 0.6896 (mptp) REVERT: B 123 MET cc_start: 0.6232 (mmp) cc_final: 0.5640 (mpm) REVERT: B 285 TYR cc_start: 0.8924 (OUTLIER) cc_final: 0.7856 (m-80) REVERT: C 30 ARG cc_start: 0.5642 (tmm-80) cc_final: 0.4885 (ttp80) REVERT: C 95 ASN cc_start: 0.8153 (t0) cc_final: 0.7836 (t0) REVERT: C 99 LYS cc_start: 0.7108 (mptp) cc_final: 0.6772 (mttp) REVERT: C 285 TYR cc_start: 0.8909 (OUTLIER) cc_final: 0.7258 (m-80) REVERT: C 396 LYS cc_start: 0.8707 (ttpp) cc_final: 0.8358 (ttpt) REVERT: D 26 GLU cc_start: 0.6294 (mt-10) cc_final: 0.5765 (pt0) REVERT: D 95 ASN cc_start: 0.8139 (t0) cc_final: 0.7771 (t0) REVERT: D 99 LYS cc_start: 0.7219 (mptp) cc_final: 0.6791 (mptp) REVERT: D 123 MET cc_start: 0.6362 (mmp) cc_final: 0.5811 (mpm) REVERT: D 285 TYR cc_start: 0.8873 (OUTLIER) cc_final: 0.7472 (m-80) REVERT: E 15 LEU cc_start: 0.7534 (tt) cc_final: 0.7215 (tm) REVERT: E 30 ARG cc_start: 0.5831 (ttp80) cc_final: 0.5253 (ttp80) REVERT: E 99 LYS cc_start: 0.6873 (mptp) cc_final: 0.6422 (mptp) REVERT: E 123 MET cc_start: 0.6228 (mmp) cc_final: 0.5617 (mpm) REVERT: E 285 TYR cc_start: 0.8914 (OUTLIER) cc_final: 0.7750 (m-80) REVERT: F 30 ARG cc_start: 0.5533 (tmm-80) cc_final: 0.4684 (tmm-80) REVERT: F 91 GLU cc_start: 0.7118 (mp0) cc_final: 0.6710 (mp0) REVERT: F 95 ASN cc_start: 0.8233 (t0) cc_final: 0.8015 (t0) REVERT: F 99 LYS cc_start: 0.7205 (mptp) cc_final: 0.6987 (mttm) REVERT: F 285 TYR cc_start: 0.8924 (OUTLIER) cc_final: 0.7262 (m-80) REVERT: G 99 LYS cc_start: 0.6950 (OUTLIER) cc_final: 0.6537 (mptp) REVERT: G 123 MET cc_start: 0.6464 (mmp) cc_final: 0.5870 (mpm) REVERT: G 285 TYR cc_start: 0.8859 (OUTLIER) cc_final: 0.7657 (m-80) REVERT: H 30 ARG cc_start: 0.5867 (ttp80) cc_final: 0.5294 (ttp80) REVERT: H 123 MET cc_start: 0.6253 (mmp) cc_final: 0.5674 (mpm) REVERT: H 232 LYS cc_start: 0.8477 (OUTLIER) cc_final: 0.8234 (mptm) REVERT: H 285 TYR cc_start: 0.8910 (OUTLIER) cc_final: 0.7738 (m-80) REVERT: H 396 LYS cc_start: 0.8593 (ttpp) cc_final: 0.8334 (ttpt) REVERT: I 30 ARG cc_start: 0.5576 (tmm-80) cc_final: 0.4739 (ttp80) REVERT: I 91 GLU cc_start: 0.7122 (mp0) cc_final: 0.6751 (mp0) REVERT: I 221 ARG cc_start: 0.6447 (OUTLIER) cc_final: 0.4740 (ttt180) REVERT: I 285 TYR cc_start: 0.8904 (OUTLIER) cc_final: 0.7259 (m-80) REVERT: J 99 LYS cc_start: 0.7333 (OUTLIER) cc_final: 0.6932 (mptp) REVERT: J 285 TYR cc_start: 0.8869 (OUTLIER) cc_final: 0.7654 (m-80) REVERT: K 15 LEU cc_start: 0.7537 (tt) cc_final: 0.7207 (tm) REVERT: K 30 ARG cc_start: 0.5569 (tmm-80) cc_final: 0.4797 (ttp80) REVERT: K 123 MET cc_start: 0.6207 (mmp) cc_final: 0.5664 (mpm) REVERT: K 232 LYS cc_start: 0.8452 (OUTLIER) cc_final: 0.8244 (mptm) REVERT: K 396 LYS cc_start: 0.8591 (ttpp) cc_final: 0.8331 (ttpt) REVERT: L 30 ARG cc_start: 0.5655 (tmm-80) cc_final: 0.4814 (tmm-80) REVERT: L 95 ASN cc_start: 0.8284 (t0) cc_final: 0.8017 (t0) REVERT: L 99 LYS cc_start: 0.7248 (mptp) cc_final: 0.7002 (mttp) REVERT: L 221 ARG cc_start: 0.6414 (OUTLIER) cc_final: 0.4668 (ttt180) REVERT: L 285 TYR cc_start: 0.8911 (OUTLIER) cc_final: 0.7263 (m-80) REVERT: L 396 LYS cc_start: 0.8714 (ttpp) cc_final: 0.8364 (ttpt) outliers start: 67 outliers final: 14 residues processed: 430 average time/residue: 0.7646 time to fit residues: 390.0093 Evaluate side-chains 403 residues out of total 4308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 371 time to evaluate : 1.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 99 LYS Chi-restraints excluded: chain A residue 285 TYR Chi-restraints excluded: chain A residue 402 MET Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 285 TYR Chi-restraints excluded: chain C residue 202 GLU Chi-restraints excluded: chain C residue 285 TYR Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain D residue 402 MET Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain E residue 389 GLN Chi-restraints excluded: chain F residue 285 TYR Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain G residue 99 LYS Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain G residue 402 MET Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain H residue 232 LYS Chi-restraints excluded: chain H residue 285 TYR Chi-restraints excluded: chain I residue 221 ARG Chi-restraints excluded: chain I residue 285 TYR Chi-restraints excluded: chain J residue 15 LEU Chi-restraints excluded: chain J residue 45 HIS Chi-restraints excluded: chain J residue 99 LYS Chi-restraints excluded: chain J residue 123 MET Chi-restraints excluded: chain J residue 285 TYR Chi-restraints excluded: chain K residue 232 LYS Chi-restraints excluded: chain L residue 221 ARG Chi-restraints excluded: chain L residue 285 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 55 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 449 optimal weight: 3.9990 chunk 377 optimal weight: 4.9990 chunk 177 optimal weight: 1.9990 chunk 103 optimal weight: 4.9990 chunk 135 optimal weight: 2.9990 chunk 432 optimal weight: 20.0000 chunk 485 optimal weight: 2.9990 chunk 170 optimal weight: 30.0000 chunk 477 optimal weight: 4.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 HIS C 19 GLN C 165 GLN D 45 HIS F 19 GLN F 37 HIS F 165 GLN I 19 GLN ** I 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 165 GLN ** J 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 19 GLN L 165 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.161251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.113579 restraints weight = 107678.410| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 2.86 r_work: 0.3035 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2921 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2908 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2908 r_free = 0.2908 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2908 r_free = 0.2908 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2908 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.1628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 40608 Z= 0.212 Angle : 0.690 8.508 54996 Z= 0.371 Chirality : 0.050 0.166 6192 Planarity : 0.006 0.063 7032 Dihedral : 5.541 53.189 5856 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 1.81 % Allowed : 9.27 % Favored : 88.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.49 (0.12), residues: 4992 helix: 1.59 (0.15), residues: 1464 sheet: 0.32 (0.16), residues: 1080 loop : -1.93 (0.11), residues: 2448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 222 TYR 0.017 0.002 TYR L 150 PHE 0.022 0.003 PHE I 183 TRP 0.011 0.002 TRP K 175 HIS 0.005 0.001 HIS F 37 Details of bonding type rmsd covalent geometry : bond 0.00492 (40572) covalent geometry : angle 0.68976 (54996) hydrogen bonds : bond 0.07164 ( 1624) hydrogen bonds : angle 4.64048 ( 4677) metal coordination : bond 0.00668 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9984 Ramachandran restraints generated. 4992 Oldfield, 0 Emsley, 4992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9984 Ramachandran restraints generated. 4992 Oldfield, 0 Emsley, 4992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 4308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 362 time to evaluate : 1.438 Fit side-chains REVERT: A 99 LYS cc_start: 0.7008 (OUTLIER) cc_final: 0.6552 (mptp) REVERT: A 123 MET cc_start: 0.6347 (mmp) cc_final: 0.5792 (mpm) REVERT: A 285 TYR cc_start: 0.9053 (OUTLIER) cc_final: 0.7631 (m-80) REVERT: B 30 ARG cc_start: 0.6121 (ttp80) cc_final: 0.5499 (ttp80) REVERT: B 91 GLU cc_start: 0.7248 (mp0) cc_final: 0.6847 (mp0) REVERT: B 123 MET cc_start: 0.6209 (mmp) cc_final: 0.5651 (mpm) REVERT: B 285 TYR cc_start: 0.9097 (OUTLIER) cc_final: 0.7548 (m-80) REVERT: B 402 MET cc_start: 0.7757 (ttm) cc_final: 0.7451 (mtt) REVERT: C 30 ARG cc_start: 0.5609 (tmm-80) cc_final: 0.4787 (tmm-80) REVERT: C 95 ASN cc_start: 0.8146 (t0) cc_final: 0.7294 (t0) REVERT: C 99 LYS cc_start: 0.7162 (mptp) cc_final: 0.6531 (mptp) REVERT: C 165 GLN cc_start: 0.7783 (OUTLIER) cc_final: 0.7170 (mm-40) REVERT: C 221 ARG cc_start: 0.6522 (OUTLIER) cc_final: 0.5107 (ttt180) REVERT: C 285 TYR cc_start: 0.9066 (OUTLIER) cc_final: 0.7578 (m-80) REVERT: D 73 MET cc_start: 0.7444 (tpp) cc_final: 0.6953 (mmm) REVERT: D 95 ASN cc_start: 0.8182 (t0) cc_final: 0.7877 (t0) REVERT: D 99 LYS cc_start: 0.7176 (OUTLIER) cc_final: 0.6683 (mptp) REVERT: D 123 MET cc_start: 0.6370 (mmp) cc_final: 0.5820 (mpm) REVERT: D 285 TYR cc_start: 0.9053 (OUTLIER) cc_final: 0.7629 (m-80) REVERT: E 30 ARG cc_start: 0.5879 (ttp80) cc_final: 0.5342 (ttp80) REVERT: E 99 LYS cc_start: 0.7000 (mptp) cc_final: 0.6518 (mptp) REVERT: E 123 MET cc_start: 0.6261 (mmp) cc_final: 0.5716 (mpm) REVERT: E 285 TYR cc_start: 0.9074 (OUTLIER) cc_final: 0.7610 (m-80) REVERT: E 402 MET cc_start: 0.7723 (ttm) cc_final: 0.7377 (mtt) REVERT: F 91 GLU cc_start: 0.7351 (mp0) cc_final: 0.6949 (mp0) REVERT: F 95 ASN cc_start: 0.8285 (t0) cc_final: 0.7918 (t0) REVERT: F 99 LYS cc_start: 0.7224 (mptp) cc_final: 0.6803 (mptp) REVERT: F 165 GLN cc_start: 0.7746 (OUTLIER) cc_final: 0.7124 (mm-40) REVERT: F 285 TYR cc_start: 0.9083 (OUTLIER) cc_final: 0.7608 (m-80) REVERT: G 26 GLU cc_start: 0.6507 (OUTLIER) cc_final: 0.6086 (pt0) REVERT: G 73 MET cc_start: 0.7383 (tpp) cc_final: 0.6837 (mmm) REVERT: G 99 LYS cc_start: 0.6923 (OUTLIER) cc_final: 0.6533 (mptp) REVERT: G 123 MET cc_start: 0.6424 (mmp) cc_final: 0.5852 (mpm) REVERT: G 285 TYR cc_start: 0.9034 (OUTLIER) cc_final: 0.7797 (m-80) REVERT: H 123 MET cc_start: 0.6077 (mmp) cc_final: 0.5512 (mpm) REVERT: H 232 LYS cc_start: 0.8481 (OUTLIER) cc_final: 0.8195 (mptm) REVERT: H 285 TYR cc_start: 0.9068 (OUTLIER) cc_final: 0.7581 (m-80) REVERT: H 402 MET cc_start: 0.7770 (ttm) cc_final: 0.7462 (mtt) REVERT: I 30 ARG cc_start: 0.5638 (tmm-80) cc_final: 0.4785 (ttp80) REVERT: I 91 GLU cc_start: 0.7351 (mp0) cc_final: 0.6957 (mp0) REVERT: I 165 GLN cc_start: 0.7771 (OUTLIER) cc_final: 0.7144 (mm-40) REVERT: I 221 ARG cc_start: 0.6522 (OUTLIER) cc_final: 0.4865 (ttt180) REVERT: I 285 TYR cc_start: 0.9070 (OUTLIER) cc_final: 0.7600 (m-80) REVERT: J 99 LYS cc_start: 0.7332 (mptp) cc_final: 0.6834 (mptp) REVERT: J 285 TYR cc_start: 0.9048 (OUTLIER) cc_final: 0.7824 (m-80) REVERT: K 123 MET cc_start: 0.6102 (mmp) cc_final: 0.5559 (mpm) REVERT: K 285 TYR cc_start: 0.9068 (OUTLIER) cc_final: 0.7606 (m-80) REVERT: K 402 MET cc_start: 0.7769 (ttm) cc_final: 0.7463 (mtt) REVERT: L 30 ARG cc_start: 0.5655 (tmm-80) cc_final: 0.4833 (tmm-80) REVERT: L 95 ASN cc_start: 0.8326 (t0) cc_final: 0.8074 (t0) REVERT: L 99 LYS cc_start: 0.7267 (mptp) cc_final: 0.6993 (mttm) REVERT: L 165 GLN cc_start: 0.7720 (OUTLIER) cc_final: 0.7093 (mm-40) REVERT: L 221 ARG cc_start: 0.6568 (OUTLIER) cc_final: 0.4890 (ttt180) REVERT: L 285 TYR cc_start: 0.9073 (OUTLIER) cc_final: 0.7594 (m-80) outliers start: 77 outliers final: 23 residues processed: 399 average time/residue: 0.7485 time to fit residues: 356.1584 Evaluate side-chains 406 residues out of total 4308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 359 time to evaluate : 1.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 99 LYS Chi-restraints excluded: chain A residue 285 TYR Chi-restraints excluded: chain A residue 402 MET Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 285 TYR Chi-restraints excluded: chain B residue 400 LYS Chi-restraints excluded: chain C residue 19 GLN Chi-restraints excluded: chain C residue 165 GLN Chi-restraints excluded: chain C residue 202 GLU Chi-restraints excluded: chain C residue 221 ARG Chi-restraints excluded: chain C residue 285 TYR Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 99 LYS Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain D residue 402 MET Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain E residue 389 GLN Chi-restraints excluded: chain F residue 19 GLN Chi-restraints excluded: chain F residue 165 GLN Chi-restraints excluded: chain F residue 285 TYR Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain G residue 26 GLU Chi-restraints excluded: chain G residue 99 LYS Chi-restraints excluded: chain G residue 127 ASP Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain G residue 402 MET Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain H residue 232 LYS Chi-restraints excluded: chain H residue 285 TYR Chi-restraints excluded: chain H residue 389 GLN Chi-restraints excluded: chain I residue 19 GLN Chi-restraints excluded: chain I residue 165 GLN Chi-restraints excluded: chain I residue 184 MET Chi-restraints excluded: chain I residue 221 ARG Chi-restraints excluded: chain I residue 285 TYR Chi-restraints excluded: chain J residue 15 LEU Chi-restraints excluded: chain J residue 45 HIS Chi-restraints excluded: chain J residue 123 MET Chi-restraints excluded: chain J residue 285 TYR Chi-restraints excluded: chain K residue 50 LEU Chi-restraints excluded: chain K residue 285 TYR Chi-restraints excluded: chain L residue 165 GLN Chi-restraints excluded: chain L residue 221 ARG Chi-restraints excluded: chain L residue 285 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 357 optimal weight: 1.9990 chunk 206 optimal weight: 0.1980 chunk 25 optimal weight: 2.9990 chunk 245 optimal weight: 7.9990 chunk 104 optimal weight: 1.9990 chunk 254 optimal weight: 0.9990 chunk 407 optimal weight: 0.6980 chunk 228 optimal weight: 6.9990 chunk 406 optimal weight: 0.6980 chunk 450 optimal weight: 4.9990 chunk 337 optimal weight: 3.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 HIS C 165 GLN D 45 HIS F 37 HIS F 165 GLN F 389 GLN G 45 HIS ** I 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 165 GLN I 389 GLN J 95 ASN L 19 GLN L 165 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.164288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.119470 restraints weight = 132647.059| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 3.34 r_work: 0.3053 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3040 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3040 r_free = 0.3040 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3040 r_free = 0.3040 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3040 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.1566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 40608 Z= 0.119 Angle : 0.564 10.008 54996 Z= 0.298 Chirality : 0.044 0.131 6192 Planarity : 0.005 0.061 7032 Dihedral : 5.145 49.286 5856 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 1.43 % Allowed : 9.81 % Favored : 88.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.37 (0.12), residues: 4992 helix: 1.79 (0.15), residues: 1476 sheet: 0.29 (0.16), residues: 1080 loop : -1.89 (0.11), residues: 2436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 98 TYR 0.015 0.001 TYR K 297 PHE 0.015 0.002 PHE J 423 TRP 0.009 0.001 TRP E 175 HIS 0.009 0.001 HIS F 37 Details of bonding type rmsd covalent geometry : bond 0.00254 (40572) covalent geometry : angle 0.56394 (54996) hydrogen bonds : bond 0.04881 ( 1624) hydrogen bonds : angle 4.37185 ( 4677) metal coordination : bond 0.00225 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9984 Ramachandran restraints generated. 4992 Oldfield, 0 Emsley, 4992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9984 Ramachandran restraints generated. 4992 Oldfield, 0 Emsley, 4992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 4308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 367 time to evaluate : 1.461 Fit side-chains revert: symmetry clash REVERT: A 99 LYS cc_start: 0.6983 (OUTLIER) cc_final: 0.6552 (mptp) REVERT: A 123 MET cc_start: 0.6279 (mmp) cc_final: 0.5661 (mpm) REVERT: A 285 TYR cc_start: 0.8922 (OUTLIER) cc_final: 0.7579 (m-80) REVERT: A 401 ASP cc_start: 0.7681 (OUTLIER) cc_final: 0.7349 (t0) REVERT: B 30 ARG cc_start: 0.6031 (ttp80) cc_final: 0.5420 (ttp80) REVERT: B 91 GLU cc_start: 0.7112 (mp0) cc_final: 0.6795 (mp0) REVERT: B 123 MET cc_start: 0.6223 (mmp) cc_final: 0.5605 (mpm) REVERT: B 285 TYR cc_start: 0.8968 (OUTLIER) cc_final: 0.7604 (m-80) REVERT: B 402 MET cc_start: 0.7411 (ttm) cc_final: 0.7063 (ttt) REVERT: C 30 ARG cc_start: 0.5623 (tmm-80) cc_final: 0.4873 (ttp80) REVERT: C 165 GLN cc_start: 0.7616 (OUTLIER) cc_final: 0.6932 (mm-40) REVERT: C 285 TYR cc_start: 0.8951 (OUTLIER) cc_final: 0.7254 (m-80) REVERT: D 73 MET cc_start: 0.7338 (tpp) cc_final: 0.6824 (mmm) REVERT: D 95 ASN cc_start: 0.8101 (t0) cc_final: 0.7751 (t0) REVERT: D 99 LYS cc_start: 0.7124 (mptp) cc_final: 0.6660 (mptp) REVERT: D 123 MET cc_start: 0.6405 (mmp) cc_final: 0.5786 (mpm) REVERT: D 285 TYR cc_start: 0.8922 (OUTLIER) cc_final: 0.7570 (m-80) REVERT: D 401 ASP cc_start: 0.7710 (OUTLIER) cc_final: 0.7387 (t0) REVERT: E 30 ARG cc_start: 0.5865 (ttp80) cc_final: 0.5325 (ttp80) REVERT: E 99 LYS cc_start: 0.6930 (mptp) cc_final: 0.6479 (mptp) REVERT: E 123 MET cc_start: 0.6242 (mmp) cc_final: 0.5621 (mpm) REVERT: E 285 TYR cc_start: 0.8968 (OUTLIER) cc_final: 0.7619 (m-80) REVERT: E 402 MET cc_start: 0.7345 (ttm) cc_final: 0.7010 (ttt) REVERT: F 91 GLU cc_start: 0.7156 (mp0) cc_final: 0.6792 (mp0) REVERT: F 95 ASN cc_start: 0.8243 (t0) cc_final: 0.7916 (t0) REVERT: F 99 LYS cc_start: 0.7259 (mptp) cc_final: 0.6859 (mptp) REVERT: F 165 GLN cc_start: 0.7605 (OUTLIER) cc_final: 0.6914 (mm-40) REVERT: F 285 TYR cc_start: 0.8958 (OUTLIER) cc_final: 0.7300 (m-80) REVERT: G 73 MET cc_start: 0.7233 (tpp) cc_final: 0.6681 (mmm) REVERT: G 99 LYS cc_start: 0.6909 (OUTLIER) cc_final: 0.6626 (mptp) REVERT: G 123 MET cc_start: 0.6384 (mmp) cc_final: 0.5763 (mpm) REVERT: G 165 GLN cc_start: 0.7852 (OUTLIER) cc_final: 0.7541 (tp40) REVERT: G 285 TYR cc_start: 0.8925 (OUTLIER) cc_final: 0.7668 (m-80) REVERT: G 401 ASP cc_start: 0.7682 (OUTLIER) cc_final: 0.7355 (t0) REVERT: H 30 ARG cc_start: 0.5908 (ttp80) cc_final: 0.5271 (ttp80) REVERT: H 123 MET cc_start: 0.6247 (mmp) cc_final: 0.5634 (mpm) REVERT: H 232 LYS cc_start: 0.8483 (OUTLIER) cc_final: 0.8282 (tptm) REVERT: H 285 TYR cc_start: 0.8968 (OUTLIER) cc_final: 0.7524 (m-80) REVERT: H 402 MET cc_start: 0.7444 (ttm) cc_final: 0.7091 (ttt) REVERT: I 30 ARG cc_start: 0.5587 (tmm-80) cc_final: 0.4725 (ttp80) REVERT: I 91 GLU cc_start: 0.7167 (mp0) cc_final: 0.6815 (mp0) REVERT: I 99 LYS cc_start: 0.7262 (mttm) cc_final: 0.6865 (mttp) REVERT: I 165 GLN cc_start: 0.7619 (OUTLIER) cc_final: 0.6913 (mm-40) REVERT: I 221 ARG cc_start: 0.6376 (OUTLIER) cc_final: 0.4714 (ttt180) REVERT: I 285 TYR cc_start: 0.8948 (OUTLIER) cc_final: 0.7273 (m-80) REVERT: J 99 LYS cc_start: 0.7287 (mptp) cc_final: 0.6818 (mptp) REVERT: J 165 GLN cc_start: 0.7915 (OUTLIER) cc_final: 0.7611 (tp40) REVERT: J 285 TYR cc_start: 0.8927 (OUTLIER) cc_final: 0.7671 (m-80) REVERT: J 401 ASP cc_start: 0.7630 (OUTLIER) cc_final: 0.7341 (t0) REVERT: K 123 MET cc_start: 0.6251 (mmp) cc_final: 0.5608 (mpm) REVERT: K 285 TYR cc_start: 0.8970 (OUTLIER) cc_final: 0.7699 (m-80) REVERT: K 402 MET cc_start: 0.7440 (ttm) cc_final: 0.7112 (ttt) REVERT: L 30 ARG cc_start: 0.5720 (tmm-80) cc_final: 0.4887 (tmm-80) REVERT: L 99 LYS cc_start: 0.7149 (mptp) cc_final: 0.6901 (mptp) REVERT: L 165 GLN cc_start: 0.7608 (OUTLIER) cc_final: 0.6908 (mm-40) REVERT: L 221 ARG cc_start: 0.6346 (OUTLIER) cc_final: 0.4687 (ttt180) REVERT: L 285 TYR cc_start: 0.8953 (OUTLIER) cc_final: 0.7278 (m-80) outliers start: 61 outliers final: 14 residues processed: 407 average time/residue: 0.7468 time to fit residues: 363.1265 Evaluate side-chains 407 residues out of total 4308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 366 time to evaluate : 1.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 99 LYS Chi-restraints excluded: chain A residue 285 TYR Chi-restraints excluded: chain A residue 401 ASP Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 285 TYR Chi-restraints excluded: chain C residue 165 GLN Chi-restraints excluded: chain C residue 202 GLU Chi-restraints excluded: chain C residue 285 TYR Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain D residue 401 ASP Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain E residue 389 GLN Chi-restraints excluded: chain F residue 165 GLN Chi-restraints excluded: chain F residue 285 TYR Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain G residue 99 LYS Chi-restraints excluded: chain G residue 127 ASP Chi-restraints excluded: chain G residue 165 GLN Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain G residue 401 ASP Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain H residue 232 LYS Chi-restraints excluded: chain H residue 285 TYR Chi-restraints excluded: chain I residue 165 GLN Chi-restraints excluded: chain I residue 221 ARG Chi-restraints excluded: chain I residue 285 TYR Chi-restraints excluded: chain J residue 15 LEU Chi-restraints excluded: chain J residue 45 HIS Chi-restraints excluded: chain J residue 123 MET Chi-restraints excluded: chain J residue 165 GLN Chi-restraints excluded: chain J residue 285 TYR Chi-restraints excluded: chain J residue 401 ASP Chi-restraints excluded: chain K residue 285 TYR Chi-restraints excluded: chain L residue 19 GLN Chi-restraints excluded: chain L residue 165 GLN Chi-restraints excluded: chain L residue 221 ARG Chi-restraints excluded: chain L residue 285 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 462 optimal weight: 20.0000 chunk 169 optimal weight: 3.9990 chunk 213 optimal weight: 2.9990 chunk 490 optimal weight: 0.6980 chunk 60 optimal weight: 0.9990 chunk 200 optimal weight: 0.9980 chunk 102 optimal weight: 3.9990 chunk 335 optimal weight: 0.9990 chunk 280 optimal weight: 0.9990 chunk 94 optimal weight: 20.0000 chunk 299 optimal weight: 6.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 HIS C 95 ASN D 45 HIS G 45 HIS ** I 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 19 GLN L 19 GLN L 95 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.164654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.118062 restraints weight = 119347.900| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 3.12 r_work: 0.3094 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2959 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2959 r_free = 0.2959 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2959 r_free = 0.2959 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2959 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.1598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 40608 Z= 0.115 Angle : 0.547 7.984 54996 Z= 0.289 Chirality : 0.044 0.131 6192 Planarity : 0.005 0.060 7032 Dihedral : 4.954 46.112 5856 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 2.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.38 % Allowed : 9.93 % Favored : 88.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.28 (0.12), residues: 4992 helix: 1.92 (0.15), residues: 1476 sheet: 0.31 (0.16), residues: 1080 loop : -1.85 (0.11), residues: 2436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 98 TYR 0.014 0.001 TYR K 297 PHE 0.016 0.002 PHE K 423 TRP 0.008 0.001 TRP E 175 HIS 0.002 0.001 HIS I 259 Details of bonding type rmsd covalent geometry : bond 0.00247 (40572) covalent geometry : angle 0.54696 (54996) hydrogen bonds : bond 0.04684 ( 1624) hydrogen bonds : angle 4.28769 ( 4677) metal coordination : bond 0.00221 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9984 Ramachandran restraints generated. 4992 Oldfield, 0 Emsley, 4992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9984 Ramachandran restraints generated. 4992 Oldfield, 0 Emsley, 4992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 4308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 372 time to evaluate : 1.550 Fit side-chains REVERT: A 99 LYS cc_start: 0.6954 (OUTLIER) cc_final: 0.6523 (mptp) REVERT: A 123 MET cc_start: 0.6321 (mmp) cc_final: 0.5736 (mpm) REVERT: A 285 TYR cc_start: 0.8983 (OUTLIER) cc_final: 0.7655 (m-80) REVERT: B 30 ARG cc_start: 0.5924 (ttp80) cc_final: 0.5280 (ttp80) REVERT: B 91 GLU cc_start: 0.7204 (mp0) cc_final: 0.6862 (mp0) REVERT: B 123 MET cc_start: 0.6278 (mmp) cc_final: 0.5685 (mpm) REVERT: B 232 LYS cc_start: 0.8470 (OUTLIER) cc_final: 0.8069 (tptm) REVERT: B 285 TYR cc_start: 0.9012 (OUTLIER) cc_final: 0.7658 (m-80) REVERT: B 402 MET cc_start: 0.7522 (ttm) cc_final: 0.7219 (ttt) REVERT: C 30 ARG cc_start: 0.5513 (tmm-80) cc_final: 0.4671 (tmm-80) REVERT: C 95 ASN cc_start: 0.8294 (t0) cc_final: 0.8080 (t0) REVERT: C 99 LYS cc_start: 0.7166 (mptp) cc_final: 0.6914 (mttm) REVERT: C 221 ARG cc_start: 0.6282 (OUTLIER) cc_final: 0.4877 (ttt180) REVERT: C 285 TYR cc_start: 0.8996 (OUTLIER) cc_final: 0.7322 (m-80) REVERT: D 26 GLU cc_start: 0.6330 (mt-10) cc_final: 0.5817 (pt0) REVERT: D 73 MET cc_start: 0.7378 (tpp) cc_final: 0.6839 (mmm) REVERT: D 95 ASN cc_start: 0.8132 (t0) cc_final: 0.7724 (t0) REVERT: D 99 LYS cc_start: 0.7044 (OUTLIER) cc_final: 0.6569 (mptp) REVERT: D 123 MET cc_start: 0.6280 (mmp) cc_final: 0.5716 (mpm) REVERT: D 285 TYR cc_start: 0.8983 (OUTLIER) cc_final: 0.7639 (m-80) REVERT: E 15 LEU cc_start: 0.7698 (tt) cc_final: 0.7490 (mt) REVERT: E 26 GLU cc_start: 0.6133 (OUTLIER) cc_final: 0.5403 (pt0) REVERT: E 30 ARG cc_start: 0.5783 (ttp80) cc_final: 0.5193 (ttp80) REVERT: E 99 LYS cc_start: 0.6930 (mptp) cc_final: 0.6501 (mptp) REVERT: E 123 MET cc_start: 0.6285 (mmp) cc_final: 0.5689 (mpm) REVERT: E 232 LYS cc_start: 0.8396 (OUTLIER) cc_final: 0.7996 (tptm) REVERT: E 285 TYR cc_start: 0.9010 (OUTLIER) cc_final: 0.7673 (m-80) REVERT: E 402 MET cc_start: 0.7388 (ttm) cc_final: 0.7087 (ttt) REVERT: F 91 GLU cc_start: 0.7225 (mp0) cc_final: 0.6913 (mp0) REVERT: F 99 LYS cc_start: 0.7266 (mptp) cc_final: 0.7034 (mttp) REVERT: F 232 LYS cc_start: 0.8424 (OUTLIER) cc_final: 0.8204 (tptm) REVERT: F 285 TYR cc_start: 0.9002 (OUTLIER) cc_final: 0.7336 (m-80) REVERT: F 400 LYS cc_start: 0.7759 (mttm) cc_final: 0.7372 (mtmp) REVERT: G 73 MET cc_start: 0.7291 (tpp) cc_final: 0.6951 (mmm) REVERT: G 123 MET cc_start: 0.6363 (mmp) cc_final: 0.5773 (mpm) REVERT: G 165 GLN cc_start: 0.7890 (OUTLIER) cc_final: 0.7566 (tp40) REVERT: G 285 TYR cc_start: 0.8960 (OUTLIER) cc_final: 0.7814 (m-80) REVERT: H 30 ARG cc_start: 0.5835 (ttp80) cc_final: 0.5168 (ttp80) REVERT: H 123 MET cc_start: 0.6293 (mmp) cc_final: 0.5699 (mpm) REVERT: H 285 TYR cc_start: 0.9009 (OUTLIER) cc_final: 0.7660 (m-80) REVERT: H 402 MET cc_start: 0.7523 (ttm) cc_final: 0.7211 (ttt) REVERT: I 30 ARG cc_start: 0.5473 (tmm-80) cc_final: 0.4610 (ttp80) REVERT: I 91 GLU cc_start: 0.7230 (mp0) cc_final: 0.6943 (mp0) REVERT: I 99 LYS cc_start: 0.7262 (mttm) cc_final: 0.6893 (mttp) REVERT: I 221 ARG cc_start: 0.6323 (OUTLIER) cc_final: 0.4709 (ttt180) REVERT: I 285 TYR cc_start: 0.8991 (OUTLIER) cc_final: 0.7305 (m-80) REVERT: J 95 ASN cc_start: 0.8265 (t0) cc_final: 0.7833 (t0) REVERT: J 99 LYS cc_start: 0.7234 (mptp) cc_final: 0.6792 (mptp) REVERT: J 165 GLN cc_start: 0.7965 (OUTLIER) cc_final: 0.7649 (tp40) REVERT: J 285 TYR cc_start: 0.8967 (OUTLIER) cc_final: 0.7814 (m-80) REVERT: K 26 GLU cc_start: 0.6217 (OUTLIER) cc_final: 0.5559 (pt0) REVERT: K 123 MET cc_start: 0.6283 (mmp) cc_final: 0.5659 (mpm) REVERT: K 285 TYR cc_start: 0.9009 (OUTLIER) cc_final: 0.7677 (m-80) REVERT: K 402 MET cc_start: 0.7508 (ttm) cc_final: 0.7206 (ttt) REVERT: L 30 ARG cc_start: 0.5570 (tmm-80) cc_final: 0.4732 (tmm-80) REVERT: L 95 ASN cc_start: 0.8304 (t0) cc_final: 0.7952 (t0) REVERT: L 99 LYS cc_start: 0.7193 (mttp) cc_final: 0.6734 (mptp) REVERT: L 221 ARG cc_start: 0.6287 (OUTLIER) cc_final: 0.4669 (ttt180) REVERT: L 232 LYS cc_start: 0.8431 (OUTLIER) cc_final: 0.8209 (tptm) REVERT: L 285 TYR cc_start: 0.8999 (OUTLIER) cc_final: 0.7296 (m-80) outliers start: 59 outliers final: 19 residues processed: 405 average time/residue: 0.7301 time to fit residues: 353.5697 Evaluate side-chains 410 residues out of total 4308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 366 time to evaluate : 1.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 99 LYS Chi-restraints excluded: chain A residue 285 TYR Chi-restraints excluded: chain A residue 402 MET Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 45 HIS Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 232 LYS Chi-restraints excluded: chain B residue 285 TYR Chi-restraints excluded: chain C residue 202 GLU Chi-restraints excluded: chain C residue 221 ARG Chi-restraints excluded: chain C residue 285 TYR Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 99 LYS Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain D residue 402 MET Chi-restraints excluded: chain E residue 26 GLU Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 232 LYS Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain E residue 389 GLN Chi-restraints excluded: chain F residue 232 LYS Chi-restraints excluded: chain F residue 285 TYR Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain G residue 127 ASP Chi-restraints excluded: chain G residue 165 GLN Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain G residue 402 MET Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain H residue 285 TYR Chi-restraints excluded: chain I residue 221 ARG Chi-restraints excluded: chain I residue 285 TYR Chi-restraints excluded: chain J residue 15 LEU Chi-restraints excluded: chain J residue 45 HIS Chi-restraints excluded: chain J residue 123 MET Chi-restraints excluded: chain J residue 165 GLN Chi-restraints excluded: chain J residue 285 TYR Chi-restraints excluded: chain K residue 19 GLN Chi-restraints excluded: chain K residue 26 GLU Chi-restraints excluded: chain K residue 50 LEU Chi-restraints excluded: chain K residue 285 TYR Chi-restraints excluded: chain L residue 221 ARG Chi-restraints excluded: chain L residue 232 LYS Chi-restraints excluded: chain L residue 285 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 192 optimal weight: 6.9990 chunk 83 optimal weight: 5.9990 chunk 300 optimal weight: 8.9990 chunk 344 optimal weight: 1.9990 chunk 251 optimal weight: 0.8980 chunk 423 optimal weight: 0.5980 chunk 116 optimal weight: 0.8980 chunk 130 optimal weight: 2.9990 chunk 405 optimal weight: 4.9990 chunk 372 optimal weight: 1.9990 chunk 286 optimal weight: 0.0570 overall best weight: 0.8900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 HIS C 165 GLN D 45 HIS F 95 ASN F 165 GLN G 45 HIS G 95 ASN H 37 HIS ** I 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 165 GLN K 19 GLN K 45 HIS L 165 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.164958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.119879 restraints weight = 131618.056| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 3.45 r_work: 0.3067 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3054 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3054 r_free = 0.3054 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3054 r_free = 0.3054 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3054 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.1631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 40608 Z= 0.112 Angle : 0.542 8.375 54996 Z= 0.286 Chirality : 0.044 0.145 6192 Planarity : 0.005 0.059 7032 Dihedral : 4.827 42.988 5856 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 2.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.27 % Allowed : 10.45 % Favored : 88.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.24 (0.12), residues: 4992 helix: 2.00 (0.15), residues: 1476 sheet: 0.27 (0.16), residues: 1080 loop : -1.84 (0.11), residues: 2436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 98 TYR 0.014 0.001 TYR H 297 PHE 0.016 0.002 PHE E 423 TRP 0.008 0.001 TRP E 175 HIS 0.008 0.001 HIS H 37 Details of bonding type rmsd covalent geometry : bond 0.00241 (40572) covalent geometry : angle 0.54177 (54996) hydrogen bonds : bond 0.04518 ( 1624) hydrogen bonds : angle 4.23619 ( 4677) metal coordination : bond 0.00209 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9984 Ramachandran restraints generated. 4992 Oldfield, 0 Emsley, 4992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9984 Ramachandran restraints generated. 4992 Oldfield, 0 Emsley, 4992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 4308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 364 time to evaluate : 1.487 Fit side-chains REVERT: A 26 GLU cc_start: 0.6370 (mt-10) cc_final: 0.5902 (pt0) REVERT: A 99 LYS cc_start: 0.6930 (OUTLIER) cc_final: 0.6534 (mptp) REVERT: A 123 MET cc_start: 0.6318 (mmp) cc_final: 0.5699 (mpm) REVERT: A 285 TYR cc_start: 0.8924 (OUTLIER) cc_final: 0.7625 (m-80) REVERT: B 30 ARG cc_start: 0.6025 (ttp80) cc_final: 0.5380 (ttp80) REVERT: B 91 GLU cc_start: 0.7099 (mp0) cc_final: 0.6816 (mp0) REVERT: B 123 MET cc_start: 0.6270 (mmp) cc_final: 0.5654 (mpm) REVERT: B 232 LYS cc_start: 0.8450 (OUTLIER) cc_final: 0.8037 (tptm) REVERT: B 285 TYR cc_start: 0.8960 (OUTLIER) cc_final: 0.7559 (m-80) REVERT: B 402 MET cc_start: 0.7350 (ttm) cc_final: 0.7039 (ttt) REVERT: C 30 ARG cc_start: 0.5598 (tmm-80) cc_final: 0.4764 (tmm-80) REVERT: C 95 ASN cc_start: 0.8272 (t0) cc_final: 0.8031 (t0) REVERT: C 99 LYS cc_start: 0.7207 (mptp) cc_final: 0.6940 (mttm) REVERT: C 221 ARG cc_start: 0.6252 (OUTLIER) cc_final: 0.4831 (ttt180) REVERT: C 285 TYR cc_start: 0.8943 (OUTLIER) cc_final: 0.7240 (m-80) REVERT: D 26 GLU cc_start: 0.6382 (mt-10) cc_final: 0.5900 (pt0) REVERT: D 73 MET cc_start: 0.7260 (tpp) cc_final: 0.6713 (mmm) REVERT: D 95 ASN cc_start: 0.8092 (t0) cc_final: 0.7662 (t0) REVERT: D 99 LYS cc_start: 0.7032 (OUTLIER) cc_final: 0.6571 (mptp) REVERT: D 123 MET cc_start: 0.6279 (mmp) cc_final: 0.5677 (mpm) REVERT: D 285 TYR cc_start: 0.8918 (OUTLIER) cc_final: 0.7607 (m-80) REVERT: E 26 GLU cc_start: 0.6112 (OUTLIER) cc_final: 0.5371 (pt0) REVERT: E 30 ARG cc_start: 0.5832 (ttp80) cc_final: 0.5273 (ttp80) REVERT: E 99 LYS cc_start: 0.6906 (mptp) cc_final: 0.6492 (mptp) REVERT: E 123 MET cc_start: 0.6285 (mmp) cc_final: 0.5662 (mpm) REVERT: E 232 LYS cc_start: 0.8437 (OUTLIER) cc_final: 0.8010 (tptm) REVERT: E 285 TYR cc_start: 0.8962 (OUTLIER) cc_final: 0.7575 (m-80) REVERT: E 402 MET cc_start: 0.7297 (ttm) cc_final: 0.7020 (ttt) REVERT: F 91 GLU cc_start: 0.7116 (mp0) cc_final: 0.6842 (mp0) REVERT: F 99 LYS cc_start: 0.7279 (mptp) cc_final: 0.7045 (mttp) REVERT: F 232 LYS cc_start: 0.8406 (OUTLIER) cc_final: 0.8191 (tptm) REVERT: F 285 TYR cc_start: 0.8946 (OUTLIER) cc_final: 0.7229 (m-80) REVERT: G 26 GLU cc_start: 0.6425 (OUTLIER) cc_final: 0.5953 (pt0) REVERT: G 73 MET cc_start: 0.7282 (tpp) cc_final: 0.6755 (mmm) REVERT: G 123 MET cc_start: 0.6297 (mmp) cc_final: 0.5668 (mpm) REVERT: G 165 GLN cc_start: 0.7873 (OUTLIER) cc_final: 0.7531 (tp40) REVERT: G 285 TYR cc_start: 0.8901 (OUTLIER) cc_final: 0.7686 (m-80) REVERT: H 30 ARG cc_start: 0.5956 (ttp80) cc_final: 0.5303 (ttp80) REVERT: H 123 MET cc_start: 0.6276 (mmp) cc_final: 0.5656 (mpm) REVERT: H 285 TYR cc_start: 0.8965 (OUTLIER) cc_final: 0.7569 (m-80) REVERT: H 402 MET cc_start: 0.7333 (ttm) cc_final: 0.7033 (ttt) REVERT: I 30 ARG cc_start: 0.5590 (tmm-80) cc_final: 0.4730 (ttp80) REVERT: I 91 GLU cc_start: 0.7110 (mp0) cc_final: 0.6839 (mp0) REVERT: I 99 LYS cc_start: 0.7299 (mttm) cc_final: 0.6971 (mttp) REVERT: I 221 ARG cc_start: 0.6314 (OUTLIER) cc_final: 0.4662 (ttt180) REVERT: I 285 TYR cc_start: 0.8940 (OUTLIER) cc_final: 0.7256 (m-80) REVERT: J 26 GLU cc_start: 0.6429 (OUTLIER) cc_final: 0.5925 (pt0) REVERT: J 99 LYS cc_start: 0.7246 (OUTLIER) cc_final: 0.6758 (mptp) REVERT: J 165 GLN cc_start: 0.7938 (OUTLIER) cc_final: 0.7597 (tp40) REVERT: J 285 TYR cc_start: 0.8903 (OUTLIER) cc_final: 0.7673 (m-80) REVERT: K 26 GLU cc_start: 0.6147 (OUTLIER) cc_final: 0.5418 (pt0) REVERT: K 123 MET cc_start: 0.6269 (mmp) cc_final: 0.5618 (mpm) REVERT: K 285 TYR cc_start: 0.8952 (OUTLIER) cc_final: 0.7507 (m-80) REVERT: K 402 MET cc_start: 0.7329 (ttm) cc_final: 0.7034 (ttt) REVERT: L 30 ARG cc_start: 0.5665 (tmm-80) cc_final: 0.4830 (tmm-80) REVERT: L 95 ASN cc_start: 0.8281 (t0) cc_final: 0.7878 (t0) REVERT: L 99 LYS cc_start: 0.7197 (mttp) cc_final: 0.6742 (mptp) REVERT: L 221 ARG cc_start: 0.6264 (OUTLIER) cc_final: 0.4610 (ttt180) REVERT: L 232 LYS cc_start: 0.8410 (OUTLIER) cc_final: 0.8183 (tptm) REVERT: L 285 TYR cc_start: 0.8942 (OUTLIER) cc_final: 0.7268 (m-80) outliers start: 54 outliers final: 17 residues processed: 395 average time/residue: 0.7284 time to fit residues: 344.4230 Evaluate side-chains 402 residues out of total 4308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 357 time to evaluate : 1.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 99 LYS Chi-restraints excluded: chain A residue 285 TYR Chi-restraints excluded: chain A residue 402 MET Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 232 LYS Chi-restraints excluded: chain B residue 285 TYR Chi-restraints excluded: chain C residue 202 GLU Chi-restraints excluded: chain C residue 221 ARG Chi-restraints excluded: chain C residue 285 TYR Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 99 LYS Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain D residue 402 MET Chi-restraints excluded: chain E residue 26 GLU Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 232 LYS Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain E residue 389 GLN Chi-restraints excluded: chain F residue 232 LYS Chi-restraints excluded: chain F residue 285 TYR Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain G residue 26 GLU Chi-restraints excluded: chain G residue 165 GLN Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain G residue 402 MET Chi-restraints excluded: chain H residue 45 HIS Chi-restraints excluded: chain H residue 285 TYR Chi-restraints excluded: chain H residue 389 GLN Chi-restraints excluded: chain I residue 221 ARG Chi-restraints excluded: chain I residue 285 TYR Chi-restraints excluded: chain J residue 15 LEU Chi-restraints excluded: chain J residue 26 GLU Chi-restraints excluded: chain J residue 45 HIS Chi-restraints excluded: chain J residue 99 LYS Chi-restraints excluded: chain J residue 123 MET Chi-restraints excluded: chain J residue 165 GLN Chi-restraints excluded: chain J residue 285 TYR Chi-restraints excluded: chain K residue 26 GLU Chi-restraints excluded: chain K residue 50 LEU Chi-restraints excluded: chain K residue 285 TYR Chi-restraints excluded: chain L residue 221 ARG Chi-restraints excluded: chain L residue 232 LYS Chi-restraints excluded: chain L residue 285 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 365 optimal weight: 6.9990 chunk 173 optimal weight: 3.9990 chunk 407 optimal weight: 4.9990 chunk 89 optimal weight: 2.9990 chunk 392 optimal weight: 2.9990 chunk 502 optimal weight: 0.9980 chunk 48 optimal weight: 8.9990 chunk 468 optimal weight: 7.9990 chunk 367 optimal weight: 1.9990 chunk 475 optimal weight: 4.9990 chunk 168 optimal weight: 20.0000 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 HIS C 37 HIS C 165 GLN D 45 HIS F 95 ASN F 165 GLN G 45 HIS H 37 HIS ** I 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 165 GLN K 45 HIS L 165 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.161579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.117406 restraints weight = 130990.229| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 3.27 r_work: 0.3001 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2981 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2981 r_free = 0.2981 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2981 r_free = 0.2981 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2981 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.1740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 40608 Z= 0.191 Angle : 0.665 9.100 54996 Z= 0.356 Chirality : 0.049 0.152 6192 Planarity : 0.005 0.060 7032 Dihedral : 5.273 43.543 5856 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 2.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 1.55 % Allowed : 10.12 % Favored : 88.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.38 (0.12), residues: 4992 helix: 1.76 (0.15), residues: 1464 sheet: 0.34 (0.16), residues: 1080 loop : -1.89 (0.11), residues: 2448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 411 TYR 0.017 0.002 TYR H 297 PHE 0.022 0.003 PHE I 183 TRP 0.010 0.002 TRP K 175 HIS 0.009 0.001 HIS H 37 Details of bonding type rmsd covalent geometry : bond 0.00439 (40572) covalent geometry : angle 0.66527 (54996) hydrogen bonds : bond 0.06763 ( 1624) hydrogen bonds : angle 4.54321 ( 4677) metal coordination : bond 0.00588 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9984 Ramachandran restraints generated. 4992 Oldfield, 0 Emsley, 4992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9984 Ramachandran restraints generated. 4992 Oldfield, 0 Emsley, 4992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 4308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 363 time to evaluate : 1.293 Fit side-chains REVERT: A 99 LYS cc_start: 0.6908 (OUTLIER) cc_final: 0.6495 (mptp) REVERT: A 123 MET cc_start: 0.6379 (mmp) cc_final: 0.5801 (mpm) REVERT: A 285 TYR cc_start: 0.8998 (OUTLIER) cc_final: 0.7629 (m-80) REVERT: B 26 GLU cc_start: 0.6180 (OUTLIER) cc_final: 0.5501 (pt0) REVERT: B 30 ARG cc_start: 0.6131 (ttp80) cc_final: 0.5459 (ttp80) REVERT: B 91 GLU cc_start: 0.7124 (mp0) cc_final: 0.6806 (mp0) REVERT: B 123 MET cc_start: 0.6187 (mmp) cc_final: 0.5595 (mpm) REVERT: B 285 TYR cc_start: 0.9044 (OUTLIER) cc_final: 0.7507 (m-80) REVERT: B 402 MET cc_start: 0.7743 (ttm) cc_final: 0.7449 (mtt) REVERT: C 30 ARG cc_start: 0.5687 (tmm-80) cc_final: 0.4863 (tmm-80) REVERT: C 99 LYS cc_start: 0.7239 (mptp) cc_final: 0.7020 (mptp) REVERT: C 165 GLN cc_start: 0.7771 (OUTLIER) cc_final: 0.7189 (mm-40) REVERT: C 221 ARG cc_start: 0.6350 (OUTLIER) cc_final: 0.4944 (ttt180) REVERT: C 285 TYR cc_start: 0.9015 (OUTLIER) cc_final: 0.7520 (m-80) REVERT: D 73 MET cc_start: 0.7294 (tpp) cc_final: 0.6757 (mmm) REVERT: D 95 ASN cc_start: 0.8134 (t0) cc_final: 0.7794 (t0) REVERT: D 99 LYS cc_start: 0.7077 (OUTLIER) cc_final: 0.6599 (mptp) REVERT: D 123 MET cc_start: 0.6370 (mmp) cc_final: 0.5784 (mpm) REVERT: D 285 TYR cc_start: 0.8999 (OUTLIER) cc_final: 0.7627 (m-80) REVERT: E 26 GLU cc_start: 0.6190 (OUTLIER) cc_final: 0.5455 (pt0) REVERT: E 30 ARG cc_start: 0.6055 (ttp80) cc_final: 0.5499 (ttp80) REVERT: E 99 LYS cc_start: 0.7019 (mptp) cc_final: 0.6510 (mptp) REVERT: E 123 MET cc_start: 0.6153 (mmp) cc_final: 0.5557 (mpm) REVERT: E 285 TYR cc_start: 0.9029 (OUTLIER) cc_final: 0.7539 (m-80) REVERT: E 402 MET cc_start: 0.7693 (ttm) cc_final: 0.7410 (mtt) REVERT: F 91 GLU cc_start: 0.7232 (mp0) cc_final: 0.6916 (mp0) REVERT: F 99 LYS cc_start: 0.7338 (mptp) cc_final: 0.7130 (mptp) REVERT: F 165 GLN cc_start: 0.7760 (OUTLIER) cc_final: 0.7169 (mm-40) REVERT: F 232 LYS cc_start: 0.8426 (OUTLIER) cc_final: 0.8182 (tptm) REVERT: F 285 TYR cc_start: 0.9032 (OUTLIER) cc_final: 0.7519 (m-80) REVERT: G 26 GLU cc_start: 0.6432 (OUTLIER) cc_final: 0.5951 (pt0) REVERT: G 73 MET cc_start: 0.7271 (tpp) cc_final: 0.6974 (mmm) REVERT: G 123 MET cc_start: 0.6393 (mmp) cc_final: 0.5792 (mpm) REVERT: G 285 TYR cc_start: 0.8986 (OUTLIER) cc_final: 0.7804 (m-80) REVERT: H 123 MET cc_start: 0.6118 (mmp) cc_final: 0.5491 (mpm) REVERT: H 285 TYR cc_start: 0.9031 (OUTLIER) cc_final: 0.7524 (m-80) REVERT: H 402 MET cc_start: 0.7761 (ttm) cc_final: 0.7471 (mtt) REVERT: I 30 ARG cc_start: 0.5760 (tmm-80) cc_final: 0.4923 (ttp80) REVERT: I 91 GLU cc_start: 0.7169 (mp0) cc_final: 0.6775 (mp0) REVERT: I 165 GLN cc_start: 0.7801 (OUTLIER) cc_final: 0.7201 (mm-40) REVERT: I 221 ARG cc_start: 0.6471 (OUTLIER) cc_final: 0.4812 (ttt180) REVERT: I 285 TYR cc_start: 0.9025 (OUTLIER) cc_final: 0.7528 (m-80) REVERT: J 95 ASN cc_start: 0.8240 (t0) cc_final: 0.7791 (t0) REVERT: J 99 LYS cc_start: 0.7287 (OUTLIER) cc_final: 0.6835 (mptp) REVERT: J 285 TYR cc_start: 0.8991 (OUTLIER) cc_final: 0.7798 (m-80) REVERT: K 26 GLU cc_start: 0.6128 (OUTLIER) cc_final: 0.5439 (pt0) REVERT: K 123 MET cc_start: 0.6162 (mmp) cc_final: 0.5571 (mpm) REVERT: K 285 TYR cc_start: 0.9038 (OUTLIER) cc_final: 0.7622 (m-80) REVERT: K 402 MET cc_start: 0.7753 (ttm) cc_final: 0.7465 (mtt) REVERT: L 30 ARG cc_start: 0.5799 (tmm-80) cc_final: 0.4934 (tmm-80) REVERT: L 95 ASN cc_start: 0.8298 (t0) cc_final: 0.7949 (t0) REVERT: L 99 LYS cc_start: 0.7214 (mttp) cc_final: 0.6926 (mttp) REVERT: L 165 GLN cc_start: 0.7749 (OUTLIER) cc_final: 0.7153 (mm-40) REVERT: L 221 ARG cc_start: 0.6417 (OUTLIER) cc_final: 0.4772 (ttt180) REVERT: L 285 TYR cc_start: 0.9025 (OUTLIER) cc_final: 0.7526 (m-80) outliers start: 66 outliers final: 13 residues processed: 398 average time/residue: 0.7543 time to fit residues: 357.7001 Evaluate side-chains 397 residues out of total 4308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 357 time to evaluate : 1.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 99 LYS Chi-restraints excluded: chain A residue 285 TYR Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 26 GLU Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 285 TYR Chi-restraints excluded: chain C residue 165 GLN Chi-restraints excluded: chain C residue 202 GLU Chi-restraints excluded: chain C residue 221 ARG Chi-restraints excluded: chain C residue 285 TYR Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 99 LYS Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain E residue 26 GLU Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain E residue 389 GLN Chi-restraints excluded: chain F residue 165 GLN Chi-restraints excluded: chain F residue 232 LYS Chi-restraints excluded: chain F residue 285 TYR Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain G residue 26 GLU Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain H residue 50 LEU Chi-restraints excluded: chain H residue 285 TYR Chi-restraints excluded: chain I residue 165 GLN Chi-restraints excluded: chain I residue 221 ARG Chi-restraints excluded: chain I residue 285 TYR Chi-restraints excluded: chain J residue 15 LEU Chi-restraints excluded: chain J residue 45 HIS Chi-restraints excluded: chain J residue 99 LYS Chi-restraints excluded: chain J residue 123 MET Chi-restraints excluded: chain J residue 285 TYR Chi-restraints excluded: chain K residue 26 GLU Chi-restraints excluded: chain K residue 285 TYR Chi-restraints excluded: chain L residue 165 GLN Chi-restraints excluded: chain L residue 221 ARG Chi-restraints excluded: chain L residue 285 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 123 optimal weight: 0.0770 chunk 154 optimal weight: 5.9990 chunk 93 optimal weight: 8.9990 chunk 274 optimal weight: 2.9990 chunk 249 optimal weight: 0.9980 chunk 457 optimal weight: 0.8980 chunk 245 optimal weight: 7.9990 chunk 317 optimal weight: 0.9980 chunk 233 optimal weight: 6.9990 chunk 75 optimal weight: 4.9990 chunk 96 optimal weight: 10.0000 overall best weight: 1.1940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 HIS C 37 HIS C 95 ASN C 165 GLN C 389 GLN D 45 HIS F 95 ASN F 165 GLN F 389 GLN G 45 HIS ** G 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 37 HIS ** I 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 165 GLN I 389 GLN L 165 GLN L 389 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.161687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.117978 restraints weight = 135979.260| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 3.20 r_work: 0.3001 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2980 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2980 r_free = 0.2980 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2980 r_free = 0.2980 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2980 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.1737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.136 40608 Z= 0.187 Angle : 0.935 59.200 54996 Z= 0.531 Chirality : 0.047 0.144 6192 Planarity : 0.005 0.060 7032 Dihedral : 5.270 43.465 5856 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 1.20 % Allowed : 10.73 % Favored : 88.08 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % 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: -0.37 (0.12), residues: 4992 helix: 1.79 (0.15), residues: 1464 sheet: 0.33 (0.16), residues: 1080 loop : -1.89 (0.11), residues: 2448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 30 TYR 0.016 0.002 TYR H 297 PHE 0.021 0.002 PHE I 183 TRP 0.011 0.002 TRP H 175 HIS 0.012 0.001 HIS H 37 Details of bonding type rmsd covalent geometry : bond 0.00405 (40572) covalent geometry : angle 0.93543 (54996) hydrogen bonds : bond 0.06663 ( 1624) hydrogen bonds : angle 4.54683 ( 4677) metal coordination : bond 0.00401 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9984 Ramachandran restraints generated. 4992 Oldfield, 0 Emsley, 4992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9984 Ramachandran restraints generated. 4992 Oldfield, 0 Emsley, 4992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 4308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 362 time to evaluate : 1.443 Fit side-chains REVERT: A 99 LYS cc_start: 0.6895 (OUTLIER) cc_final: 0.6478 (mptp) REVERT: A 123 MET cc_start: 0.6373 (mmp) cc_final: 0.5796 (mpm) REVERT: A 285 TYR cc_start: 0.8993 (OUTLIER) cc_final: 0.7628 (m-80) REVERT: B 26 GLU cc_start: 0.6175 (OUTLIER) cc_final: 0.5489 (pt0) REVERT: B 30 ARG cc_start: 0.6115 (ttp80) cc_final: 0.5445 (ttp80) REVERT: B 91 GLU cc_start: 0.7104 (mp0) cc_final: 0.6789 (mp0) REVERT: B 123 MET cc_start: 0.6181 (mmp) cc_final: 0.5583 (mpm) REVERT: B 285 TYR cc_start: 0.9033 (OUTLIER) cc_final: 0.7494 (m-80) REVERT: B 402 MET cc_start: 0.7737 (ttm) cc_final: 0.7444 (mtt) REVERT: C 30 ARG cc_start: 0.5671 (tmm-80) cc_final: 0.4840 (tmm-80) REVERT: C 99 LYS cc_start: 0.7217 (mptp) cc_final: 0.7009 (mptp) REVERT: C 221 ARG cc_start: 0.6343 (OUTLIER) cc_final: 0.4935 (ttt180) REVERT: C 285 TYR cc_start: 0.9011 (OUTLIER) cc_final: 0.7516 (m-80) REVERT: D 73 MET cc_start: 0.7294 (tpp) cc_final: 0.6755 (mmm) REVERT: D 95 ASN cc_start: 0.8128 (t0) cc_final: 0.7781 (t0) REVERT: D 99 LYS cc_start: 0.7068 (OUTLIER) cc_final: 0.6602 (mptp) REVERT: D 123 MET cc_start: 0.6361 (mmp) cc_final: 0.5771 (mpm) REVERT: D 285 TYR cc_start: 0.8992 (OUTLIER) cc_final: 0.7621 (m-80) REVERT: E 26 GLU cc_start: 0.6178 (OUTLIER) cc_final: 0.5446 (pt0) REVERT: E 30 ARG cc_start: 0.6040 (ttp80) cc_final: 0.5488 (ttp80) REVERT: E 99 LYS cc_start: 0.7002 (mptp) cc_final: 0.6521 (mptp) REVERT: E 123 MET cc_start: 0.6145 (mmp) cc_final: 0.5546 (mpm) REVERT: E 285 TYR cc_start: 0.9026 (OUTLIER) cc_final: 0.7530 (m-80) REVERT: E 402 MET cc_start: 0.7683 (ttm) cc_final: 0.7401 (mtt) REVERT: F 91 GLU cc_start: 0.7217 (mp0) cc_final: 0.6900 (mp0) REVERT: F 99 LYS cc_start: 0.7327 (mptp) cc_final: 0.7116 (mptp) REVERT: F 232 LYS cc_start: 0.8426 (OUTLIER) cc_final: 0.8185 (tptm) REVERT: F 285 TYR cc_start: 0.9032 (OUTLIER) cc_final: 0.7519 (m-80) REVERT: G 26 GLU cc_start: 0.6432 (OUTLIER) cc_final: 0.5955 (pt0) REVERT: G 73 MET cc_start: 0.7267 (tpp) cc_final: 0.6973 (mmm) REVERT: G 123 MET cc_start: 0.6386 (mmp) cc_final: 0.5778 (mpm) REVERT: G 285 TYR cc_start: 0.8981 (OUTLIER) cc_final: 0.7799 (m-80) REVERT: H 123 MET cc_start: 0.6108 (mmp) cc_final: 0.5474 (mpm) REVERT: H 285 TYR cc_start: 0.9030 (OUTLIER) cc_final: 0.7526 (m-80) REVERT: H 402 MET cc_start: 0.7759 (ttm) cc_final: 0.7468 (mtt) REVERT: I 30 ARG cc_start: 0.5736 (tmm-80) cc_final: 0.4898 (ttp80) REVERT: I 91 GLU cc_start: 0.7163 (mp0) cc_final: 0.6763 (mp0) REVERT: I 221 ARG cc_start: 0.6470 (OUTLIER) cc_final: 0.4819 (ttt180) REVERT: I 285 TYR cc_start: 0.9023 (OUTLIER) cc_final: 0.7530 (m-80) REVERT: J 95 ASN cc_start: 0.8230 (t0) cc_final: 0.7779 (t0) REVERT: J 99 LYS cc_start: 0.7278 (OUTLIER) cc_final: 0.6821 (mptp) REVERT: J 285 TYR cc_start: 0.8988 (OUTLIER) cc_final: 0.7797 (m-80) REVERT: K 26 GLU cc_start: 0.6126 (OUTLIER) cc_final: 0.5435 (pt0) REVERT: K 123 MET cc_start: 0.6151 (mmp) cc_final: 0.5556 (mpm) REVERT: K 285 TYR cc_start: 0.9035 (OUTLIER) cc_final: 0.7550 (m-80) REVERT: K 402 MET cc_start: 0.7747 (ttm) cc_final: 0.7457 (mtt) REVERT: L 30 ARG cc_start: 0.5777 (tmm-80) cc_final: 0.4913 (tmm-80) REVERT: L 95 ASN cc_start: 0.8294 (t0) cc_final: 0.7853 (t0) REVERT: L 99 LYS cc_start: 0.7208 (mttp) cc_final: 0.6718 (mptp) REVERT: L 221 ARG cc_start: 0.6413 (OUTLIER) cc_final: 0.4767 (ttt180) REVERT: L 285 TYR cc_start: 0.9026 (OUTLIER) cc_final: 0.7533 (m-80) outliers start: 51 outliers final: 16 residues processed: 387 average time/residue: 0.7520 time to fit residues: 347.6763 Evaluate side-chains 396 residues out of total 4308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 357 time to evaluate : 1.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 99 LYS Chi-restraints excluded: chain A residue 285 TYR Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 26 GLU Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 285 TYR Chi-restraints excluded: chain C residue 202 GLU Chi-restraints excluded: chain C residue 221 ARG Chi-restraints excluded: chain C residue 285 TYR Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 99 LYS Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain E residue 26 GLU Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 202 GLU Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain E residue 389 GLN Chi-restraints excluded: chain F residue 232 LYS Chi-restraints excluded: chain F residue 285 TYR Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain G residue 26 GLU Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain H residue 50 LEU Chi-restraints excluded: chain H residue 285 TYR Chi-restraints excluded: chain I residue 184 MET Chi-restraints excluded: chain I residue 221 ARG Chi-restraints excluded: chain I residue 285 TYR Chi-restraints excluded: chain J residue 15 LEU Chi-restraints excluded: chain J residue 45 HIS Chi-restraints excluded: chain J residue 99 LYS Chi-restraints excluded: chain J residue 123 MET Chi-restraints excluded: chain J residue 285 TYR Chi-restraints excluded: chain K residue 15 LEU Chi-restraints excluded: chain K residue 26 GLU Chi-restraints excluded: chain K residue 285 TYR Chi-restraints excluded: chain L residue 221 ARG Chi-restraints excluded: chain L residue 285 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 174 optimal weight: 8.9990 chunk 102 optimal weight: 7.9990 chunk 54 optimal weight: 30.0000 chunk 214 optimal weight: 0.5980 chunk 137 optimal weight: 9.9990 chunk 486 optimal weight: 4.9990 chunk 211 optimal weight: 0.9990 chunk 71 optimal weight: 0.9990 chunk 294 optimal weight: 20.0000 chunk 483 optimal weight: 0.0670 chunk 472 optimal weight: 4.9990 overall best weight: 1.5324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 HIS C 37 HIS C 95 ASN C 165 GLN D 45 HIS F 95 ASN F 165 GLN G 45 HIS ** G 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 37 HIS ** I 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 165 GLN L 165 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.161670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.116632 restraints weight = 133112.734| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 3.37 r_work: 0.3004 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2984 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2984 r_free = 0.2984 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2984 r_free = 0.2984 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2984 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.1746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.136 40608 Z= 0.187 Angle : 0.935 59.200 54996 Z= 0.531 Chirality : 0.047 0.144 6192 Planarity : 0.005 0.060 7032 Dihedral : 5.270 43.465 5856 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 1.06 % Allowed : 10.89 % Favored : 88.05 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % 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: -0.37 (0.12), residues: 4992 helix: 1.79 (0.15), residues: 1464 sheet: 0.33 (0.16), residues: 1080 loop : -1.89 (0.11), residues: 2448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 30 TYR 0.016 0.002 TYR H 297 PHE 0.021 0.002 PHE I 183 TRP 0.011 0.002 TRP H 175 HIS 0.012 0.001 HIS H 37 Details of bonding type rmsd covalent geometry : bond 0.00405 (40572) covalent geometry : angle 0.93543 (54996) hydrogen bonds : bond 0.06663 ( 1624) hydrogen bonds : angle 4.54683 ( 4677) metal coordination : bond 0.00401 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14869.27 seconds wall clock time: 253 minutes 25.18 seconds (15205.18 seconds total)