Starting phenix.real_space_refine on Wed Aug 27 00:57:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jce_36159/08_2025/8jce_36159.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jce_36159/08_2025/8jce_36159.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.41 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8jce_36159/08_2025/8jce_36159.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jce_36159/08_2025/8jce_36159.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8jce_36159/08_2025/8jce_36159.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jce_36159/08_2025/8jce_36159.map" } resolution = 2.41 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= 0.001 sd= 0.026 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 12 6.06 5 P 48 5.49 5 Mg 12 5.21 5 S 348 5.16 5 C 27420 2.51 5 N 7584 2.21 5 O 8880 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 127 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 44304 Number of models: 1 Model: "" Number of chains: 36 Chain: "A" Number of atoms: 3543 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 453, 3537 Classifications: {'peptide': 453} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 22, 'TRANS': 430} Chain breaks: 3 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 11 Conformer: "B" Number of residues, atoms: 453, 3537 Classifications: {'peptide': 453} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 22, 'TRANS': 430} Chain breaks: 3 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 11 bond proxies already assigned to first conformer: 3605 Chain: "B" Number of atoms: 3543 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 453, 3537 Classifications: {'peptide': 453} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 22, 'TRANS': 430} Chain breaks: 3 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 11 Conformer: "B" Number of residues, atoms: 453, 3537 Classifications: {'peptide': 453} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 22, 'TRANS': 430} Chain breaks: 3 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 11 bond proxies already assigned to first conformer: 3605 Chain: "C" Number of atoms: 3543 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 453, 3537 Classifications: {'peptide': 453} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 22, 'TRANS': 430} Chain breaks: 3 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 11 Conformer: "B" Number of residues, atoms: 453, 3537 Classifications: {'peptide': 453} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 22, 'TRANS': 430} Chain breaks: 3 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 11 bond proxies already assigned to first conformer: 3605 Chain: "D" Number of atoms: 3543 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 453, 3537 Classifications: {'peptide': 453} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 22, 'TRANS': 430} Chain breaks: 3 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 11 Conformer: "B" Number of residues, atoms: 453, 3537 Classifications: {'peptide': 453} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 22, 'TRANS': 430} Chain breaks: 3 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 11 bond proxies already assigned to first conformer: 3605 Chain: "E" Number of atoms: 3543 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 453, 3537 Classifications: {'peptide': 453} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 22, 'TRANS': 430} Chain breaks: 3 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 11 Conformer: "B" Number of residues, atoms: 453, 3537 Classifications: {'peptide': 453} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 22, 'TRANS': 430} Chain breaks: 3 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 11 bond proxies already assigned to first conformer: 3605 Chain: "F" Number of atoms: 3543 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 453, 3537 Classifications: {'peptide': 453} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 22, 'TRANS': 430} Chain breaks: 3 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 11 Conformer: "B" Number of residues, atoms: 453, 3537 Classifications: {'peptide': 453} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 22, 'TRANS': 430} Chain breaks: 3 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 11 bond proxies already assigned to first conformer: 3605 Chain: "G" Number of atoms: 3543 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 453, 3537 Classifications: {'peptide': 453} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 22, 'TRANS': 430} Chain breaks: 3 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 11 Conformer: "B" Number of residues, atoms: 453, 3537 Classifications: {'peptide': 453} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 22, 'TRANS': 430} Chain breaks: 3 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 11 bond proxies already assigned to first conformer: 3605 Chain: "H" Number of atoms: 3543 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 453, 3537 Classifications: {'peptide': 453} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 22, 'TRANS': 430} Chain breaks: 3 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 11 Conformer: "B" Number of residues, atoms: 453, 3537 Classifications: {'peptide': 453} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 22, 'TRANS': 430} Chain breaks: 3 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 11 bond proxies already assigned to first conformer: 3605 Chain: "I" Number of atoms: 3543 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 453, 3537 Classifications: {'peptide': 453} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 22, 'TRANS': 430} Chain breaks: 3 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 11 Conformer: "B" Number of residues, atoms: 453, 3537 Classifications: {'peptide': 453} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 22, 'TRANS': 430} Chain breaks: 3 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 11 bond proxies already assigned to first conformer: 3605 Chain: "J" Number of atoms: 3543 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 453, 3537 Classifications: {'peptide': 453} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 22, 'TRANS': 430} Chain breaks: 3 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 11 Conformer: "B" Number of residues, atoms: 453, 3537 Classifications: {'peptide': 453} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 22, 'TRANS': 430} Chain breaks: 3 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 11 bond proxies already assigned to first conformer: 3605 Chain: "K" Number of atoms: 3543 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 453, 3537 Classifications: {'peptide': 453} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 22, 'TRANS': 430} Chain breaks: 3 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 11 Conformer: "B" Number of residues, atoms: 453, 3537 Classifications: {'peptide': 453} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 22, 'TRANS': 430} Chain breaks: 3 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 11 bond proxies already assigned to first conformer: 3605 Chain: "L" Number of atoms: 3543 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 453, 3537 Classifications: {'peptide': 453} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 22, 'TRANS': 430} Chain breaks: 3 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 11 Conformer: "B" Number of residues, atoms: 453, 3537 Classifications: {'peptide': 453} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 22, 'TRANS': 430} Chain breaks: 3 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 11 bond proxies already assigned to first conformer: 3605 Chain: "A" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 100 Unusual residues: {' MG': 1, ' ZN': 1, 'YG4': 1} Classifications: {'peptide': 1, 'undetermined': 3} Link IDs: {None: 3} Chain: "B" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 100 Unusual residues: {' MG': 1, ' ZN': 1, 'YG4': 1} Classifications: {'peptide': 1, 'undetermined': 3} Link IDs: {None: 3} Chain: "C" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 100 Unusual residues: {' MG': 1, ' ZN': 1, 'YG4': 1} Classifications: {'peptide': 1, 'undetermined': 3} Link IDs: {None: 3} Chain: "D" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 100 Unusual residues: {' MG': 1, ' ZN': 1, 'YG4': 1} Classifications: {'peptide': 1, 'undetermined': 3} Link IDs: {None: 3} Chain: "E" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 100 Unusual residues: {' MG': 1, ' ZN': 1, 'YG4': 1} Classifications: {'peptide': 1, 'undetermined': 3} Link IDs: {None: 3} Chain: "F" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 100 Unusual residues: {' MG': 1, ' ZN': 1, 'YG4': 1} Classifications: {'peptide': 1, 'undetermined': 3} Link IDs: {None: 3} Chain: "G" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 100 Unusual residues: {' MG': 1, ' ZN': 1, 'YG4': 1} Classifications: {'peptide': 1, 'undetermined': 3} Link IDs: {None: 3} Chain: "H" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 100 Unusual residues: {' MG': 1, ' ZN': 1, 'YG4': 1} Classifications: {'peptide': 1, 'undetermined': 3} Link IDs: {None: 3} Chain: "I" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 100 Unusual residues: {' MG': 1, ' ZN': 1, 'YG4': 1} Classifications: {'peptide': 1, 'undetermined': 3} Link IDs: {None: 3} Chain: "J" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 100 Unusual residues: {' MG': 1, ' ZN': 1, 'YG4': 1} Classifications: {'peptide': 1, 'undetermined': 3} Link IDs: {None: 3} Chain: "K" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 100 Unusual residues: {' MG': 1, ' ZN': 1, 'YG4': 1} Classifications: {'peptide': 1, 'undetermined': 3} Link IDs: {None: 3} Chain: "L" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 100 Unusual residues: {' MG': 1, ' ZN': 1, 'YG4': 1} Classifications: {'peptide': 1, 'undetermined': 3} Link IDs: {None: 3} Chain: "A" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 50 Classifications: {'water': 50} Link IDs: {None: 49} Chain: "B" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 48 Classifications: {'water': 48} Link IDs: {None: 47} Chain: "C" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 49 Classifications: {'water': 49} Link IDs: {None: 48} Chain: "D" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 50 Classifications: {'water': 50} Link IDs: {None: 49} Chain: "E" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 48 Classifications: {'water': 48} Link IDs: {None: 47} Chain: "F" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 49 Classifications: {'water': 49} Link IDs: {None: 48} Chain: "G" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 50 Classifications: {'water': 50} Link IDs: {None: 49} Chain: "H" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 48 Classifications: {'water': 48} Link IDs: {None: 47} Chain: "I" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 49 Classifications: {'water': 49} Link IDs: {None: 48} Chain: "J" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 50 Classifications: {'water': 50} Link IDs: {None: 49} Chain: "K" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 48 Classifications: {'water': 48} Link IDs: {None: 47} Chain: "L" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 49 Classifications: {'water': 49} Link IDs: {None: 48} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1019 SG CYS A 134 20.276 131.099 61.518 1.00 77.67 S ATOM 1071 SG CYS A 141 20.951 135.121 60.817 1.00 74.94 S ATOM 4562 SG CYS B 134 17.158 86.013 61.522 1.00 77.73 S ATOM 4614 SG CYS B 141 15.854 89.824 60.792 1.00 71.40 S ATOM 8105 SG CYS C 134 37.093 45.420 61.509 1.00 77.84 S ATOM 8157 SG CYS C 141 33.968 48.043 60.817 1.00 71.12 S ATOM 11648 SG CYS D 134 74.601 20.266 61.521 1.00 77.78 S ATOM 11700 SG CYS D 141 70.579 20.941 60.818 1.00 75.09 S ATOM 15191 SG CYS E 134 119.679 17.158 61.523 1.00 77.58 S ATOM 15243 SG CYS E 141 115.873 15.847 60.793 1.00 71.62 S ATOM 18734 SG CYS F 134 160.280 37.085 61.510 1.00 77.76 S ATOM 18786 SG CYS F 141 157.649 33.970 60.813 1.00 70.84 S ATOM 22277 SG CYS G 134 185.436 74.590 61.523 1.00 77.43 S ATOM 22329 SG CYS G 141 184.762 70.570 60.819 1.00 74.90 S ATOM 25820 SG CYS H 134 188.557 119.679 61.526 1.00 77.73 S ATOM 25872 SG CYS H 141 189.852 115.862 60.790 1.00 71.72 S ATOM 29363 SG CYS I 134 168.604 160.290 61.515 1.00 77.79 S ATOM 29415 SG CYS I 141 171.725 157.648 60.813 1.00 70.94 S ATOM 32906 SG CYS J 134 131.110 185.426 61.520 1.00 77.55 S ATOM 32958 SG CYS J 141 135.130 184.752 60.818 1.00 74.97 S ATOM 36449 SG CYS K 134 86.021 188.547 61.525 1.00 77.52 S ATOM 36501 SG CYS K 141 89.835 189.842 60.792 1.00 71.38 S ATOM 39992 SG CYS L 134 45.427 168.606 61.508 1.00 77.81 S ATOM 40044 SG CYS L 141 48.058 171.723 60.813 1.00 70.83 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: 15.82, per 1000 atoms: 0.36 Number of scatterers: 44304 At special positions: 0 Unit cell: (206.55, 206.55, 90.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 12 29.99 S 348 16.00 P 48 15.00 Mg 12 11.99 O 8880 8.00 N 7584 7.00 C 27420 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: 3.13 Conformation dependent library (CDL) restraints added in 2.8 seconds Enol-peptide restraints added in 953.7 nanoseconds 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 B 602 " pdb="ZN ZN B 602 " - pdb=" NE2 HIS B 79 " pdb="ZN ZN B 602 " - pdb=" SG CYS B 141 " pdb="ZN ZN B 602 " - pdb=" SG CYS B 134 " pdb=" ZN C 602 " pdb="ZN ZN C 602 " - pdb=" NE2 HIS C 79 " pdb="ZN ZN C 602 " - pdb=" SG CYS C 141 " pdb="ZN ZN C 602 " - pdb=" SG CYS C 134 " pdb=" ZN D 602 " pdb="ZN ZN D 602 " - pdb=" NE2 HIS D 79 " pdb="ZN ZN D 602 " - pdb=" SG CYS D 141 " pdb="ZN ZN D 602 " - pdb=" SG CYS D 134 " pdb=" ZN E 602 " pdb="ZN ZN E 602 " - pdb=" NE2 HIS E 79 " pdb="ZN ZN E 602 " - pdb=" SG CYS E 141 " pdb="ZN ZN E 602 " - pdb=" SG CYS E 134 " pdb=" ZN F 602 " pdb="ZN ZN F 602 " - pdb=" NE2 HIS F 79 " pdb="ZN ZN F 602 " - pdb=" SG CYS F 141 " pdb="ZN ZN F 602 " - pdb=" SG CYS F 134 " pdb=" ZN G 602 " pdb="ZN ZN G 602 " - pdb=" NE2 HIS G 79 " pdb="ZN ZN G 602 " - pdb=" SG CYS G 141 " pdb="ZN ZN G 602 " - pdb=" SG CYS G 134 " pdb=" ZN H 602 " pdb="ZN ZN H 602 " - pdb=" NE2 HIS H 79 " pdb="ZN ZN H 602 " - pdb=" SG CYS H 141 " pdb="ZN ZN H 602 " - pdb=" SG CYS H 134 " pdb=" ZN I 602 " pdb="ZN ZN I 602 " - pdb=" NE2 HIS I 79 " pdb="ZN ZN I 602 " - pdb=" SG CYS I 141 " pdb="ZN ZN I 602 " - pdb=" SG CYS I 134 " pdb=" ZN J 602 " pdb="ZN ZN J 602 " - pdb=" NE2 HIS J 79 " pdb="ZN ZN J 602 " - pdb=" SG CYS J 141 " pdb="ZN ZN J 602 " - pdb=" SG CYS J 134 " pdb=" ZN K 602 " pdb="ZN ZN K 602 " - pdb=" NE2 HIS K 79 " pdb="ZN ZN K 602 " - pdb=" SG CYS K 141 " pdb="ZN ZN K 602 " - pdb=" SG CYS K 134 " pdb=" ZN L 602 " pdb="ZN ZN L 602 " - pdb=" NE2 HIS L 79 " pdb="ZN ZN L 602 " - pdb=" SG CYS L 141 " pdb="ZN ZN L 602 " - pdb=" SG CYS L 134 " 10752 Ramachandran restraints generated. 5376 Oldfield, 0 Emsley, 5376 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10368 Finding SS restraints... Secondary structure from input PDB file: 204 helices and 48 sheets defined 35.1% alpha, 22.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.31 Creating SS restraints... Processing helix chain 'A' and resid 13 through 22 removed outlier: 4.290A pdb=" N ALA A 17 " --> pdb=" O ALA A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 55 removed outlier: 3.541A pdb=" N LYS A 49 " --> pdb=" O HIS A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 72 removed outlier: 3.661A pdb=" N MET A 72 " --> pdb=" O ALA A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 102 removed outlier: 3.505A 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 Processing helix chain 'A' and resid 180 through 185 removed outlier: 3.539A pdb=" N MET A 184 " --> pdb=" O THR A 180 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR A 185 " --> pdb=" O THR A 181 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 180 through 185' Processing helix chain 'A' and resid 193 through 195 No H-bonds generated for 'chain 'A' and resid 193 through 195' 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 341 Processing helix chain 'A' and resid 342 through 343 No H-bonds generated for 'chain 'A' and resid 342 through 343' Processing helix chain 'A' and resid 344 through 348 removed outlier: 3.520A pdb=" N THR A 348 " --> pdb=" O ILE A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 364 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 removed outlier: 3.519A pdb=" N GLU A 403 " --> pdb=" O ARG A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 473 Processing helix chain 'B' and resid 13 through 22 removed outlier: 4.366A pdb=" N ALA B 17 " --> pdb=" O ALA B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 55 removed outlier: 3.547A pdb=" N LYS B 49 " --> pdb=" O HIS B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 72 removed outlier: 3.681A pdb=" N MET B 72 " --> pdb=" O ALA B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 102 Processing helix chain 'B' and resid 111 through 125 Processing helix chain 'B' and resid 157 through 167 Processing helix chain 'B' and resid 180 through 185 removed outlier: 3.513A pdb=" N MET B 184 " --> pdb=" O THR B 180 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N TYR B 185 " --> pdb=" O THR B 181 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 180 through 185' Processing helix chain 'B' and resid 193 through 195 No H-bonds generated for 'chain 'B' and resid 193 through 195' 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 341 Processing helix chain 'B' and resid 342 through 343 No H-bonds generated for 'chain 'B' and resid 342 through 343' Processing helix chain 'B' and resid 344 through 348 removed outlier: 3.572A pdb=" N THR B 348 " --> pdb=" O ILE B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 364 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 removed outlier: 3.533A pdb=" N GLU B 403 " --> pdb=" O ARG B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 473 Processing helix chain 'C' and resid 13 through 22 removed outlier: 4.344A pdb=" N ALA C 17 " --> pdb=" O ALA C 13 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 55 removed outlier: 3.589A pdb=" N LYS C 49 " --> pdb=" O HIS C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 72 removed outlier: 3.687A pdb=" N MET C 72 " --> pdb=" O ALA C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 102 Processing helix chain 'C' and resid 111 through 125 Processing helix chain 'C' and resid 157 through 167 Processing helix chain 'C' and resid 180 through 185 removed outlier: 3.543A pdb=" N MET C 184 " --> pdb=" O THR C 180 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 195 No H-bonds generated for 'chain 'C' and resid 193 through 195' 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 341 Processing helix chain 'C' and resid 342 through 343 No H-bonds generated for 'chain 'C' and resid 342 through 343' Processing helix chain 'C' and resid 344 through 348 removed outlier: 3.527A pdb=" N THR C 348 " --> pdb=" O ILE C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 364 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 removed outlier: 3.611A pdb=" N GLU C 403 " --> pdb=" O ARG C 399 " (cutoff:3.500A) Processing helix chain 'C' and resid 461 through 473 Processing helix chain 'D' and resid 13 through 22 removed outlier: 4.293A pdb=" N ALA D 17 " --> pdb=" O ALA D 13 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 55 removed outlier: 3.542A pdb=" N LYS D 49 " --> pdb=" O HIS D 45 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 72 removed outlier: 3.668A pdb=" N MET D 72 " --> pdb=" O ALA D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 102 removed outlier: 3.504A 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 Processing helix chain 'D' and resid 180 through 185 removed outlier: 3.540A pdb=" N MET D 184 " --> pdb=" O THR D 180 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR D 185 " --> pdb=" O THR D 181 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 180 through 185' Processing helix chain 'D' and resid 193 through 195 No H-bonds generated for 'chain 'D' and resid 193 through 195' 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 341 Processing helix chain 'D' and resid 342 through 343 No H-bonds generated for 'chain 'D' and resid 342 through 343' Processing helix chain 'D' and resid 344 through 348 removed outlier: 3.521A pdb=" N THR D 348 " --> pdb=" O ILE D 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 351 through 364 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 removed outlier: 3.520A pdb=" N GLU D 403 " --> pdb=" O ARG D 399 " (cutoff:3.500A) Processing helix chain 'D' and resid 461 through 473 Processing helix chain 'E' and resid 13 through 22 removed outlier: 4.388A pdb=" N ALA E 17 " --> pdb=" O ALA E 13 " (cutoff:3.500A) Processing helix chain 'E' and resid 37 through 55 removed outlier: 3.547A pdb=" N LYS E 49 " --> pdb=" O HIS E 45 " (cutoff:3.500A) Processing helix chain 'E' and resid 67 through 72 removed outlier: 3.646A pdb=" N MET E 72 " --> pdb=" O ALA E 69 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 102 Processing helix chain 'E' and resid 111 through 125 Processing helix chain 'E' and resid 157 through 167 Processing helix chain 'E' and resid 180 through 185 removed outlier: 3.513A pdb=" N MET E 184 " --> pdb=" O THR E 180 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TYR E 185 " --> pdb=" O THR E 181 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 180 through 185' Processing helix chain 'E' and resid 193 through 195 No H-bonds generated for 'chain 'E' and resid 193 through 195' 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 341 Processing helix chain 'E' and resid 342 through 343 No H-bonds generated for 'chain 'E' and resid 342 through 343' Processing helix chain 'E' and resid 344 through 348 removed outlier: 3.574A pdb=" N THR E 348 " --> pdb=" O ILE E 345 " (cutoff:3.500A) Processing helix chain 'E' and resid 351 through 364 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 removed outlier: 3.532A pdb=" N GLU E 403 " --> pdb=" O ARG E 399 " (cutoff:3.500A) Processing helix chain 'E' and resid 461 through 473 Processing helix chain 'F' and resid 13 through 22 removed outlier: 4.344A pdb=" N ALA F 17 " --> pdb=" O ALA F 13 " (cutoff:3.500A) Processing helix chain 'F' and resid 37 through 55 removed outlier: 3.593A pdb=" N LYS F 49 " --> pdb=" O HIS F 45 " (cutoff:3.500A) Processing helix chain 'F' and resid 67 through 72 removed outlier: 3.688A pdb=" N MET F 72 " --> pdb=" O ALA F 69 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 102 Processing helix chain 'F' and resid 111 through 125 Processing helix chain 'F' and resid 157 through 167 Processing helix chain 'F' and resid 180 through 185 removed outlier: 3.544A pdb=" N MET F 184 " --> pdb=" O THR F 180 " (cutoff:3.500A) Processing helix chain 'F' and resid 193 through 195 No H-bonds generated for 'chain 'F' and resid 193 through 195' 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 341 Processing helix chain 'F' and resid 342 through 343 No H-bonds generated for 'chain 'F' and resid 342 through 343' Processing helix chain 'F' and resid 344 through 348 removed outlier: 3.530A pdb=" N THR F 348 " --> pdb=" O ILE F 345 " (cutoff:3.500A) Processing helix chain 'F' and resid 351 through 364 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 removed outlier: 3.610A pdb=" N GLU F 403 " --> pdb=" O ARG F 399 " (cutoff:3.500A) Processing helix chain 'F' and resid 461 through 473 Processing helix chain 'G' and resid 13 through 22 removed outlier: 4.291A pdb=" N ALA G 17 " --> pdb=" O ALA G 13 " (cutoff:3.500A) Processing helix chain 'G' and resid 37 through 55 removed outlier: 3.540A pdb=" N LYS G 49 " --> pdb=" O HIS G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 67 through 72 removed outlier: 3.669A pdb=" N MET G 72 " --> pdb=" O ALA G 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 88 through 102 removed outlier: 3.504A 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 Processing helix chain 'G' and resid 180 through 185 removed outlier: 3.540A pdb=" N MET G 184 " --> pdb=" O THR G 180 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N TYR G 185 " --> pdb=" O THR G 181 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 180 through 185' Processing helix chain 'G' and resid 193 through 195 No H-bonds generated for 'chain 'G' and resid 193 through 195' 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 341 Processing helix chain 'G' and resid 342 through 343 No H-bonds generated for 'chain 'G' and resid 342 through 343' Processing helix chain 'G' and resid 344 through 348 removed outlier: 3.521A pdb=" N THR G 348 " --> pdb=" O ILE G 345 " (cutoff:3.500A) Processing helix chain 'G' and resid 351 through 364 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 removed outlier: 3.509A pdb=" N GLU G 403 " --> pdb=" O ARG G 399 " (cutoff:3.500A) Processing helix chain 'G' and resid 461 through 473 Processing helix chain 'H' and resid 13 through 22 removed outlier: 4.373A pdb=" N ALA H 17 " --> pdb=" O ALA H 13 " (cutoff:3.500A) Processing helix chain 'H' and resid 37 through 55 removed outlier: 3.549A pdb=" N LYS H 49 " --> pdb=" O HIS H 45 " (cutoff:3.500A) Processing helix chain 'H' and resid 67 through 72 removed outlier: 3.658A pdb=" N MET H 72 " --> pdb=" O ALA H 69 " (cutoff:3.500A) Processing helix chain 'H' and resid 88 through 102 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: 3.514A pdb=" N MET H 184 " --> pdb=" O THR H 180 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TYR H 185 " --> pdb=" O THR H 181 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 180 through 185' Processing helix chain 'H' and resid 193 through 195 No H-bonds generated for 'chain 'H' and resid 193 through 195' 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 341 Processing helix chain 'H' and resid 342 through 343 No H-bonds generated for 'chain 'H' and resid 342 through 343' Processing helix chain 'H' and resid 344 through 348 removed outlier: 3.568A pdb=" N THR H 348 " --> pdb=" O ILE H 345 " (cutoff:3.500A) Processing helix chain 'H' and resid 351 through 364 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 removed outlier: 3.521A pdb=" N GLU H 403 " --> pdb=" O ARG H 399 " (cutoff:3.500A) Processing helix chain 'H' and resid 461 through 473 Processing helix chain 'I' and resid 13 through 22 removed outlier: 4.348A pdb=" N ALA I 17 " --> pdb=" O ALA I 13 " (cutoff:3.500A) Processing helix chain 'I' and resid 37 through 55 removed outlier: 3.591A pdb=" N LYS I 49 " --> pdb=" O HIS I 45 " (cutoff:3.500A) Processing helix chain 'I' and resid 67 through 72 removed outlier: 3.689A pdb=" N MET I 72 " --> pdb=" O ALA I 69 " (cutoff:3.500A) Processing helix chain 'I' and resid 88 through 102 Processing helix chain 'I' and resid 111 through 125 Processing helix chain 'I' and resid 157 through 167 Processing helix chain 'I' and resid 180 through 185 removed outlier: 3.545A pdb=" N MET I 184 " --> pdb=" O THR I 180 " (cutoff:3.500A) Processing helix chain 'I' and resid 193 through 195 No H-bonds generated for 'chain 'I' and resid 193 through 195' 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 341 Processing helix chain 'I' and resid 342 through 343 No H-bonds generated for 'chain 'I' and resid 342 through 343' Processing helix chain 'I' and resid 344 through 348 removed outlier: 3.532A pdb=" N THR I 348 " --> pdb=" O ILE I 345 " (cutoff:3.500A) Processing helix chain 'I' and resid 351 through 364 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 removed outlier: 3.606A pdb=" N GLU I 403 " --> pdb=" O ARG I 399 " (cutoff:3.500A) Processing helix chain 'I' and resid 461 through 473 Processing helix chain 'J' and resid 13 through 22 removed outlier: 4.288A pdb=" N ALA J 17 " --> pdb=" O ALA J 13 " (cutoff:3.500A) Processing helix chain 'J' and resid 37 through 55 removed outlier: 3.539A pdb=" N LYS J 49 " --> pdb=" O HIS J 45 " (cutoff:3.500A) Processing helix chain 'J' and resid 67 through 72 removed outlier: 3.661A pdb=" N MET J 72 " --> pdb=" O ALA J 69 " (cutoff:3.500A) Processing helix chain 'J' and resid 88 through 102 removed outlier: 3.516A 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 Processing helix chain 'J' and resid 180 through 185 removed outlier: 3.539A pdb=" N MET J 184 " --> pdb=" O THR J 180 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N TYR J 185 " --> pdb=" O THR J 181 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 180 through 185' Processing helix chain 'J' and resid 193 through 195 No H-bonds generated for 'chain 'J' and resid 193 through 195' 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 341 Processing helix chain 'J' and resid 342 through 343 No H-bonds generated for 'chain 'J' and resid 342 through 343' Processing helix chain 'J' and resid 344 through 348 removed outlier: 3.520A pdb=" N THR J 348 " --> pdb=" O ILE J 345 " (cutoff:3.500A) Processing helix chain 'J' and resid 351 through 364 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 removed outlier: 3.514A pdb=" N GLU J 403 " --> pdb=" O ARG J 399 " (cutoff:3.500A) Processing helix chain 'J' and resid 461 through 473 Processing helix chain 'K' and resid 13 through 22 removed outlier: 4.362A pdb=" N ALA K 17 " --> pdb=" O ALA K 13 " (cutoff:3.500A) Processing helix chain 'K' and resid 37 through 55 removed outlier: 3.549A pdb=" N LYS K 49 " --> pdb=" O HIS K 45 " (cutoff:3.500A) Processing helix chain 'K' and resid 67 through 72 removed outlier: 3.668A pdb=" N MET K 72 " --> pdb=" O ALA K 69 " (cutoff:3.500A) Processing helix chain 'K' and resid 88 through 102 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: 3.515A pdb=" N MET K 184 " --> pdb=" O THR K 180 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N TYR K 185 " --> pdb=" O THR K 181 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 180 through 185' Processing helix chain 'K' and resid 193 through 195 No H-bonds generated for 'chain 'K' and resid 193 through 195' 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 341 Processing helix chain 'K' and resid 342 through 343 No H-bonds generated for 'chain 'K' and resid 342 through 343' Processing helix chain 'K' and resid 344 through 348 removed outlier: 3.570A pdb=" N THR K 348 " --> pdb=" O ILE K 345 " (cutoff:3.500A) Processing helix chain 'K' and resid 351 through 364 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 removed outlier: 3.521A pdb=" N GLU K 403 " --> pdb=" O ARG K 399 " (cutoff:3.500A) Processing helix chain 'K' and resid 461 through 473 Processing helix chain 'L' and resid 13 through 22 removed outlier: 4.349A pdb=" N ALA L 17 " --> pdb=" O ALA L 13 " (cutoff:3.500A) Processing helix chain 'L' and resid 37 through 55 removed outlier: 3.585A pdb=" N LYS L 49 " --> pdb=" O HIS L 45 " (cutoff:3.500A) Processing helix chain 'L' and resid 67 through 72 removed outlier: 3.685A pdb=" N MET L 72 " --> pdb=" O ALA L 69 " (cutoff:3.500A) Processing helix chain 'L' and resid 88 through 102 Processing helix chain 'L' and resid 111 through 125 Processing helix chain 'L' and resid 157 through 167 Processing helix chain 'L' and resid 180 through 185 removed outlier: 3.543A pdb=" N MET L 184 " --> pdb=" O THR L 180 " (cutoff:3.500A) Processing helix chain 'L' and resid 193 through 195 No H-bonds generated for 'chain 'L' and resid 193 through 195' 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 341 Processing helix chain 'L' and resid 342 through 343 No H-bonds generated for 'chain 'L' and resid 342 through 343' Processing helix chain 'L' and resid 344 through 348 removed outlier: 3.533A pdb=" N THR L 348 " --> pdb=" O ILE L 345 " (cutoff:3.500A) Processing helix chain 'L' and resid 351 through 364 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 removed outlier: 3.613A pdb=" N GLU L 403 " --> pdb=" O ARG L 399 " (cutoff:3.500A) Processing helix chain 'L' and resid 461 through 473 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: 8.274A pdb=" N CYS A 134 " --> pdb=" O TYR A 78 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N CYS A 80 " --> pdb=" O CYS A 134 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ILE A 61 " --> pdb=" O HIS A 79 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N VAL A 81 " --> pdb=" O ILE A 61 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ASP A 63 " --> pdb=" O VAL A 81 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N GLN A 151 " --> pdb=" O ILE A 64 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N ALA A 148 " --> pdb=" O TYR A 174 " (cutoff:3.500A) removed outlier: 8.506A pdb=" N VAL A 176 " --> pdb=" O ALA A 148 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N TYR A 150 " --> pdb=" O VAL A 176 " (cutoff:3.500A) removed outlier: 9.004A pdb=" N PHE A 178 " --> pdb=" O TYR A 150 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N TYR A 285 " --> pdb=" O SER A 281 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N SER A 281 " --> pdb=" O TYR A 285 " (cutoff:3.500A) removed outlier: 6.667A 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: 6.873A pdb=" N ALA A 189 " --> pdb=" O CYS A 331 " (cutoff:3.500A) removed outlier: 9.249A pdb=" N TYR A 333 " --> pdb=" O ALA A 189 " (cutoff:3.500A) removed outlier: 8.251A 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: 4.070A pdb=" N THR A 437 " --> pdb=" O HIS A 308 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 3 through 6 Processing sheet with id=AA6, first strand: chain 'B' and resid 133 through 134 removed outlier: 8.270A pdb=" N CYS B 134 " --> pdb=" O TYR B 78 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N CYS B 80 " --> pdb=" O CYS B 134 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ILE B 61 " --> pdb=" O HIS B 79 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N VAL B 81 " --> pdb=" O ILE B 61 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ASP B 63 " --> pdb=" O VAL B 81 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N GLN B 151 " --> pdb=" O ILE B 64 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N TYR B 285 " --> pdb=" O SER B 281 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N SER B 281 " --> pdb=" O TYR B 285 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N VAL B 287 " --> pdb=" O VAL B 279 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 246 through 251 removed outlier: 6.879A pdb=" N ALA B 189 " --> pdb=" O CYS B 331 " (cutoff:3.500A) removed outlier: 9.260A pdb=" N TYR B 333 " --> pdb=" O ALA B 189 " (cutoff:3.500A) removed outlier: 8.307A 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: 3.983A pdb=" N THR B 437 " --> pdb=" O HIS B 308 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 3 through 6 Processing sheet with id=AB1, first strand: chain 'C' and resid 133 through 134 removed outlier: 8.203A pdb=" N CYS C 134 " --> pdb=" O TYR C 78 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N CYS C 80 " --> pdb=" O CYS C 134 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N GLN C 151 " --> pdb=" O ILE C 64 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLY C 177 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N TYR C 285 " --> pdb=" O SER C 281 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N SER C 281 " --> pdb=" O TYR C 285 " (cutoff:3.500A) removed outlier: 6.583A 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: 6.858A pdb=" N ALA C 189 " --> pdb=" O CYS C 331 " (cutoff:3.500A) removed outlier: 9.241A pdb=" N TYR C 333 " --> pdb=" O ALA C 189 " (cutoff:3.500A) removed outlier: 8.278A 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: 4.085A 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: 8.273A pdb=" N CYS D 134 " --> pdb=" O TYR D 78 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N CYS D 80 " --> pdb=" O CYS D 134 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N GLN D 151 " --> pdb=" O ILE D 64 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N ALA D 148 " --> pdb=" O TYR D 174 " (cutoff:3.500A) removed outlier: 8.507A pdb=" N VAL D 176 " --> pdb=" O ALA D 148 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N TYR D 150 " --> pdb=" O VAL D 176 " (cutoff:3.500A) removed outlier: 9.005A pdb=" N PHE D 178 " --> pdb=" O TYR D 150 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N TYR D 285 " --> pdb=" O SER D 281 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N SER D 281 " --> pdb=" O TYR D 285 " (cutoff:3.500A) removed outlier: 6.664A 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: 6.868A pdb=" N ALA D 189 " --> pdb=" O CYS D 331 " (cutoff:3.500A) removed outlier: 9.248A pdb=" N TYR D 333 " --> pdb=" O ALA D 189 " (cutoff:3.500A) removed outlier: 8.247A 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: 4.068A pdb=" N THR D 437 " --> pdb=" O HIS D 308 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 3 through 6 Processing sheet with id=AB9, first strand: chain 'E' and resid 133 through 134 removed outlier: 8.271A pdb=" N CYS E 134 " --> pdb=" O TYR E 78 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N CYS E 80 " --> pdb=" O CYS E 134 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ILE E 61 " --> pdb=" O HIS E 79 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N VAL E 81 " --> pdb=" O ILE E 61 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ASP E 63 " --> pdb=" O VAL E 81 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N GLN E 151 " --> pdb=" O ILE E 64 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N TYR E 285 " --> pdb=" O SER E 281 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N SER E 281 " --> pdb=" O TYR E 285 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N VAL E 287 " --> pdb=" O VAL E 279 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 246 through 251 removed outlier: 6.880A pdb=" N ALA E 189 " --> pdb=" O CYS E 331 " (cutoff:3.500A) removed outlier: 9.262A pdb=" N TYR E 333 " --> pdb=" O ALA E 189 " (cutoff:3.500A) removed outlier: 8.311A 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: 3.981A 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: 8.200A pdb=" N CYS F 134 " --> pdb=" O TYR F 78 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N CYS F 80 " --> pdb=" O CYS F 134 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ILE F 61 " --> pdb=" O HIS F 79 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N VAL F 81 " --> pdb=" O ILE F 61 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ASP F 63 " --> pdb=" O VAL F 81 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N GLN F 151 " --> pdb=" O ILE F 64 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLY F 177 " --> pdb=" O VAL F 286 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N TYR F 285 " --> pdb=" O SER F 281 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N SER F 281 " --> pdb=" O TYR F 285 " (cutoff:3.500A) removed outlier: 6.582A 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: 6.865A pdb=" N ALA F 189 " --> pdb=" O CYS F 331 " (cutoff:3.500A) removed outlier: 9.247A pdb=" N TYR F 333 " --> pdb=" O ALA F 189 " (cutoff:3.500A) removed outlier: 8.277A 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: 4.086A pdb=" N THR F 437 " --> pdb=" O HIS F 308 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 3 through 6 Processing sheet with id=AC8, first strand: chain 'G' and resid 133 through 134 removed outlier: 8.273A pdb=" N CYS G 134 " --> pdb=" O TYR G 78 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N CYS G 80 " --> pdb=" O CYS G 134 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N GLN G 151 " --> pdb=" O ILE G 64 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ALA G 148 " --> pdb=" O TYR G 174 " (cutoff:3.500A) removed outlier: 8.504A pdb=" N VAL G 176 " --> pdb=" O ALA G 148 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N TYR G 150 " --> pdb=" O VAL G 176 " (cutoff:3.500A) removed outlier: 9.002A pdb=" N PHE G 178 " --> pdb=" O TYR G 150 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N TYR G 285 " --> pdb=" O SER G 281 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N SER G 281 " --> pdb=" O TYR G 285 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N VAL G 287 " --> pdb=" O VAL G 279 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 246 through 251 removed outlier: 6.874A pdb=" N ALA G 189 " --> pdb=" O CYS G 331 " (cutoff:3.500A) removed outlier: 9.251A pdb=" N TYR G 333 " --> pdb=" O ALA G 189 " (cutoff:3.500A) removed outlier: 8.248A 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: 4.054A 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: 8.265A pdb=" N CYS H 134 " --> pdb=" O TYR H 78 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N CYS H 80 " --> pdb=" O CYS H 134 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ILE H 61 " --> pdb=" O HIS H 79 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N VAL H 81 " --> pdb=" O ILE H 61 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ASP H 63 " --> pdb=" O VAL H 81 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N GLN H 151 " --> pdb=" O ILE H 64 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N TYR H 285 " --> pdb=" O SER H 281 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N SER H 281 " --> pdb=" O TYR H 285 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N VAL H 287 " --> pdb=" O VAL H 279 " (cutoff:3.500A) removed outlier: 8.842A pdb=" N PHE H 447 " --> pdb=" O VAL H 263 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N HIS H 265 " --> pdb=" O PHE H 447 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 246 through 251 removed outlier: 6.878A pdb=" N ALA H 189 " --> pdb=" O CYS H 331 " (cutoff:3.500A) removed outlier: 9.260A pdb=" N TYR H 333 " --> pdb=" O ALA H 189 " (cutoff:3.500A) removed outlier: 8.310A 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: 3.984A 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: 8.205A pdb=" N CYS I 134 " --> pdb=" O TYR I 78 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N CYS I 80 " --> pdb=" O CYS I 134 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N GLN I 151 " --> pdb=" O ILE I 64 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLY I 177 " --> pdb=" O VAL I 286 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N TYR I 285 " --> pdb=" O SER I 281 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N SER I 281 " --> pdb=" O TYR I 285 " (cutoff:3.500A) removed outlier: 6.589A 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: 6.868A pdb=" N ALA I 189 " --> pdb=" O CYS I 331 " (cutoff:3.500A) removed outlier: 9.247A pdb=" N TYR I 333 " --> pdb=" O ALA I 189 " (cutoff:3.500A) removed outlier: 8.279A 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: 4.083A 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: 8.274A pdb=" N CYS J 134 " --> pdb=" O TYR J 78 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N CYS J 80 " --> pdb=" O CYS J 134 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ILE J 61 " --> pdb=" O HIS J 79 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N VAL J 81 " --> pdb=" O ILE J 61 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ASP J 63 " --> pdb=" O VAL J 81 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N GLN J 151 " --> pdb=" O ILE J 64 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ALA J 148 " --> pdb=" O TYR J 174 " (cutoff:3.500A) removed outlier: 8.503A pdb=" N VAL J 176 " --> pdb=" O ALA J 148 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N TYR J 150 " --> pdb=" O VAL J 176 " (cutoff:3.500A) removed outlier: 9.003A pdb=" N PHE J 178 " --> pdb=" O TYR J 150 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N TYR J 285 " --> pdb=" O SER J 281 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N SER J 281 " --> pdb=" O TYR J 285 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N VAL J 287 " --> pdb=" O VAL J 279 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 246 through 251 removed outlier: 6.875A pdb=" N ALA J 189 " --> pdb=" O CYS J 331 " (cutoff:3.500A) removed outlier: 9.250A pdb=" N TYR J 333 " --> pdb=" O ALA J 189 " (cutoff:3.500A) removed outlier: 8.250A 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: 4.054A pdb=" N THR J 437 " --> pdb=" O HIS J 308 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'K' and resid 3 through 6 Processing sheet with id=AE6, first strand: chain 'K' and resid 133 through 134 removed outlier: 8.273A pdb=" N CYS K 134 " --> pdb=" O TYR K 78 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N CYS K 80 " --> pdb=" O CYS K 134 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ILE K 61 " --> pdb=" O HIS K 79 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N VAL K 81 " --> pdb=" O ILE K 61 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ASP K 63 " --> pdb=" O VAL K 81 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N GLN K 151 " --> pdb=" O ILE K 64 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N TYR K 285 " --> pdb=" O SER K 281 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N SER K 281 " --> pdb=" O TYR K 285 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N VAL K 287 " --> pdb=" O VAL K 279 " (cutoff:3.500A) removed outlier: 8.842A pdb=" N PHE K 447 " --> pdb=" O VAL K 263 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N HIS K 265 " --> pdb=" O PHE K 447 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'K' and resid 246 through 251 removed outlier: 6.880A pdb=" N ALA K 189 " --> pdb=" O CYS K 331 " (cutoff:3.500A) removed outlier: 9.263A pdb=" N TYR K 333 " --> pdb=" O ALA K 189 " (cutoff:3.500A) removed outlier: 8.309A 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: 3.984A 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: 8.203A pdb=" N CYS L 134 " --> pdb=" O TYR L 78 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N CYS L 80 " --> pdb=" O CYS L 134 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N GLN L 151 " --> pdb=" O ILE L 64 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLY L 177 " --> pdb=" O VAL L 286 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N TYR L 285 " --> pdb=" O SER L 281 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N SER L 281 " --> pdb=" O TYR L 285 " (cutoff:3.500A) removed outlier: 6.590A 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: 6.859A pdb=" N ALA L 189 " --> pdb=" O CYS L 331 " (cutoff:3.500A) removed outlier: 9.241A pdb=" N TYR L 333 " --> pdb=" O ALA L 189 " (cutoff:3.500A) removed outlier: 8.277A 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: 4.082A pdb=" N THR L 437 " --> pdb=" O HIS L 308 " (cutoff:3.500A) 1868 hydrogen bonds defined for protein. 5310 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: 8.42 Time building geometry restraints manager: 4.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 13912 1.34 - 1.46: 8300 1.46 - 1.58: 21876 1.58 - 1.69: 96 1.69 - 1.81: 528 Bond restraints: 44712 Sorted by residual: bond pdb=" O8 YG4 G 604 " pdb=" P1 YG4 G 604 " ideal model delta sigma weight residual 1.656 1.599 0.057 2.00e-02 2.50e+03 8.09e+00 bond pdb=" O8 YG4 E 604 " pdb=" P1 YG4 E 604 " ideal model delta sigma weight residual 1.656 1.599 0.057 2.00e-02 2.50e+03 8.07e+00 bond pdb=" O8 YG4 B 604 " pdb=" P1 YG4 B 604 " ideal model delta sigma weight residual 1.656 1.600 0.056 2.00e-02 2.50e+03 7.97e+00 bond pdb=" O8 YG4 K 604 " pdb=" P1 YG4 K 604 " ideal model delta sigma weight residual 1.656 1.600 0.056 2.00e-02 2.50e+03 7.96e+00 bond pdb=" O8 YG4 J 604 " pdb=" P1 YG4 J 604 " ideal model delta sigma weight residual 1.656 1.600 0.056 2.00e-02 2.50e+03 7.95e+00 ... (remaining 44707 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.25: 59772 2.25 - 4.49: 812 4.49 - 6.74: 96 6.74 - 8.99: 104 8.99 - 11.24: 32 Bond angle restraints: 60816 Sorted by residual: angle pdb=" CG SAH B 603 " pdb=" SD SAH B 603 " pdb=" C5' SAH B 603 " ideal model delta sigma weight residual 101.77 90.53 11.24 3.00e+00 1.11e-01 1.40e+01 angle pdb=" CG SAH E 603 " pdb=" SD SAH E 603 " pdb=" C5' SAH E 603 " ideal model delta sigma weight residual 101.77 90.55 11.22 3.00e+00 1.11e-01 1.40e+01 angle pdb=" CG SAH H 603 " pdb=" SD SAH H 603 " pdb=" C5' SAH H 603 " ideal model delta sigma weight residual 101.77 90.55 11.22 3.00e+00 1.11e-01 1.40e+01 angle pdb=" CG SAH K 603 " pdb=" SD SAH K 603 " pdb=" C5' SAH K 603 " ideal model delta sigma weight residual 101.77 90.56 11.21 3.00e+00 1.11e-01 1.40e+01 angle pdb=" CG SAH F 603 " pdb=" SD SAH F 603 " pdb=" C5' SAH F 603 " ideal model delta sigma weight residual 101.77 90.56 11.21 3.00e+00 1.11e-01 1.40e+01 ... (remaining 60811 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.00: 26157 34.00 - 68.00: 1234 68.00 - 102.00: 209 102.00 - 136.00: 8 136.00 - 170.00: 16 Dihedral angle restraints: 27624 sinusoidal: 11628 harmonic: 15996 Sorted by residual: dihedral pdb=" C14 YG4 L 604 " pdb=" O16 YG4 L 604 " pdb=" P4 YG4 L 604 " pdb=" O18 YG4 L 604 " ideal model delta sinusoidal sigma weight residual 184.82 14.82 170.00 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" C14 YG4 F 604 " pdb=" O16 YG4 F 604 " pdb=" P4 YG4 F 604 " pdb=" O18 YG4 F 604 " ideal model delta sinusoidal sigma weight residual 184.82 14.87 169.95 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" C14 YG4 C 604 " pdb=" O16 YG4 C 604 " pdb=" P4 YG4 C 604 " pdb=" O18 YG4 C 604 " ideal model delta sinusoidal sigma weight residual 184.82 14.91 169.91 1 3.00e+01 1.11e-03 2.12e+01 ... (remaining 27621 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 5940 0.064 - 0.128: 845 0.128 - 0.192: 31 0.192 - 0.257: 24 0.257 - 0.321: 12 Chirality restraints: 6852 Sorted by residual: chirality pdb=" C16 YG4 A1003 " pdb=" C15 YG4 A1003 " pdb=" N6 YG4 A1003 " pdb=" O15 YG4 A1003 " both_signs ideal model delta sigma weight residual False 2.46 2.14 0.32 2.00e-01 2.50e+01 2.57e+00 chirality pdb=" C16 YG4 D 604 " pdb=" C15 YG4 D 604 " pdb=" N6 YG4 D 604 " pdb=" O15 YG4 D 604 " both_signs ideal model delta sigma weight residual False 2.46 2.14 0.32 2.00e-01 2.50e+01 2.56e+00 chirality pdb=" C16 YG4 G 604 " pdb=" C15 YG4 G 604 " pdb=" N6 YG4 G 604 " pdb=" O15 YG4 G 604 " both_signs ideal model delta sigma weight residual False 2.46 2.15 0.32 2.00e-01 2.50e+01 2.53e+00 ... (remaining 6849 not shown) Planarity restraints: 7548 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C27 YG4 F 604 " -0.056 2.00e-02 2.50e+03 2.67e-02 1.60e+01 pdb=" C28 YG4 F 604 " 0.006 2.00e-02 2.50e+03 pdb=" C29 YG4 F 604 " -0.006 2.00e-02 2.50e+03 pdb=" C30 YG4 F 604 " 0.017 2.00e-02 2.50e+03 pdb=" C31 YG4 F 604 " 0.032 2.00e-02 2.50e+03 pdb=" N11 YG4 F 604 " 0.016 2.00e-02 2.50e+03 pdb=" N12 YG4 F 604 " -0.011 2.00e-02 2.50e+03 pdb=" O24 YG4 F 604 " 0.028 2.00e-02 2.50e+03 pdb=" O25 YG4 F 604 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C27 YG4 L 604 " 0.056 2.00e-02 2.50e+03 2.66e-02 1.60e+01 pdb=" C28 YG4 L 604 " -0.006 2.00e-02 2.50e+03 pdb=" C29 YG4 L 604 " 0.006 2.00e-02 2.50e+03 pdb=" C30 YG4 L 604 " -0.016 2.00e-02 2.50e+03 pdb=" C31 YG4 L 604 " -0.032 2.00e-02 2.50e+03 pdb=" N11 YG4 L 604 " -0.017 2.00e-02 2.50e+03 pdb=" N12 YG4 L 604 " 0.011 2.00e-02 2.50e+03 pdb=" O24 YG4 L 604 " -0.028 2.00e-02 2.50e+03 pdb=" O25 YG4 L 604 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C27 YG4 C 604 " 0.056 2.00e-02 2.50e+03 2.66e-02 1.59e+01 pdb=" C28 YG4 C 604 " -0.006 2.00e-02 2.50e+03 pdb=" C29 YG4 C 604 " 0.005 2.00e-02 2.50e+03 pdb=" C30 YG4 C 604 " -0.016 2.00e-02 2.50e+03 pdb=" C31 YG4 C 604 " -0.032 2.00e-02 2.50e+03 pdb=" N11 YG4 C 604 " -0.016 2.00e-02 2.50e+03 pdb=" N12 YG4 C 604 " 0.011 2.00e-02 2.50e+03 pdb=" O24 YG4 C 604 " -0.028 2.00e-02 2.50e+03 pdb=" O25 YG4 C 604 " 0.026 2.00e-02 2.50e+03 ... (remaining 7545 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 304 2.60 - 3.17: 32804 3.17 - 3.75: 62593 3.75 - 4.32: 96138 4.32 - 4.90: 156263 Nonbonded interactions: 348102 Sorted by model distance: nonbonded pdb="MG MG H 601 " pdb=" O HOH G 703 " model vdw 2.023 2.170 nonbonded pdb="MG MG E 601 " pdb=" O HOH D 703 " model vdw 2.025 2.170 nonbonded pdb="MG MG B 601 " pdb=" O HOH A1103 " model vdw 2.025 2.170 nonbonded pdb="MG MG K 601 " pdb=" O HOH J 703 " model vdw 2.025 2.170 nonbonded pdb="MG MG J 601 " pdb=" O HOH I 712 " model vdw 2.032 2.170 ... (remaining 348097 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 474)) selection = (chain 'B' and (resid 2 through 235 or resid 237 through 474)) selection = (chain 'C' and (resid 2 through 235 or resid 237 through 474)) selection = (chain 'D' and (resid 2 through 235 or resid 237 through 474)) selection = (chain 'E' and (resid 2 through 235 or resid 237 through 474)) selection = (chain 'F' and (resid 2 through 235 or resid 237 through 474)) selection = (chain 'G' and (resid 2 through 235 or resid 237 through 474)) selection = (chain 'H' and (resid 2 through 235 or resid 237 through 474)) selection = (chain 'I' and (resid 2 through 235 or resid 237 through 474)) selection = (chain 'J' and (resid 2 through 235 or resid 237 through 474)) selection = (chain 'K' and (resid 2 through 235 or resid 237 through 474)) selection = (chain 'L' and (resid 2 through 235 or resid 237 through 474)) } 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: 9.200 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: 0.020 Extract box with map and model: 0.520 Check model and map are aligned: 0.130 Set scattering table: 0.120 Process input model: 48.850 Find NCS groups from input model: 1.220 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8837 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 44748 Z= 0.225 Angle : 0.750 11.236 60816 Z= 0.332 Chirality : 0.047 0.321 6852 Planarity : 0.005 0.046 7548 Dihedral : 20.044 169.999 17256 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.59 % Allowed : 20.23 % Favored : 79.18 % 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 aren not related in a simple way. whole: -0.35 (0.10), residues: 5376 helix: 0.74 (0.12), residues: 1572 sheet: 0.78 (0.15), residues: 1140 loop : -1.32 (0.10), residues: 2664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 20 TYR 0.012 0.001 TYR L 285 PHE 0.010 0.001 PHE F 183 TRP 0.006 0.001 TRP D 199 HIS 0.002 0.001 HIS D 259 Details of bonding type rmsd covalent geometry : bond 0.00462 (44712) covalent geometry : angle 0.74963 (60816) hydrogen bonds : bond 0.28381 ( 1868) hydrogen bonds : angle 6.43692 ( 5310) metal coordination : bond 0.00134 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10752 Ramachandran restraints generated. 5376 Oldfield, 0 Emsley, 5376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10752 Ramachandran restraints generated. 5376 Oldfield, 0 Emsley, 5376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 4668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 260 time to evaluate : 1.402 Fit side-chains outliers start: 27 outliers final: 19 residues processed: 287 average time/residue: 0.7762 time to fit residues: 272.1825 Evaluate side-chains 268 residues out of total 4668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 249 time to evaluate : 1.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain A residue 396 LYS Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 214 SER Chi-restraints excluded: chain D residue 214 SER Chi-restraints excluded: chain D residue 396 LYS Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain F residue 139 VAL Chi-restraints excluded: chain F residue 214 SER Chi-restraints excluded: chain G residue 214 SER Chi-restraints excluded: chain G residue 396 LYS Chi-restraints excluded: chain H residue 139 VAL Chi-restraints excluded: chain I residue 139 VAL Chi-restraints excluded: chain I residue 214 SER Chi-restraints excluded: chain J residue 214 SER Chi-restraints excluded: chain J residue 396 LYS Chi-restraints excluded: chain L residue 139 VAL Chi-restraints excluded: chain L residue 214 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 394 optimal weight: 7.9990 chunk 430 optimal weight: 0.4980 chunk 41 optimal weight: 1.9990 chunk 265 optimal weight: 1.9990 chunk 523 optimal weight: 5.9990 chunk 497 optimal weight: 6.9990 chunk 414 optimal weight: 0.9980 chunk 310 optimal weight: 0.0570 chunk 488 optimal weight: 6.9990 chunk 366 optimal weight: 0.8980 chunk 223 optimal weight: 10.0000 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 95 ASN A 364 GLN A 377 ASN B 95 ASN C 95 ASN D 95 ASN D 364 GLN D 377 ASN E 95 ASN F 53 GLN F 95 ASN G 364 GLN G 377 ASN H 95 ASN I 53 GLN I 95 ASN J 95 ASN J 364 GLN J 377 ASN K 95 ASN L 53 GLN L 95 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.089870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.065260 restraints weight = 200132.139| |-----------------------------------------------------------------------------| r_work (start): 0.2902 rms_B_bonded: 3.53 r_work: 0.2759 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2756 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2756 r_free = 0.2756 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2756 r_free = 0.2756 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2756 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8934 moved from start: 0.1086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 44748 Z= 0.121 Angle : 0.553 8.556 60816 Z= 0.288 Chirality : 0.043 0.184 6852 Planarity : 0.005 0.042 7548 Dihedral : 16.806 151.220 7219 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 1.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.09 % Allowed : 19.15 % Favored : 79.77 % 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 aren not related in a simple way. whole: 0.53 (0.11), residues: 5376 helix: 2.41 (0.13), residues: 1584 sheet: 0.92 (0.15), residues: 1140 loop : -1.28 (0.11), residues: 2652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 71 TYR 0.012 0.001 TYR E 382 PHE 0.012 0.001 PHE F 264 TRP 0.010 0.001 TRP F 470 HIS 0.004 0.001 HIS F 45 Details of bonding type rmsd covalent geometry : bond 0.00252 (44712) covalent geometry : angle 0.55302 (60816) hydrogen bonds : bond 0.05729 ( 1868) hydrogen bonds : angle 4.65878 ( 5310) metal coordination : bond 0.00225 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10752 Ramachandran restraints generated. 5376 Oldfield, 0 Emsley, 5376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10752 Ramachandran restraints generated. 5376 Oldfield, 0 Emsley, 5376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 4668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 252 time to evaluate : 1.640 Fit side-chains REVERT: A 9 ASP cc_start: 0.8678 (t0) cc_final: 0.8351 (t0) REVERT: A 441 GLN cc_start: 0.8967 (OUTLIER) cc_final: 0.8311 (mp10) REVERT: C 285 TYR cc_start: 0.8952 (OUTLIER) cc_final: 0.6184 (m-80) REVERT: C 441 GLN cc_start: 0.8925 (OUTLIER) cc_final: 0.7926 (mt0) REVERT: D 9 ASP cc_start: 0.8676 (t0) cc_final: 0.8344 (t0) REVERT: D 441 GLN cc_start: 0.8967 (OUTLIER) cc_final: 0.8311 (mp10) REVERT: E 364 GLN cc_start: 0.8028 (OUTLIER) cc_final: 0.7546 (mt0) REVERT: F 285 TYR cc_start: 0.8964 (OUTLIER) cc_final: 0.6214 (m-80) REVERT: F 441 GLN cc_start: 0.8924 (OUTLIER) cc_final: 0.7930 (mt0) REVERT: G 9 ASP cc_start: 0.8671 (t0) cc_final: 0.8336 (t0) REVERT: H 364 GLN cc_start: 0.8034 (OUTLIER) cc_final: 0.7546 (mt0) REVERT: I 441 GLN cc_start: 0.8904 (OUTLIER) cc_final: 0.7900 (mt0) REVERT: J 9 ASP cc_start: 0.8662 (t0) cc_final: 0.8333 (t0) REVERT: K 364 GLN cc_start: 0.8027 (OUTLIER) cc_final: 0.7535 (mt0) REVERT: L 285 TYR cc_start: 0.9037 (OUTLIER) cc_final: 0.6314 (m-80) REVERT: L 441 GLN cc_start: 0.8896 (OUTLIER) cc_final: 0.7889 (mt0) outliers start: 50 outliers final: 5 residues processed: 294 average time/residue: 0.7930 time to fit residues: 280.5308 Evaluate side-chains 267 residues out of total 4668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 250 time to evaluate : 1.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 396 LYS Chi-restraints excluded: chain A residue 441 GLN Chi-restraints excluded: chain C residue 285 TYR Chi-restraints excluded: chain C residue 441 GLN Chi-restraints excluded: chain D residue 396 LYS Chi-restraints excluded: chain D residue 441 GLN Chi-restraints excluded: chain E residue 364 GLN Chi-restraints excluded: chain F residue 285 TYR Chi-restraints excluded: chain F residue 441 GLN Chi-restraints excluded: chain G residue 396 LYS Chi-restraints excluded: chain H residue 364 GLN Chi-restraints excluded: chain I residue 441 GLN Chi-restraints excluded: chain J residue 396 LYS Chi-restraints excluded: chain K residue 109 ASP Chi-restraints excluded: chain K residue 364 GLN Chi-restraints excluded: chain L residue 285 TYR Chi-restraints excluded: chain L residue 441 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 51 optimal weight: 8.9990 chunk 448 optimal weight: 6.9990 chunk 524 optimal weight: 2.9990 chunk 189 optimal weight: 6.9990 chunk 376 optimal weight: 0.9990 chunk 342 optimal weight: 4.9990 chunk 67 optimal weight: 8.9990 chunk 258 optimal weight: 0.7980 chunk 181 optimal weight: 3.9990 chunk 165 optimal weight: 8.9990 chunk 389 optimal weight: 5.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 364 GLN B 95 ASN C 53 GLN C 95 ASN D 364 GLN E 95 ASN F 95 ASN G 364 GLN I 95 ASN J 364 GLN L 95 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.086972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.062267 restraints weight = 216956.650| |-----------------------------------------------------------------------------| r_work (start): 0.2847 rms_B_bonded: 3.60 r_work: 0.2702 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2702 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2692 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2692 r_free = 0.2692 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2692 r_free = 0.2692 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2692 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8991 moved from start: 0.1124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 44748 Z= 0.183 Angle : 0.629 8.597 60816 Z= 0.330 Chirality : 0.046 0.242 6852 Planarity : 0.005 0.045 7548 Dihedral : 16.143 153.674 7204 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 1.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.98 % Allowed : 19.19 % Favored : 79.83 % 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 aren not related in a simple way. whole: 0.47 (0.11), residues: 5376 helix: 2.61 (0.14), residues: 1656 sheet: 0.63 (0.15), residues: 1056 loop : -1.41 (0.11), residues: 2664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 222 TYR 0.018 0.002 TYR F 285 PHE 0.017 0.002 PHE F 183 TRP 0.008 0.002 TRP C 470 HIS 0.004 0.001 HIS J 164 Details of bonding type rmsd covalent geometry : bond 0.00436 (44712) covalent geometry : angle 0.62872 (60816) hydrogen bonds : bond 0.06983 ( 1868) hydrogen bonds : angle 4.60931 ( 5310) metal coordination : bond 0.00193 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10752 Ramachandran restraints generated. 5376 Oldfield, 0 Emsley, 5376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10752 Ramachandran restraints generated. 5376 Oldfield, 0 Emsley, 5376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 4668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 255 time to evaluate : 1.202 Fit side-chains REVERT: A 9 ASP cc_start: 0.8690 (t0) cc_final: 0.8358 (t0) REVERT: A 441 GLN cc_start: 0.9003 (OUTLIER) cc_final: 0.8302 (mp10) REVERT: C 285 TYR cc_start: 0.9278 (OUTLIER) cc_final: 0.6390 (m-80) REVERT: C 441 GLN cc_start: 0.8956 (OUTLIER) cc_final: 0.7920 (mt0) REVERT: D 9 ASP cc_start: 0.8686 (t0) cc_final: 0.8331 (t0) REVERT: D 441 GLN cc_start: 0.8994 (OUTLIER) cc_final: 0.8287 (mp10) REVERT: E 364 GLN cc_start: 0.8128 (OUTLIER) cc_final: 0.7662 (mt0) REVERT: F 285 TYR cc_start: 0.9282 (OUTLIER) cc_final: 0.6393 (m-80) REVERT: F 441 GLN cc_start: 0.8952 (OUTLIER) cc_final: 0.7914 (mt0) REVERT: G 9 ASP cc_start: 0.8676 (t0) cc_final: 0.8342 (t0) REVERT: H 364 GLN cc_start: 0.8133 (OUTLIER) cc_final: 0.7668 (mt0) REVERT: I 285 TYR cc_start: 0.9286 (OUTLIER) cc_final: 0.6560 (m-80) REVERT: I 441 GLN cc_start: 0.8936 (OUTLIER) cc_final: 0.7901 (mt0) REVERT: J 9 ASP cc_start: 0.8669 (t0) cc_final: 0.8340 (t0) REVERT: K 364 GLN cc_start: 0.8136 (OUTLIER) cc_final: 0.7696 (mt0) REVERT: L 285 TYR cc_start: 0.9258 (OUTLIER) cc_final: 0.6615 (m-80) REVERT: L 441 GLN cc_start: 0.8937 (OUTLIER) cc_final: 0.7901 (mt0) outliers start: 45 outliers final: 2 residues processed: 288 average time/residue: 0.7499 time to fit residues: 263.1525 Evaluate side-chains 265 residues out of total 4668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 250 time to evaluate : 1.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 441 GLN Chi-restraints excluded: chain B residue 109 ASP Chi-restraints excluded: chain C residue 285 TYR Chi-restraints excluded: chain C residue 441 GLN Chi-restraints excluded: chain D residue 441 GLN Chi-restraints excluded: chain E residue 364 GLN Chi-restraints excluded: chain F residue 285 TYR Chi-restraints excluded: chain F residue 441 GLN Chi-restraints excluded: chain H residue 364 GLN Chi-restraints excluded: chain I residue 285 TYR Chi-restraints excluded: chain I residue 441 GLN Chi-restraints excluded: chain K residue 109 ASP Chi-restraints excluded: chain K residue 364 GLN Chi-restraints excluded: chain L residue 285 TYR Chi-restraints excluded: chain L residue 441 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 61.6636 > 50: distance: 7 - 31: 12.459 distance: 11 - 39: 11.841 distance: 17 - 48: 26.621 distance: 25 - 31: 15.437 distance: 26 - 57: 25.414 distance: 31 - 32: 20.594 distance: 32 - 33: 34.495 distance: 32 - 35: 18.319 distance: 33 - 34: 37.617 distance: 33 - 39: 18.547 distance: 34 - 66: 41.646 distance: 35 - 36: 33.425 distance: 35 - 37: 23.558 distance: 36 - 38: 39.030 distance: 39 - 40: 17.779 distance: 40 - 41: 12.144 distance: 40 - 43: 23.278 distance: 41 - 42: 15.081 distance: 41 - 48: 20.150 distance: 43 - 44: 15.329 distance: 44 - 45: 20.429 distance: 45 - 46: 3.103 distance: 45 - 47: 14.689 distance: 48 - 49: 30.269 distance: 49 - 50: 22.927 distance: 49 - 52: 49.630 distance: 50 - 51: 14.674 distance: 50 - 57: 41.201 distance: 52 - 53: 43.391 distance: 53 - 54: 11.632 distance: 54 - 55: 16.141 distance: 54 - 56: 13.530 distance: 57 - 58: 23.998 distance: 58 - 59: 15.340 distance: 58 - 61: 17.720 distance: 59 - 60: 28.074 distance: 59 - 66: 42.440 distance: 61 - 62: 20.531 distance: 62 - 63: 13.316 distance: 63 - 64: 17.527 distance: 63 - 65: 27.443 distance: 66 - 67: 11.122 distance: 67 - 68: 43.717 distance: 67 - 70: 33.941 distance: 68 - 69: 43.385 distance: 68 - 74: 33.920 distance: 70 - 71: 53.098 distance: 70 - 72: 26.934 distance: 71 - 73: 39.769 distance: 74 - 75: 6.899 distance: 75 - 76: 31.761 distance: 75 - 78: 40.173 distance: 76 - 77: 11.894 distance: 76 - 82: 7.271 distance: 78 - 79: 15.433 distance: 79 - 80: 49.139 distance: 79 - 81: 42.295 distance: 82 - 83: 12.504 distance: 82 - 88: 19.212 distance: 83 - 84: 7.113 distance: 83 - 86: 12.328 distance: 84 - 85: 22.570 distance: 84 - 89: 14.356 distance: 86 - 87: 37.698 distance: 87 - 88: 15.274 distance: 89 - 90: 23.108 distance: 90 - 91: 19.278 distance: 90 - 93: 26.562 distance: 91 - 92: 28.246 distance: 91 - 97: 10.847 distance: 93 - 94: 13.755 distance: 94 - 95: 39.767 distance: 94 - 96: 23.610 distance: 97 - 98: 19.319 distance: 98 - 99: 11.882 distance: 98 - 101: 27.547 distance: 99 - 100: 28.093 distance: 99 - 103: 35.755 distance: 101 - 102: 30.521 distance: 103 - 104: 16.900 distance: 104 - 105: 17.878 distance: 104 - 107: 38.181 distance: 105 - 106: 20.622 distance: 105 - 110: 15.696 distance: 106 - 151: 30.541 distance: 107 - 108: 49.812 distance: 107 - 109: 35.081