Starting phenix.real_space_refine on Wed Jan 15 17:58:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7kdv_22830/01_2025/7kdv_22830.cif Found real_map, /net/cci-nas-00/data/ceres_data/7kdv_22830/01_2025/7kdv_22830.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7kdv_22830/01_2025/7kdv_22830.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7kdv_22830/01_2025/7kdv_22830.map" model { file = "/net/cci-nas-00/data/ceres_data/7kdv_22830/01_2025/7kdv_22830.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7kdv_22830/01_2025/7kdv_22830.cif" } resolution = 4.59 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.002 sd= 0.052 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 246 5.16 5 C 33312 2.51 5 N 8484 2.21 5 O 9654 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 42 residue(s): 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 51696 Number of models: 1 Model: "" Number of chains: 42 Chain: "A" Number of atoms: 4823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 600, 4823 Classifications: {'peptide': 600} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PCIS': 4, 'PTRANS': 41, 'TRANS': 552} Chain breaks: 1 Chain: "B" Number of atoms: 3628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 3628 Classifications: {'peptide': 452} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 26, 'TRANS': 423} Chain: "C" Number of atoms: 4823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 600, 4823 Classifications: {'peptide': 600} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PCIS': 4, 'PTRANS': 41, 'TRANS': 552} Chain breaks: 1 Chain: "D" Number of atoms: 3628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 3628 Classifications: {'peptide': 452} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 26, 'TRANS': 423} Chain: "E" Number of atoms: 4823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 600, 4823 Classifications: {'peptide': 600} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PCIS': 4, 'PTRANS': 41, 'TRANS': 552} Chain breaks: 1 Chain: "F" Number of atoms: 3628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 3628 Classifications: {'peptide': 452} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 26, 'TRANS': 423} Chain: "G" Number of atoms: 4823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 600, 4823 Classifications: {'peptide': 600} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PCIS': 4, 'PTRANS': 41, 'TRANS': 552} Chain breaks: 1 Chain: "H" Number of atoms: 3628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 3628 Classifications: {'peptide': 452} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 26, 'TRANS': 423} Chain: "I" Number of atoms: 4823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 600, 4823 Classifications: {'peptide': 600} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PCIS': 4, 'PTRANS': 41, 'TRANS': 552} Chain breaks: 1 Chain: "J" Number of atoms: 3628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 3628 Classifications: {'peptide': 452} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 26, 'TRANS': 423} Chain: "K" Number of atoms: 4823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 600, 4823 Classifications: {'peptide': 600} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PCIS': 4, 'PTRANS': 41, 'TRANS': 552} Chain breaks: 1 Chain: "L" Number of atoms: 3628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 3628 Classifications: {'peptide': 452} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 26, 'TRANS': 423} Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "H" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "I" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "J" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "K" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "L" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 23.64, per 1000 atoms: 0.46 Number of scatterers: 51696 At special positions: 0 Unit cell: (237.93, 221.45, 143.17, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 246 16.00 O 9654 8.00 N 8484 7.00 C 33312 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 196 " - pdb=" SG CYS A 231 " distance=2.03 Simple disulfide: pdb=" SG CYS A 628 " - pdb=" SG CYS A 636 " distance=2.03 Simple disulfide: pdb=" SG CYS B 83 " - pdb=" SG CYS B 356 " distance=2.03 Simple disulfide: pdb=" SG CYS B 235 " - pdb=" SG CYS B 251 " distance=2.03 Simple disulfide: pdb=" SG CYS B 236 " - pdb=" SG CYS B 241 " distance=2.04 Simple disulfide: pdb=" SG CYS B 276 " - pdb=" SG CYS B 325 " distance=2.03 Simple disulfide: pdb=" SG CYS C 196 " - pdb=" SG CYS C 231 " distance=2.03 Simple disulfide: pdb=" SG CYS C 628 " - pdb=" SG CYS C 636 " distance=2.03 Simple disulfide: pdb=" SG CYS D 83 " - pdb=" SG CYS D 356 " distance=2.03 Simple disulfide: pdb=" SG CYS D 235 " - pdb=" SG CYS D 251 " distance=2.03 Simple disulfide: pdb=" SG CYS D 236 " - pdb=" SG CYS D 241 " distance=2.04 Simple disulfide: pdb=" SG CYS D 276 " - pdb=" SG CYS D 325 " distance=2.03 Simple disulfide: pdb=" SG CYS E 196 " - pdb=" SG CYS E 231 " distance=2.03 Simple disulfide: pdb=" SG CYS E 628 " - pdb=" SG CYS E 636 " distance=2.03 Simple disulfide: pdb=" SG CYS F 83 " - pdb=" SG CYS F 356 " distance=2.03 Simple disulfide: pdb=" SG CYS F 235 " - pdb=" SG CYS F 251 " distance=2.03 Simple disulfide: pdb=" SG CYS F 236 " - pdb=" SG CYS F 241 " distance=2.04 Simple disulfide: pdb=" SG CYS F 276 " - pdb=" SG CYS F 325 " distance=2.03 Simple disulfide: pdb=" SG CYS G 196 " - pdb=" SG CYS G 231 " distance=2.03 Simple disulfide: pdb=" SG CYS G 628 " - pdb=" SG CYS G 636 " distance=2.03 Simple disulfide: pdb=" SG CYS H 83 " - pdb=" SG CYS H 356 " distance=2.03 Simple disulfide: pdb=" SG CYS H 235 " - pdb=" SG CYS H 251 " distance=2.03 Simple disulfide: pdb=" SG CYS H 236 " - pdb=" SG CYS H 241 " distance=2.04 Simple disulfide: pdb=" SG CYS H 276 " - pdb=" SG CYS H 325 " distance=2.03 Simple disulfide: pdb=" SG CYS I 196 " - pdb=" SG CYS I 231 " distance=2.03 Simple disulfide: pdb=" SG CYS I 628 " - pdb=" SG CYS I 636 " distance=2.03 Simple disulfide: pdb=" SG CYS J 83 " - pdb=" SG CYS J 356 " distance=2.03 Simple disulfide: pdb=" SG CYS J 235 " - pdb=" SG CYS J 251 " distance=2.03 Simple disulfide: pdb=" SG CYS J 236 " - pdb=" SG CYS J 241 " distance=2.04 Simple disulfide: pdb=" SG CYS J 276 " - pdb=" SG CYS J 325 " distance=2.03 Simple disulfide: pdb=" SG CYS K 196 " - pdb=" SG CYS K 231 " distance=2.03 Simple disulfide: pdb=" SG CYS K 628 " - pdb=" SG CYS K 636 " distance=2.03 Simple disulfide: pdb=" SG CYS L 83 " - pdb=" SG CYS L 356 " distance=2.03 Simple disulfide: pdb=" SG CYS L 235 " - pdb=" SG CYS L 251 " distance=2.03 Simple disulfide: pdb=" SG CYS L 236 " - pdb=" SG CYS L 241 " distance=2.04 Simple disulfide: pdb=" SG CYS L 276 " - pdb=" SG CYS L 325 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " NAG-ASN " NAG A 701 " - " ASN A 248 " " NAG A 702 " - " ASN A 504 " " NAG A 703 " - " ASN A 510 " " NAG A 704 " - " ASN A 557 " " NAG B 501 " - " ASN B 140 " " NAG C 701 " - " ASN C 248 " " NAG C 702 " - " ASN C 504 " " NAG C 703 " - " ASN C 510 " " NAG C 704 " - " ASN C 557 " " NAG D 501 " - " ASN D 140 " " NAG E 701 " - " ASN E 248 " " NAG E 702 " - " ASN E 504 " " NAG E 703 " - " ASN E 510 " " NAG E 704 " - " ASN E 557 " " NAG F 501 " - " ASN F 140 " " NAG G 701 " - " ASN G 248 " " NAG G 702 " - " ASN G 504 " " NAG G 703 " - " ASN G 510 " " NAG G 704 " - " ASN G 557 " " NAG H 501 " - " ASN H 140 " " NAG I 701 " - " ASN I 248 " " NAG I 702 " - " ASN I 504 " " NAG I 703 " - " ASN I 510 " " NAG I 704 " - " ASN I 557 " " NAG J 501 " - " ASN J 140 " " NAG K 701 " - " ASN K 248 " " NAG K 702 " - " ASN K 504 " " NAG K 703 " - " ASN K 510 " " NAG K 704 " - " ASN K 557 " " NAG L 501 " - " ASN L 140 " " NAG M 1 " - " ASN A 500 " " NAG N 1 " - " ASN A 617 " " NAG O 1 " - " ASN B 327 " " NAG P 1 " - " ASN C 500 " " NAG Q 1 " - " ASN C 617 " " NAG R 1 " - " ASN D 327 " " NAG S 1 " - " ASN E 500 " " NAG T 1 " - " ASN E 617 " " NAG U 1 " - " ASN F 327 " " NAG V 1 " - " ASN G 500 " " NAG W 1 " - " ASN G 617 " " NAG X 1 " - " ASN H 327 " " NAG Y 1 " - " ASN I 500 " " NAG Z 1 " - " ASN I 617 " " NAG a 1 " - " ASN J 327 " " NAG b 1 " - " ASN K 500 " " NAG c 1 " - " ASN K 617 " " NAG d 1 " - " ASN L 327 " Time building additional restraints: 10.71 Conformation dependent library (CDL) restraints added in 5.0 seconds 12552 Ramachandran restraints generated. 6276 Oldfield, 0 Emsley, 6276 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11700 Finding SS restraints... Secondary structure from input PDB file: 204 helices and 78 sheets defined 32.2% alpha, 20.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.75 Creating SS restraints... Processing helix chain 'A' and resid 62 through 64 No H-bonds generated for 'chain 'A' and resid 62 through 64' Processing helix chain 'A' and resid 65 through 77 Processing helix chain 'A' and resid 86 through 91 removed outlier: 3.666A pdb=" N HIS A 90 " --> pdb=" O PRO A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 103 Processing helix chain 'A' and resid 104 through 115 Processing helix chain 'A' and resid 131 through 136 Processing helix chain 'A' and resid 137 through 143 removed outlier: 3.556A pdb=" N LYS A 143 " --> pdb=" O LEU A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 171 Proline residue: A 168 - end of helix Processing helix chain 'A' and resid 172 through 178 removed outlier: 6.067A pdb=" N TYR A 175 " --> pdb=" O PRO A 172 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLN A 176 " --> pdb=" O LEU A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 193 Processing helix chain 'A' and resid 197 through 213 removed outlier: 3.675A pdb=" N LEU A 201 " --> pdb=" O ASP A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 233 removed outlier: 3.534A pdb=" N LEU A 229 " --> pdb=" O SER A 225 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N CYS A 231 " --> pdb=" O LYS A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 260 removed outlier: 3.614A pdb=" N PHE A 259 " --> pdb=" O VAL A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 300 Processing helix chain 'A' and resid 345 through 356 Processing helix chain 'A' and resid 389 through 394 Processing helix chain 'A' and resid 517 through 525 Processing helix chain 'A' and resid 606 through 610 Processing helix chain 'B' and resid 67 through 71 Processing helix chain 'B' and resid 85 through 91 removed outlier: 3.927A pdb=" N LEU B 89 " --> pdb=" O SER B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 115 removed outlier: 3.504A pdb=" N ILE B 115 " --> pdb=" O TRP B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 159 Processing helix chain 'B' and resid 160 through 163 Processing helix chain 'B' and resid 174 through 188 removed outlier: 3.538A pdb=" N TYR B 178 " --> pdb=" O TYR B 174 " (cutoff:3.500A) Proline residue: B 180 - end of helix Processing helix chain 'B' and resid 205 through 220 Processing helix chain 'B' and resid 224 through 236 removed outlier: 3.590A pdb=" N CYS B 236 " --> pdb=" O GLN B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 265 removed outlier: 3.571A pdb=" N SER B 265 " --> pdb=" O ILE B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 336 Processing helix chain 'B' and resid 337 through 344 Processing helix chain 'B' and resid 357 through 363 Processing helix chain 'B' and resid 371 through 382 removed outlier: 4.069A pdb=" N SER B 381 " --> pdb=" O LYS B 377 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N GLN B 382 " --> pdb=" O LEU B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 409 removed outlier: 3.637A pdb=" N ASP B 402 " --> pdb=" O ASN B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 457 Processing helix chain 'B' and resid 457 through 470 Processing helix chain 'C' and resid 62 through 64 No H-bonds generated for 'chain 'C' and resid 62 through 64' Processing helix chain 'C' and resid 65 through 77 Processing helix chain 'C' and resid 86 through 91 removed outlier: 3.667A pdb=" N HIS C 90 " --> pdb=" O PRO C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 103 Processing helix chain 'C' and resid 104 through 115 Processing helix chain 'C' and resid 131 through 136 Processing helix chain 'C' and resid 137 through 143 removed outlier: 3.556A pdb=" N LYS C 143 " --> pdb=" O LEU C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 171 Proline residue: C 168 - end of helix Processing helix chain 'C' and resid 172 through 178 removed outlier: 6.066A pdb=" N TYR C 175 " --> pdb=" O PRO C 172 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N GLN C 176 " --> pdb=" O LEU C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 193 Processing helix chain 'C' and resid 197 through 213 removed outlier: 3.675A pdb=" N LEU C 201 " --> pdb=" O ASP C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 233 removed outlier: 3.534A pdb=" N LEU C 229 " --> pdb=" O SER C 225 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N CYS C 231 " --> pdb=" O LYS C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 248 through 260 removed outlier: 3.615A pdb=" N PHE C 259 " --> pdb=" O VAL C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 300 Processing helix chain 'C' and resid 345 through 356 Processing helix chain 'C' and resid 389 through 394 Processing helix chain 'C' and resid 517 through 525 Processing helix chain 'C' and resid 606 through 610 Processing helix chain 'D' and resid 67 through 71 Processing helix chain 'D' and resid 85 through 91 removed outlier: 3.927A pdb=" N LEU D 89 " --> pdb=" O SER D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 115 removed outlier: 3.503A pdb=" N ILE D 115 " --> pdb=" O TRP D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 141 through 159 Processing helix chain 'D' and resid 160 through 163 Processing helix chain 'D' and resid 174 through 188 removed outlier: 3.539A pdb=" N TYR D 178 " --> pdb=" O TYR D 174 " (cutoff:3.500A) Proline residue: D 180 - end of helix Processing helix chain 'D' and resid 205 through 220 Processing helix chain 'D' and resid 224 through 236 removed outlier: 3.590A pdb=" N CYS D 236 " --> pdb=" O GLN D 232 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 265 removed outlier: 3.570A pdb=" N SER D 265 " --> pdb=" O ILE D 261 " (cutoff:3.500A) Processing helix chain 'D' and resid 328 through 336 Processing helix chain 'D' and resid 337 through 344 Processing helix chain 'D' and resid 357 through 363 Processing helix chain 'D' and resid 371 through 382 removed outlier: 4.070A pdb=" N SER D 381 " --> pdb=" O LYS D 377 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N GLN D 382 " --> pdb=" O LEU D 378 " (cutoff:3.500A) Processing helix chain 'D' and resid 398 through 409 removed outlier: 3.637A pdb=" N ASP D 402 " --> pdb=" O ASN D 398 " (cutoff:3.500A) Processing helix chain 'D' and resid 452 through 457 Processing helix chain 'D' and resid 457 through 470 Processing helix chain 'E' and resid 62 through 64 No H-bonds generated for 'chain 'E' and resid 62 through 64' Processing helix chain 'E' and resid 65 through 77 Processing helix chain 'E' and resid 86 through 91 removed outlier: 3.666A pdb=" N HIS E 90 " --> pdb=" O PRO E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 100 through 103 Processing helix chain 'E' and resid 104 through 115 Processing helix chain 'E' and resid 131 through 136 Processing helix chain 'E' and resid 137 through 143 removed outlier: 3.556A pdb=" N LYS E 143 " --> pdb=" O LEU E 140 " (cutoff:3.500A) Processing helix chain 'E' and resid 152 through 171 Proline residue: E 168 - end of helix Processing helix chain 'E' and resid 172 through 178 removed outlier: 6.067A pdb=" N TYR E 175 " --> pdb=" O PRO E 172 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N GLN E 176 " --> pdb=" O LEU E 173 " (cutoff:3.500A) Processing helix chain 'E' and resid 189 through 193 Processing helix chain 'E' and resid 197 through 213 removed outlier: 3.675A pdb=" N LEU E 201 " --> pdb=" O ASP E 197 " (cutoff:3.500A) Processing helix chain 'E' and resid 225 through 233 removed outlier: 3.535A pdb=" N LEU E 229 " --> pdb=" O SER E 225 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N CYS E 231 " --> pdb=" O LYS E 227 " (cutoff:3.500A) Processing helix chain 'E' and resid 248 through 260 removed outlier: 3.615A pdb=" N PHE E 259 " --> pdb=" O VAL E 255 " (cutoff:3.500A) Processing helix chain 'E' and resid 286 through 300 Processing helix chain 'E' and resid 345 through 356 Processing helix chain 'E' and resid 389 through 394 Processing helix chain 'E' and resid 517 through 525 Processing helix chain 'E' and resid 606 through 610 Processing helix chain 'F' and resid 67 through 71 Processing helix chain 'F' and resid 85 through 91 removed outlier: 3.926A pdb=" N LEU F 89 " --> pdb=" O SER F 85 " (cutoff:3.500A) Processing helix chain 'F' and resid 111 through 115 removed outlier: 3.504A pdb=" N ILE F 115 " --> pdb=" O TRP F 112 " (cutoff:3.500A) Processing helix chain 'F' and resid 141 through 159 Processing helix chain 'F' and resid 160 through 163 Processing helix chain 'F' and resid 174 through 188 removed outlier: 3.538A pdb=" N TYR F 178 " --> pdb=" O TYR F 174 " (cutoff:3.500A) Proline residue: F 180 - end of helix Processing helix chain 'F' and resid 205 through 220 Processing helix chain 'F' and resid 224 through 236 removed outlier: 3.590A pdb=" N CYS F 236 " --> pdb=" O GLN F 232 " (cutoff:3.500A) Processing helix chain 'F' and resid 248 through 265 removed outlier: 3.570A pdb=" N SER F 265 " --> pdb=" O ILE F 261 " (cutoff:3.500A) Processing helix chain 'F' and resid 328 through 336 Processing helix chain 'F' and resid 337 through 344 Processing helix chain 'F' and resid 357 through 363 Processing helix chain 'F' and resid 371 through 382 removed outlier: 4.069A pdb=" N SER F 381 " --> pdb=" O LYS F 377 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N GLN F 382 " --> pdb=" O LEU F 378 " (cutoff:3.500A) Processing helix chain 'F' and resid 398 through 409 removed outlier: 3.637A pdb=" N ASP F 402 " --> pdb=" O ASN F 398 " (cutoff:3.500A) Processing helix chain 'F' and resid 452 through 457 Processing helix chain 'F' and resid 457 through 470 Processing helix chain 'G' and resid 62 through 64 No H-bonds generated for 'chain 'G' and resid 62 through 64' Processing helix chain 'G' and resid 65 through 77 Processing helix chain 'G' and resid 86 through 91 removed outlier: 3.666A pdb=" N HIS G 90 " --> pdb=" O PRO G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 100 through 103 Processing helix chain 'G' and resid 104 through 115 Processing helix chain 'G' and resid 131 through 136 Processing helix chain 'G' and resid 137 through 143 removed outlier: 3.555A pdb=" N LYS G 143 " --> pdb=" O LEU G 140 " (cutoff:3.500A) Processing helix chain 'G' and resid 152 through 171 Proline residue: G 168 - end of helix Processing helix chain 'G' and resid 172 through 178 removed outlier: 6.067A pdb=" N TYR G 175 " --> pdb=" O PRO G 172 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLN G 176 " --> pdb=" O LEU G 173 " (cutoff:3.500A) Processing helix chain 'G' and resid 189 through 193 Processing helix chain 'G' and resid 197 through 213 removed outlier: 3.676A pdb=" N LEU G 201 " --> pdb=" O ASP G 197 " (cutoff:3.500A) Processing helix chain 'G' and resid 225 through 233 removed outlier: 3.535A pdb=" N LEU G 229 " --> pdb=" O SER G 225 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N CYS G 231 " --> pdb=" O LYS G 227 " (cutoff:3.500A) Processing helix chain 'G' and resid 248 through 260 removed outlier: 3.615A pdb=" N PHE G 259 " --> pdb=" O VAL G 255 " (cutoff:3.500A) Processing helix chain 'G' and resid 286 through 300 Processing helix chain 'G' and resid 345 through 356 Processing helix chain 'G' and resid 389 through 394 Processing helix chain 'G' and resid 517 through 525 Processing helix chain 'G' and resid 606 through 610 Processing helix chain 'H' and resid 67 through 71 Processing helix chain 'H' and resid 85 through 91 removed outlier: 3.927A pdb=" N LEU H 89 " --> pdb=" O SER H 85 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 115 removed outlier: 3.503A pdb=" N ILE H 115 " --> pdb=" O TRP H 112 " (cutoff:3.500A) Processing helix chain 'H' and resid 141 through 159 Processing helix chain 'H' and resid 160 through 163 Processing helix chain 'H' and resid 174 through 188 removed outlier: 3.537A pdb=" N TYR H 178 " --> pdb=" O TYR H 174 " (cutoff:3.500A) Proline residue: H 180 - end of helix Processing helix chain 'H' and resid 205 through 220 Processing helix chain 'H' and resid 224 through 236 removed outlier: 3.590A pdb=" N CYS H 236 " --> pdb=" O GLN H 232 " (cutoff:3.500A) Processing helix chain 'H' and resid 248 through 265 removed outlier: 3.571A pdb=" N SER H 265 " --> pdb=" O ILE H 261 " (cutoff:3.500A) Processing helix chain 'H' and resid 328 through 336 Processing helix chain 'H' and resid 337 through 344 Processing helix chain 'H' and resid 357 through 363 Processing helix chain 'H' and resid 371 through 382 removed outlier: 4.069A pdb=" N SER H 381 " --> pdb=" O LYS H 377 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N GLN H 382 " --> pdb=" O LEU H 378 " (cutoff:3.500A) Processing helix chain 'H' and resid 398 through 409 removed outlier: 3.638A pdb=" N ASP H 402 " --> pdb=" O ASN H 398 " (cutoff:3.500A) Processing helix chain 'H' and resid 452 through 457 Processing helix chain 'H' and resid 457 through 470 Processing helix chain 'I' and resid 62 through 64 No H-bonds generated for 'chain 'I' and resid 62 through 64' Processing helix chain 'I' and resid 65 through 77 Processing helix chain 'I' and resid 86 through 91 removed outlier: 3.666A pdb=" N HIS I 90 " --> pdb=" O PRO I 86 " (cutoff:3.500A) Processing helix chain 'I' and resid 100 through 103 Processing helix chain 'I' and resid 104 through 115 Processing helix chain 'I' and resid 131 through 136 Processing helix chain 'I' and resid 137 through 143 removed outlier: 3.556A pdb=" N LYS I 143 " --> pdb=" O LEU I 140 " (cutoff:3.500A) Processing helix chain 'I' and resid 152 through 171 Proline residue: I 168 - end of helix Processing helix chain 'I' and resid 172 through 178 removed outlier: 6.067A pdb=" N TYR I 175 " --> pdb=" O PRO I 172 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLN I 176 " --> pdb=" O LEU I 173 " (cutoff:3.500A) Processing helix chain 'I' and resid 189 through 193 Processing helix chain 'I' and resid 197 through 213 removed outlier: 3.675A pdb=" N LEU I 201 " --> pdb=" O ASP I 197 " (cutoff:3.500A) Processing helix chain 'I' and resid 225 through 233 removed outlier: 3.536A pdb=" N LEU I 229 " --> pdb=" O SER I 225 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N CYS I 231 " --> pdb=" O LYS I 227 " (cutoff:3.500A) Processing helix chain 'I' and resid 248 through 260 removed outlier: 3.614A pdb=" N PHE I 259 " --> pdb=" O VAL I 255 " (cutoff:3.500A) Processing helix chain 'I' and resid 286 through 300 Processing helix chain 'I' and resid 345 through 356 Processing helix chain 'I' and resid 389 through 394 Processing helix chain 'I' and resid 517 through 525 Processing helix chain 'I' and resid 606 through 610 Processing helix chain 'J' and resid 67 through 71 Processing helix chain 'J' and resid 85 through 91 removed outlier: 3.927A pdb=" N LEU J 89 " --> pdb=" O SER J 85 " (cutoff:3.500A) Processing helix chain 'J' and resid 111 through 115 removed outlier: 3.504A pdb=" N ILE J 115 " --> pdb=" O TRP J 112 " (cutoff:3.500A) Processing helix chain 'J' and resid 141 through 159 Processing helix chain 'J' and resid 160 through 163 Processing helix chain 'J' and resid 174 through 188 removed outlier: 3.539A pdb=" N TYR J 178 " --> pdb=" O TYR J 174 " (cutoff:3.500A) Proline residue: J 180 - end of helix Processing helix chain 'J' and resid 205 through 220 Processing helix chain 'J' and resid 224 through 236 removed outlier: 3.591A pdb=" N CYS J 236 " --> pdb=" O GLN J 232 " (cutoff:3.500A) Processing helix chain 'J' and resid 248 through 265 removed outlier: 3.571A pdb=" N SER J 265 " --> pdb=" O ILE J 261 " (cutoff:3.500A) Processing helix chain 'J' and resid 328 through 336 Processing helix chain 'J' and resid 337 through 344 Processing helix chain 'J' and resid 357 through 363 Processing helix chain 'J' and resid 371 through 382 removed outlier: 4.069A pdb=" N SER J 381 " --> pdb=" O LYS J 377 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N GLN J 382 " --> pdb=" O LEU J 378 " (cutoff:3.500A) Processing helix chain 'J' and resid 398 through 409 removed outlier: 3.638A pdb=" N ASP J 402 " --> pdb=" O ASN J 398 " (cutoff:3.500A) Processing helix chain 'J' and resid 452 through 457 Processing helix chain 'J' and resid 457 through 470 Processing helix chain 'K' and resid 62 through 64 No H-bonds generated for 'chain 'K' and resid 62 through 64' Processing helix chain 'K' and resid 65 through 77 Processing helix chain 'K' and resid 86 through 91 removed outlier: 3.666A pdb=" N HIS K 90 " --> pdb=" O PRO K 86 " (cutoff:3.500A) Processing helix chain 'K' and resid 100 through 103 Processing helix chain 'K' and resid 104 through 115 Processing helix chain 'K' and resid 131 through 136 Processing helix chain 'K' and resid 137 through 143 removed outlier: 3.556A pdb=" N LYS K 143 " --> pdb=" O LEU K 140 " (cutoff:3.500A) Processing helix chain 'K' and resid 152 through 171 Proline residue: K 168 - end of helix Processing helix chain 'K' and resid 172 through 178 removed outlier: 6.067A pdb=" N TYR K 175 " --> pdb=" O PRO K 172 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLN K 176 " --> pdb=" O LEU K 173 " (cutoff:3.500A) Processing helix chain 'K' and resid 189 through 193 Processing helix chain 'K' and resid 197 through 213 removed outlier: 3.675A pdb=" N LEU K 201 " --> pdb=" O ASP K 197 " (cutoff:3.500A) Processing helix chain 'K' and resid 225 through 233 removed outlier: 3.535A pdb=" N LEU K 229 " --> pdb=" O SER K 225 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N CYS K 231 " --> pdb=" O LYS K 227 " (cutoff:3.500A) Processing helix chain 'K' and resid 248 through 260 removed outlier: 3.614A pdb=" N PHE K 259 " --> pdb=" O VAL K 255 " (cutoff:3.500A) Processing helix chain 'K' and resid 286 through 300 Processing helix chain 'K' and resid 345 through 356 Processing helix chain 'K' and resid 389 through 394 Processing helix chain 'K' and resid 517 through 525 Processing helix chain 'K' and resid 606 through 610 Processing helix chain 'L' and resid 67 through 71 Processing helix chain 'L' and resid 85 through 91 removed outlier: 3.926A pdb=" N LEU L 89 " --> pdb=" O SER L 85 " (cutoff:3.500A) Processing helix chain 'L' and resid 111 through 115 removed outlier: 3.504A pdb=" N ILE L 115 " --> pdb=" O TRP L 112 " (cutoff:3.500A) Processing helix chain 'L' and resid 141 through 159 Processing helix chain 'L' and resid 160 through 163 Processing helix chain 'L' and resid 174 through 188 removed outlier: 3.538A pdb=" N TYR L 178 " --> pdb=" O TYR L 174 " (cutoff:3.500A) Proline residue: L 180 - end of helix Processing helix chain 'L' and resid 205 through 220 Processing helix chain 'L' and resid 224 through 236 removed outlier: 3.590A pdb=" N CYS L 236 " --> pdb=" O GLN L 232 " (cutoff:3.500A) Processing helix chain 'L' and resid 248 through 265 removed outlier: 3.571A pdb=" N SER L 265 " --> pdb=" O ILE L 261 " (cutoff:3.500A) Processing helix chain 'L' and resid 328 through 336 Processing helix chain 'L' and resid 337 through 344 Processing helix chain 'L' and resid 357 through 363 Processing helix chain 'L' and resid 371 through 382 removed outlier: 4.069A pdb=" N SER L 381 " --> pdb=" O LYS L 377 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N GLN L 382 " --> pdb=" O LEU L 378 " (cutoff:3.500A) Processing helix chain 'L' and resid 398 through 409 removed outlier: 3.637A pdb=" N ASP L 402 " --> pdb=" O ASN L 398 " (cutoff:3.500A) Processing helix chain 'L' and resid 452 through 457 Processing helix chain 'L' and resid 457 through 470 Processing sheet with id=AA1, first strand: chain 'A' and resid 33 through 36 Processing sheet with id=AA2, first strand: chain 'A' and resid 52 through 55 removed outlier: 6.196A pdb=" N ILE A 52 " --> pdb=" O ALA A 80 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N GLN A 82 " --> pdb=" O ILE A 52 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N GLY A 54 " --> pdb=" O GLN A 82 " (cutoff:3.500A) removed outlier: 8.638A pdb=" N TYR A 84 " --> pdb=" O GLY A 54 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N ILE A 81 " --> pdb=" O ILE A 120 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N ARG A 122 " --> pdb=" O ILE A 81 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N MET A 83 " --> pdb=" O ARG A 122 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N VAL A 119 " --> pdb=" O ILE A 182 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N VAL A 184 " --> pdb=" O VAL A 119 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N LEU A 121 " --> pdb=" O VAL A 184 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N PHE A 219 " --> pdb=" O ILE A 182 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N VAL A 184 " --> pdb=" O PHE A 219 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N THR A 221 " --> pdb=" O VAL A 184 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N LEU A 218 " --> pdb=" O TYR A 238 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N THR A 240 " --> pdb=" O LEU A 218 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N THR A 220 " --> pdb=" O THR A 240 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ASP A 242 " --> pdb=" O THR A 220 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N ASP A 222 " --> pdb=" O ASP A 242 " (cutoff:3.500A) removed outlier: 8.352A pdb=" N ALA A 239 " --> pdb=" O ILE A 266 " (cutoff:3.500A) removed outlier: 8.578A pdb=" N SER A 268 " --> pdb=" O ALA A 239 " (cutoff:3.500A) removed outlier: 8.332A pdb=" N VAL A 241 " --> pdb=" O SER A 268 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N PHE A 270 " --> pdb=" O VAL A 241 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N GLU A 269 " --> pdb=" O ASN A 305 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N TYR A 307 " --> pdb=" O GLU A 269 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N TYR A 271 " --> pdb=" O TYR A 307 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 321 through 322 removed outlier: 3.769A pdb=" N ASN A 322 " --> pdb=" O GLU A 326 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLU A 326 " --> pdb=" O ASN A 322 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 376 through 379 Processing sheet with id=AA5, first strand: chain 'A' and resid 382 through 385 removed outlier: 6.438A pdb=" N PHE A 553 " --> pdb=" O PHE A 383 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLY A 591 " --> pdb=" O VAL A 583 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ILE A 585 " --> pdb=" O ASN A 589 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N ASN A 589 " --> pdb=" O ILE A 585 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 399 through 401 removed outlier: 3.774A pdb=" N ARG A 444 " --> pdb=" O GLU A 480 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ALA A 445 " --> pdb=" O ILE A 456 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N ILE A 456 " --> pdb=" O ALA A 445 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N VAL A 447 " --> pdb=" O GLN A 454 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 427 through 433 removed outlier: 6.277A pdb=" N ASN A 429 " --> pdb=" O GLY A 469 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N GLY A 469 " --> pdb=" O ASN A 429 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 441 through 442 Processing sheet with id=AA9, first strand: chain 'B' and resid 44 through 50 removed outlier: 3.541A pdb=" N TYR B 131 " --> pdb=" O HIS B 56 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 44 through 50 removed outlier: 3.895A pdb=" N HIS B 58 " --> pdb=" O GLU B 122 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N LEU B 167 " --> pdb=" O GLN B 195 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N LEU B 197 " --> pdb=" O LEU B 167 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N LEU B 169 " --> pdb=" O LEU B 197 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N VAL B 199 " --> pdb=" O LEU B 169 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N GLY B 171 " --> pdb=" O VAL B 199 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N PHE B 434 " --> pdb=" O THR B 445 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N VAL B 431 " --> pdb=" O VAL B 422 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N VAL B 422 " --> pdb=" O VAL B 431 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLY B 433 " --> pdb=" O TRP B 420 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N GLU B 437 " --> pdb=" O GLN B 416 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N GLN B 416 " --> pdb=" O GLU B 437 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 96 through 98 Processing sheet with id=AB3, first strand: chain 'B' and resid 139 through 140 removed outlier: 6.978A pdb=" N THR B 139 " --> pdb=" O ARG B 365 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'B' and resid 289 through 292 removed outlier: 5.906A pdb=" N LEU B 290 " --> pdb=" O ARG B 320 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'C' and resid 33 through 36 Processing sheet with id=AB6, first strand: chain 'C' and resid 52 through 55 removed outlier: 6.197A pdb=" N ILE C 52 " --> pdb=" O ALA C 80 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N GLN C 82 " --> pdb=" O ILE C 52 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N GLY C 54 " --> pdb=" O GLN C 82 " (cutoff:3.500A) removed outlier: 8.637A pdb=" N TYR C 84 " --> pdb=" O GLY C 54 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N ILE C 81 " --> pdb=" O ILE C 120 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N ARG C 122 " --> pdb=" O ILE C 81 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N MET C 83 " --> pdb=" O ARG C 122 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N VAL C 119 " --> pdb=" O ILE C 182 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N VAL C 184 " --> pdb=" O VAL C 119 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N LEU C 121 " --> pdb=" O VAL C 184 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N PHE C 219 " --> pdb=" O ILE C 182 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N VAL C 184 " --> pdb=" O PHE C 219 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N THR C 221 " --> pdb=" O VAL C 184 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N LEU C 218 " --> pdb=" O TYR C 238 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N THR C 240 " --> pdb=" O LEU C 218 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N THR C 220 " --> pdb=" O THR C 240 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ASP C 242 " --> pdb=" O THR C 220 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N ASP C 222 " --> pdb=" O ASP C 242 " (cutoff:3.500A) removed outlier: 8.352A pdb=" N ALA C 239 " --> pdb=" O ILE C 266 " (cutoff:3.500A) removed outlier: 8.577A pdb=" N SER C 268 " --> pdb=" O ALA C 239 " (cutoff:3.500A) removed outlier: 8.331A pdb=" N VAL C 241 " --> pdb=" O SER C 268 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N PHE C 270 " --> pdb=" O VAL C 241 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N GLU C 269 " --> pdb=" O ASN C 305 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N TYR C 307 " --> pdb=" O GLU C 269 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N TYR C 271 " --> pdb=" O TYR C 307 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 321 through 322 removed outlier: 3.770A pdb=" N ASN C 322 " --> pdb=" O GLU C 326 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLU C 326 " --> pdb=" O ASN C 322 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'C' and resid 376 through 379 Processing sheet with id=AB9, first strand: chain 'C' and resid 382 through 385 removed outlier: 6.438A pdb=" N PHE C 553 " --> pdb=" O PHE C 383 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLY C 591 " --> pdb=" O VAL C 583 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ILE C 585 " --> pdb=" O ASN C 589 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N ASN C 589 " --> pdb=" O ILE C 585 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 399 through 401 removed outlier: 3.773A pdb=" N ARG C 444 " --> pdb=" O GLU C 480 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ALA C 445 " --> pdb=" O ILE C 456 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N ILE C 456 " --> pdb=" O ALA C 445 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N VAL C 447 " --> pdb=" O GLN C 454 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 427 through 433 removed outlier: 6.277A pdb=" N ASN C 429 " --> pdb=" O GLY C 469 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N GLY C 469 " --> pdb=" O ASN C 429 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 441 through 442 Processing sheet with id=AC4, first strand: chain 'D' and resid 44 through 50 removed outlier: 3.542A pdb=" N TYR D 131 " --> pdb=" O HIS D 56 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 44 through 50 removed outlier: 3.895A pdb=" N HIS D 58 " --> pdb=" O GLU D 122 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N LEU D 167 " --> pdb=" O GLN D 195 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N LEU D 197 " --> pdb=" O LEU D 167 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N LEU D 169 " --> pdb=" O LEU D 197 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N VAL D 199 " --> pdb=" O LEU D 169 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N GLY D 171 " --> pdb=" O VAL D 199 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N PHE D 434 " --> pdb=" O THR D 445 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N VAL D 431 " --> pdb=" O VAL D 422 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N VAL D 422 " --> pdb=" O VAL D 431 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLY D 433 " --> pdb=" O TRP D 420 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N GLU D 437 " --> pdb=" O GLN D 416 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N GLN D 416 " --> pdb=" O GLU D 437 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 96 through 98 Processing sheet with id=AC7, first strand: chain 'D' and resid 139 through 140 removed outlier: 6.977A pdb=" N THR D 139 " --> pdb=" O ARG D 365 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'D' and resid 289 through 292 removed outlier: 5.905A pdb=" N LEU D 290 " --> pdb=" O ARG D 320 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'E' and resid 33 through 36 Processing sheet with id=AD1, first strand: chain 'E' and resid 52 through 55 removed outlier: 6.196A pdb=" N ILE E 52 " --> pdb=" O ALA E 80 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N GLN E 82 " --> pdb=" O ILE E 52 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N GLY E 54 " --> pdb=" O GLN E 82 " (cutoff:3.500A) removed outlier: 8.637A pdb=" N TYR E 84 " --> pdb=" O GLY E 54 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N ILE E 81 " --> pdb=" O ILE E 120 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N ARG E 122 " --> pdb=" O ILE E 81 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N MET E 83 " --> pdb=" O ARG E 122 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N VAL E 119 " --> pdb=" O ILE E 182 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N VAL E 184 " --> pdb=" O VAL E 119 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N LEU E 121 " --> pdb=" O VAL E 184 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N PHE E 219 " --> pdb=" O ILE E 182 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N VAL E 184 " --> pdb=" O PHE E 219 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N THR E 221 " --> pdb=" O VAL E 184 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N LEU E 218 " --> pdb=" O TYR E 238 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N THR E 240 " --> pdb=" O LEU E 218 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N THR E 220 " --> pdb=" O THR E 240 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ASP E 242 " --> pdb=" O THR E 220 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N ASP E 222 " --> pdb=" O ASP E 242 " (cutoff:3.500A) removed outlier: 8.353A pdb=" N ALA E 239 " --> pdb=" O ILE E 266 " (cutoff:3.500A) removed outlier: 8.578A pdb=" N SER E 268 " --> pdb=" O ALA E 239 " (cutoff:3.500A) removed outlier: 8.331A pdb=" N VAL E 241 " --> pdb=" O SER E 268 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N PHE E 270 " --> pdb=" O VAL E 241 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N GLU E 269 " --> pdb=" O ASN E 305 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N TYR E 307 " --> pdb=" O GLU E 269 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N TYR E 271 " --> pdb=" O TYR E 307 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 321 through 322 removed outlier: 3.769A pdb=" N ASN E 322 " --> pdb=" O GLU E 326 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLU E 326 " --> pdb=" O ASN E 322 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'E' and resid 376 through 379 Processing sheet with id=AD4, first strand: chain 'E' and resid 382 through 385 removed outlier: 6.437A pdb=" N PHE E 553 " --> pdb=" O PHE E 383 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLY E 591 " --> pdb=" O VAL E 583 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ILE E 585 " --> pdb=" O ASN E 589 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N ASN E 589 " --> pdb=" O ILE E 585 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 399 through 401 removed outlier: 3.773A pdb=" N ARG E 444 " --> pdb=" O GLU E 480 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ALA E 445 " --> pdb=" O ILE E 456 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N ILE E 456 " --> pdb=" O ALA E 445 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N VAL E 447 " --> pdb=" O GLN E 454 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 427 through 433 removed outlier: 6.277A pdb=" N ASN E 429 " --> pdb=" O GLY E 469 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N GLY E 469 " --> pdb=" O ASN E 429 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 441 through 442 Processing sheet with id=AD8, first strand: chain 'F' and resid 44 through 50 removed outlier: 3.541A pdb=" N TYR F 131 " --> pdb=" O HIS F 56 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 44 through 50 removed outlier: 3.895A pdb=" N HIS F 58 " --> pdb=" O GLU F 122 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N LEU F 167 " --> pdb=" O GLN F 195 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N LEU F 197 " --> pdb=" O LEU F 167 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N LEU F 169 " --> pdb=" O LEU F 197 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N VAL F 199 " --> pdb=" O LEU F 169 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N GLY F 171 " --> pdb=" O VAL F 199 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N PHE F 434 " --> pdb=" O THR F 445 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N VAL F 431 " --> pdb=" O VAL F 422 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N VAL F 422 " --> pdb=" O VAL F 431 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLY F 433 " --> pdb=" O TRP F 420 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N GLU F 437 " --> pdb=" O GLN F 416 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N GLN F 416 " --> pdb=" O GLU F 437 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'F' and resid 96 through 98 Processing sheet with id=AE2, first strand: chain 'F' and resid 139 through 140 removed outlier: 6.978A pdb=" N THR F 139 " --> pdb=" O ARG F 365 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'F' and resid 289 through 292 removed outlier: 5.905A pdb=" N LEU F 290 " --> pdb=" O ARG F 320 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'G' and resid 33 through 36 Processing sheet with id=AE5, first strand: chain 'G' and resid 52 through 55 removed outlier: 6.196A pdb=" N ILE G 52 " --> pdb=" O ALA G 80 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N GLN G 82 " --> pdb=" O ILE G 52 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N GLY G 54 " --> pdb=" O GLN G 82 " (cutoff:3.500A) removed outlier: 8.638A pdb=" N TYR G 84 " --> pdb=" O GLY G 54 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N ILE G 81 " --> pdb=" O ILE G 120 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N ARG G 122 " --> pdb=" O ILE G 81 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N MET G 83 " --> pdb=" O ARG G 122 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N VAL G 119 " --> pdb=" O ILE G 182 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N VAL G 184 " --> pdb=" O VAL G 119 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N LEU G 121 " --> pdb=" O VAL G 184 " (cutoff:3.500A) removed outlier: 8.070A pdb=" N PHE G 219 " --> pdb=" O ILE G 182 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N VAL G 184 " --> pdb=" O PHE G 219 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N THR G 221 " --> pdb=" O VAL G 184 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N LEU G 218 " --> pdb=" O TYR G 238 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N THR G 240 " --> pdb=" O LEU G 218 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N THR G 220 " --> pdb=" O THR G 240 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ASP G 242 " --> pdb=" O THR G 220 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N ASP G 222 " --> pdb=" O ASP G 242 " (cutoff:3.500A) removed outlier: 8.352A pdb=" N ALA G 239 " --> pdb=" O ILE G 266 " (cutoff:3.500A) removed outlier: 8.577A pdb=" N SER G 268 " --> pdb=" O ALA G 239 " (cutoff:3.500A) removed outlier: 8.331A pdb=" N VAL G 241 " --> pdb=" O SER G 268 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N PHE G 270 " --> pdb=" O VAL G 241 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N GLU G 269 " --> pdb=" O ASN G 305 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N TYR G 307 " --> pdb=" O GLU G 269 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N TYR G 271 " --> pdb=" O TYR G 307 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 321 through 322 removed outlier: 3.769A pdb=" N ASN G 322 " --> pdb=" O GLU G 326 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLU G 326 " --> pdb=" O ASN G 322 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'G' and resid 376 through 379 Processing sheet with id=AE8, first strand: chain 'G' and resid 382 through 385 removed outlier: 6.437A pdb=" N PHE G 553 " --> pdb=" O PHE G 383 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLY G 591 " --> pdb=" O VAL G 583 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ILE G 585 " --> pdb=" O ASN G 589 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N ASN G 589 " --> pdb=" O ILE G 585 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'G' and resid 399 through 401 removed outlier: 3.774A pdb=" N ARG G 444 " --> pdb=" O GLU G 480 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ALA G 445 " --> pdb=" O ILE G 456 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N ILE G 456 " --> pdb=" O ALA G 445 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N VAL G 447 " --> pdb=" O GLN G 454 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'G' and resid 427 through 433 removed outlier: 6.277A pdb=" N ASN G 429 " --> pdb=" O GLY G 469 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N GLY G 469 " --> pdb=" O ASN G 429 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'G' and resid 441 through 442 Processing sheet with id=AF3, first strand: chain 'H' and resid 44 through 50 removed outlier: 3.541A pdb=" N TYR H 131 " --> pdb=" O HIS H 56 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'H' and resid 44 through 50 removed outlier: 3.895A pdb=" N HIS H 58 " --> pdb=" O GLU H 122 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N LEU H 167 " --> pdb=" O GLN H 195 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N LEU H 197 " --> pdb=" O LEU H 167 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N LEU H 169 " --> pdb=" O LEU H 197 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N VAL H 199 " --> pdb=" O LEU H 169 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N GLY H 171 " --> pdb=" O VAL H 199 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N PHE H 434 " --> pdb=" O THR H 445 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N VAL H 431 " --> pdb=" O VAL H 422 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N VAL H 422 " --> pdb=" O VAL H 431 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLY H 433 " --> pdb=" O TRP H 420 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N GLU H 437 " --> pdb=" O GLN H 416 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N GLN H 416 " --> pdb=" O GLU H 437 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'H' and resid 96 through 98 Processing sheet with id=AF6, first strand: chain 'H' and resid 139 through 140 removed outlier: 6.978A pdb=" N THR H 139 " --> pdb=" O ARG H 365 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF6 Processing sheet with id=AF7, first strand: chain 'H' and resid 289 through 292 removed outlier: 5.906A pdb=" N LEU H 290 " --> pdb=" O ARG H 320 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF7 Processing sheet with id=AF8, first strand: chain 'I' and resid 33 through 36 Processing sheet with id=AF9, first strand: chain 'I' and resid 52 through 55 removed outlier: 6.197A pdb=" N ILE I 52 " --> pdb=" O ALA I 80 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N GLN I 82 " --> pdb=" O ILE I 52 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N GLY I 54 " --> pdb=" O GLN I 82 " (cutoff:3.500A) removed outlier: 8.638A pdb=" N TYR I 84 " --> pdb=" O GLY I 54 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N ILE I 81 " --> pdb=" O ILE I 120 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N ARG I 122 " --> pdb=" O ILE I 81 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N MET I 83 " --> pdb=" O ARG I 122 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N VAL I 119 " --> pdb=" O ILE I 182 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N VAL I 184 " --> pdb=" O VAL I 119 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N LEU I 121 " --> pdb=" O VAL I 184 " (cutoff:3.500A) removed outlier: 8.070A pdb=" N PHE I 219 " --> pdb=" O ILE I 182 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N VAL I 184 " --> pdb=" O PHE I 219 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N THR I 221 " --> pdb=" O VAL I 184 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N LEU I 218 " --> pdb=" O TYR I 238 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N THR I 240 " --> pdb=" O LEU I 218 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N THR I 220 " --> pdb=" O THR I 240 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ASP I 242 " --> pdb=" O THR I 220 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N ASP I 222 " --> pdb=" O ASP I 242 " (cutoff:3.500A) removed outlier: 8.352A pdb=" N ALA I 239 " --> pdb=" O ILE I 266 " (cutoff:3.500A) removed outlier: 8.577A pdb=" N SER I 268 " --> pdb=" O ALA I 239 " (cutoff:3.500A) removed outlier: 8.331A pdb=" N VAL I 241 " --> pdb=" O SER I 268 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N PHE I 270 " --> pdb=" O VAL I 241 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N GLU I 269 " --> pdb=" O ASN I 305 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N TYR I 307 " --> pdb=" O GLU I 269 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N TYR I 271 " --> pdb=" O TYR I 307 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'I' and resid 321 through 322 removed outlier: 3.769A pdb=" N ASN I 322 " --> pdb=" O GLU I 326 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLU I 326 " --> pdb=" O ASN I 322 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG1 Processing sheet with id=AG2, first strand: chain 'I' and resid 376 through 379 Processing sheet with id=AG3, first strand: chain 'I' and resid 382 through 385 removed outlier: 6.438A pdb=" N PHE I 553 " --> pdb=" O PHE I 383 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N GLY I 591 " --> pdb=" O VAL I 583 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ILE I 585 " --> pdb=" O ASN I 589 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N ASN I 589 " --> pdb=" O ILE I 585 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'I' and resid 399 through 401 removed outlier: 3.773A pdb=" N ARG I 444 " --> pdb=" O GLU I 480 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ALA I 445 " --> pdb=" O ILE I 456 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N ILE I 456 " --> pdb=" O ALA I 445 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N VAL I 447 " --> pdb=" O GLN I 454 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'I' and resid 427 through 433 removed outlier: 6.278A pdb=" N ASN I 429 " --> pdb=" O GLY I 469 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N GLY I 469 " --> pdb=" O ASN I 429 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'I' and resid 441 through 442 Processing sheet with id=AG7, first strand: chain 'J' and resid 44 through 50 removed outlier: 3.541A pdb=" N TYR J 131 " --> pdb=" O HIS J 56 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'J' and resid 44 through 50 removed outlier: 3.895A pdb=" N HIS J 58 " --> pdb=" O GLU J 122 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N LEU J 167 " --> pdb=" O GLN J 195 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N LEU J 197 " --> pdb=" O LEU J 167 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N LEU J 169 " --> pdb=" O LEU J 197 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N VAL J 199 " --> pdb=" O LEU J 169 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N GLY J 171 " --> pdb=" O VAL J 199 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N PHE J 434 " --> pdb=" O THR J 445 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N VAL J 431 " --> pdb=" O VAL J 422 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N VAL J 422 " --> pdb=" O VAL J 431 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLY J 433 " --> pdb=" O TRP J 420 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N GLU J 437 " --> pdb=" O GLN J 416 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N GLN J 416 " --> pdb=" O GLU J 437 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'J' and resid 96 through 98 Processing sheet with id=AH1, first strand: chain 'J' and resid 139 through 140 removed outlier: 6.978A pdb=" N THR J 139 " --> pdb=" O ARG J 365 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH1 Processing sheet with id=AH2, first strand: chain 'J' and resid 289 through 292 removed outlier: 5.906A pdb=" N LEU J 290 " --> pdb=" O ARG J 320 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH2 Processing sheet with id=AH3, first strand: chain 'K' and resid 33 through 36 Processing sheet with id=AH4, first strand: chain 'K' and resid 52 through 55 removed outlier: 6.196A pdb=" N ILE K 52 " --> pdb=" O ALA K 80 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N GLN K 82 " --> pdb=" O ILE K 52 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N GLY K 54 " --> pdb=" O GLN K 82 " (cutoff:3.500A) removed outlier: 8.638A pdb=" N TYR K 84 " --> pdb=" O GLY K 54 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N ILE K 81 " --> pdb=" O ILE K 120 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N ARG K 122 " --> pdb=" O ILE K 81 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N MET K 83 " --> pdb=" O ARG K 122 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N VAL K 119 " --> pdb=" O ILE K 182 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N VAL K 184 " --> pdb=" O VAL K 119 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N LEU K 121 " --> pdb=" O VAL K 184 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N PHE K 219 " --> pdb=" O ILE K 182 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N VAL K 184 " --> pdb=" O PHE K 219 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N THR K 221 " --> pdb=" O VAL K 184 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N LEU K 218 " --> pdb=" O TYR K 238 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N THR K 240 " --> pdb=" O LEU K 218 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N THR K 220 " --> pdb=" O THR K 240 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ASP K 242 " --> pdb=" O THR K 220 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N ASP K 222 " --> pdb=" O ASP K 242 " (cutoff:3.500A) removed outlier: 8.352A pdb=" N ALA K 239 " --> pdb=" O ILE K 266 " (cutoff:3.500A) removed outlier: 8.578A pdb=" N SER K 268 " --> pdb=" O ALA K 239 " (cutoff:3.500A) removed outlier: 8.331A pdb=" N VAL K 241 " --> pdb=" O SER K 268 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N PHE K 270 " --> pdb=" O VAL K 241 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N GLU K 269 " --> pdb=" O ASN K 305 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N TYR K 307 " --> pdb=" O GLU K 269 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N TYR K 271 " --> pdb=" O TYR K 307 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'K' and resid 321 through 322 removed outlier: 3.769A pdb=" N ASN K 322 " --> pdb=" O GLU K 326 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLU K 326 " --> pdb=" O ASN K 322 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH5 Processing sheet with id=AH6, first strand: chain 'K' and resid 376 through 379 Processing sheet with id=AH7, first strand: chain 'K' and resid 382 through 385 removed outlier: 6.438A pdb=" N PHE K 553 " --> pdb=" O PHE K 383 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLY K 591 " --> pdb=" O VAL K 583 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ILE K 585 " --> pdb=" O ASN K 589 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N ASN K 589 " --> pdb=" O ILE K 585 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'K' and resid 399 through 401 removed outlier: 3.773A pdb=" N ARG K 444 " --> pdb=" O GLU K 480 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ALA K 445 " --> pdb=" O ILE K 456 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N ILE K 456 " --> pdb=" O ALA K 445 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N VAL K 447 " --> pdb=" O GLN K 454 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'K' and resid 427 through 433 removed outlier: 6.277A pdb=" N ASN K 429 " --> pdb=" O GLY K 469 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N GLY K 469 " --> pdb=" O ASN K 429 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'K' and resid 441 through 442 Processing sheet with id=AI2, first strand: chain 'L' and resid 44 through 50 removed outlier: 3.542A pdb=" N TYR L 131 " --> pdb=" O HIS L 56 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'L' and resid 44 through 50 removed outlier: 3.895A pdb=" N HIS L 58 " --> pdb=" O GLU L 122 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N LEU L 167 " --> pdb=" O GLN L 195 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N LEU L 197 " --> pdb=" O LEU L 167 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N LEU L 169 " --> pdb=" O LEU L 197 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N VAL L 199 " --> pdb=" O LEU L 169 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N GLY L 171 " --> pdb=" O VAL L 199 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N PHE L 434 " --> pdb=" O THR L 445 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N VAL L 431 " --> pdb=" O VAL L 422 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N VAL L 422 " --> pdb=" O VAL L 431 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLY L 433 " --> pdb=" O TRP L 420 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N GLU L 437 " --> pdb=" O GLN L 416 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N GLN L 416 " --> pdb=" O GLU L 437 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'L' and resid 96 through 98 Processing sheet with id=AI5, first strand: chain 'L' and resid 139 through 140 removed outlier: 6.978A pdb=" N THR L 139 " --> pdb=" O ARG L 365 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI5 Processing sheet with id=AI6, first strand: chain 'L' and resid 289 through 292 removed outlier: 5.906A pdb=" N LEU L 290 " --> pdb=" O ARG L 320 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI6 1842 hydrogen bonds defined for protein. 4950 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: 21.80 Time building geometry restraints manager: 12.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 16349 1.35 - 1.47: 13837 1.47 - 1.59: 22608 1.59 - 1.71: 0 1.71 - 1.83: 390 Bond restraints: 53184 Sorted by residual: bond pdb=" C1 NAG F 501 " pdb=" O5 NAG F 501 " ideal model delta sigma weight residual 1.406 1.442 -0.036 2.00e-02 2.50e+03 3.19e+00 bond pdb=" C1 NAG B 501 " pdb=" O5 NAG B 501 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.15e+00 bond pdb=" C1 NAG J 501 " pdb=" O5 NAG J 501 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.14e+00 bond pdb=" C1 NAG D 501 " pdb=" O5 NAG D 501 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.12e+00 bond pdb=" C1 NAG L 501 " pdb=" O5 NAG L 501 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.11e+00 ... (remaining 53179 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.79: 68633 1.79 - 3.57: 3265 3.57 - 5.36: 438 5.36 - 7.15: 60 7.15 - 8.93: 24 Bond angle restraints: 72420 Sorted by residual: angle pdb=" C ALA I 316 " pdb=" N TYR I 317 " pdb=" CA TYR I 317 " ideal model delta sigma weight residual 122.49 115.02 7.47 1.57e+00 4.06e-01 2.27e+01 angle pdb=" C ALA A 316 " pdb=" N TYR A 317 " pdb=" CA TYR A 317 " ideal model delta sigma weight residual 122.49 115.05 7.44 1.57e+00 4.06e-01 2.25e+01 angle pdb=" C ALA E 316 " pdb=" N TYR E 317 " pdb=" CA TYR E 317 " ideal model delta sigma weight residual 122.49 115.06 7.43 1.57e+00 4.06e-01 2.24e+01 angle pdb=" C ALA K 316 " pdb=" N TYR K 317 " pdb=" CA TYR K 317 " ideal model delta sigma weight residual 122.49 115.06 7.43 1.57e+00 4.06e-01 2.24e+01 angle pdb=" C ALA C 316 " pdb=" N TYR C 317 " pdb=" CA TYR C 317 " ideal model delta sigma weight residual 122.49 115.06 7.43 1.57e+00 4.06e-01 2.24e+01 ... (remaining 72415 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.30: 30631 21.30 - 42.61: 1349 42.61 - 63.91: 252 63.91 - 85.22: 90 85.22 - 106.52: 36 Dihedral angle restraints: 32358 sinusoidal: 13998 harmonic: 18360 Sorted by residual: dihedral pdb=" CA PRO G 432 " pdb=" C PRO G 432 " pdb=" N ILE G 433 " pdb=" CA ILE G 433 " ideal model delta harmonic sigma weight residual 180.00 156.42 23.58 0 5.00e+00 4.00e-02 2.22e+01 dihedral pdb=" CA PRO E 432 " pdb=" C PRO E 432 " pdb=" N ILE E 433 " pdb=" CA ILE E 433 " ideal model delta harmonic sigma weight residual 180.00 156.44 23.56 0 5.00e+00 4.00e-02 2.22e+01 dihedral pdb=" CA PRO K 432 " pdb=" C PRO K 432 " pdb=" N ILE K 433 " pdb=" CA ILE K 433 " ideal model delta harmonic sigma weight residual 180.00 156.44 23.56 0 5.00e+00 4.00e-02 2.22e+01 ... (remaining 32355 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 6046 0.054 - 0.108: 1566 0.108 - 0.162: 259 0.162 - 0.215: 19 0.215 - 0.269: 12 Chirality restraints: 7902 Sorted by residual: chirality pdb=" C5 BMA R 3 " pdb=" C4 BMA R 3 " pdb=" C6 BMA R 3 " pdb=" O5 BMA R 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" C5 BMA O 3 " pdb=" C4 BMA O 3 " pdb=" C6 BMA O 3 " pdb=" O5 BMA O 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" C5 BMA X 3 " pdb=" C4 BMA X 3 " pdb=" C6 BMA X 3 " pdb=" O5 BMA X 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.80e+00 ... (remaining 7899 not shown) Planarity restraints: 9360 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL F 184 " -0.019 2.00e-02 2.50e+03 3.73e-02 1.39e+01 pdb=" C VAL F 184 " 0.065 2.00e-02 2.50e+03 pdb=" O VAL F 184 " -0.024 2.00e-02 2.50e+03 pdb=" N LEU F 185 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL L 184 " -0.019 2.00e-02 2.50e+03 3.70e-02 1.37e+01 pdb=" C VAL L 184 " 0.064 2.00e-02 2.50e+03 pdb=" O VAL L 184 " -0.024 2.00e-02 2.50e+03 pdb=" N LEU L 185 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL H 184 " 0.019 2.00e-02 2.50e+03 3.70e-02 1.37e+01 pdb=" C VAL H 184 " -0.064 2.00e-02 2.50e+03 pdb=" O VAL H 184 " 0.024 2.00e-02 2.50e+03 pdb=" N LEU H 185 " 0.021 2.00e-02 2.50e+03 ... (remaining 9357 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 1283 2.67 - 3.23: 51622 3.23 - 3.78: 85706 3.78 - 4.34: 117673 4.34 - 4.90: 185560 Nonbonded interactions: 441844 Sorted by model distance: nonbonded pdb=" O ILE L 261 " pdb=" OG SER L 265 " model vdw 2.109 3.040 nonbonded pdb=" O ILE D 261 " pdb=" OG SER D 265 " model vdw 2.109 3.040 nonbonded pdb=" O ILE H 261 " pdb=" OG SER H 265 " model vdw 2.110 3.040 nonbonded pdb=" O ILE F 261 " pdb=" OG SER F 265 " model vdw 2.110 3.040 nonbonded pdb=" O ILE B 261 " pdb=" OG SER B 265 " model vdw 2.110 3.040 ... (remaining 441839 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: 0.13 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'P' selection = chain 'Q' selection = chain 'S' selection = chain 'T' selection = chain 'V' selection = chain 'W' selection = chain 'Y' selection = chain 'Z' selection = chain 'b' selection = chain 'c' } ncs_group { reference = chain 'O' selection = chain 'R' selection = chain 'U' selection = chain 'X' selection = chain 'a' selection = chain 'd' } Set up NCS constraints Number of NCS constrained groups: 4 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' } pdb_interpretation.ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' } pdb_interpretation.ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'P' selection = chain 'Q' selection = chain 'S' selection = chain 'T' selection = chain 'V' selection = chain 'W' selection = chain 'Y' selection = chain 'Z' selection = chain 'b' selection = chain 'c' } pdb_interpretation.ncs_group { reference = chain 'O' selection = chain 'R' selection = chain 'U' selection = chain 'X' selection = chain 'a' selection = chain 'd' } Set refine NCS operators NCS operators will be refined. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 1.680 Check model and map are aligned: 0.310 Set scattering table: 0.380 Process input model: 95.280 Find NCS groups from input model: 2.320 Set up NCS constraints: 0.280 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.020 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 104.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 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 0.046 53184 Z= 0.304 Angle : 0.849 8.933 72420 Z= 0.467 Chirality : 0.050 0.269 7902 Planarity : 0.007 0.062 9312 Dihedral : 13.451 106.520 20550 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.38 % Allowed : 5.45 % Favored : 94.17 % Rotamer: Outliers : 0.98 % Allowed : 4.02 % Favored : 95.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.22 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.10), residues: 6276 helix: -0.42 (0.13), residues: 1536 sheet: -0.43 (0.14), residues: 1146 loop : -1.32 (0.10), residues: 3594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP L 420 HIS 0.004 0.001 HIS B 451 PHE 0.021 0.002 PHE D 42 TYR 0.025 0.004 TYR F 273 ARG 0.009 0.001 ARG A 484 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12552 Ramachandran restraints generated. 6276 Oldfield, 0 Emsley, 6276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12552 Ramachandran restraints generated. 6276 Oldfield, 0 Emsley, 6276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 52 time to evaluate : 0.435 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 70 LEU cc_start: 0.8985 (mt) cc_final: 0.8771 (mt) outliers start: 6 outliers final: 1 residues processed: 58 average time/residue: 0.2120 time to fit residues: 14.9242 Evaluate side-chains 31 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 30 time to evaluate : 0.441 Evaluate side-chains 68 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 65 time to evaluate : 0.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 90 LEU cc_start: 0.8660 (mt) cc_final: 0.8121 (mp) REVERT: B 371 MET cc_start: 0.8793 (mmp) cc_final: 0.7477 (mmm) REVERT: B 387 LEU cc_start: 0.8585 (tp) cc_final: 0.8296 (tp) outliers start: 3 outliers final: 0 residues processed: 67 average time/residue: 0.1906 time to fit residues: 14.9129 Evaluate side-chains 38 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 0.326 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.004 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0019 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0023 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 630 random chunks: chunk 531 optimal weight: 10.0000 chunk 477 optimal weight: 0.0670 chunk 264 optimal weight: 0.6980 chunk 163 optimal weight: 0.8980 chunk 322 optimal weight: 0.9990 chunk 255 optimal weight: 0.0970 chunk 493 optimal weight: 0.1980 chunk 191 optimal weight: 0.0870 chunk 300 optimal weight: 0.9990 chunk 367 optimal weight: 0.0470 chunk 572 optimal weight: 0.9990 overall best weight: 0.0992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 82 GLN E 188 ASN Total number of N/Q/H flips: 2 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 147 ASN L 297 ASN Total number of N/Q/H flips: 2 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2672 r_free = 0.2672 target = 0.025400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2409 r_free = 0.2409 target = 0.019060 restraints weight = 68718.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2442 r_free = 0.2442 target = 0.019897 restraints weight = 44861.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2465 r_free = 0.2465 target = 0.020512 restraints weight = 32782.779| |-----------------------------------------------------------------------------| r_work (final): 0.2485 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.033765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2632 r_free = 0.2632 target = 0.024645 restraints weight = 46679.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.2658 r_free = 0.2658 target = 0.025375 restraints weight = 34568.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2677 r_free = 0.2677 target = 0.025920 restraints weight = 27509.532| |-----------------------------------------------------------------------------| r_work (final): 0.2636 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2483 r_free = 0.2483 target = 0.043638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2486 r_free = 0.2486 target = 0.042331 restraints weight = 372.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2480 r_free = 0.2480 target = 0.042680 restraints weight = 104.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2479 r_free = 0.2479 target = 0.042975 restraints weight = 53.565| |-----------------------------------------------------------------------------| r_work (final): 0.2471 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2565 r_free = 0.2565 target = 0.040488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2599 r_free = 0.2599 target = 0.039289 restraints weight = 909.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2579 r_free = 0.2579 target = 0.039754 restraints weight = 397.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2572 r_free = 0.2572 target = 0.039896 restraints weight = 253.960| |-----------------------------------------------------------------------------| r_work (final): 0.2556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8719 moved from start: 0.2139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 53184 Z= 0.213 Angle : 0.680 8.869 72420 Z= 0.348 Chirality : 0.044 0.171 7902 Planarity : 0.005 0.047 9312 Dihedral : 8.004 72.723 8448 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.22 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.10), residues: 6276 helix: 1.22 (0.14), residues: 1596 sheet: -0.33 (0.14), residues: 1110 loop : -0.96 (0.10), residues: 3570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 139 HIS 0.004 0.001 HIS C 277 PHE 0.027 0.002 PHE F 405 TYR 0.023 0.002 TYR I 307 ARG 0.007 0.001 ARG G 444 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11360 Ramachandran restraints generated. 5680 Oldfield, 0 Emsley, 5680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11360 Ramachandran restraints generated. 5680 Oldfield, 0 Emsley, 5680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 70 LEU cc_start: 0.9749 (mt) cc_final: 0.9522 (mt) REVERT: E 308 MET cc_start: 0.9209 (mmp) cc_final: 0.8361 (mmm) REVERT: E 521 MET cc_start: 0.9567 (tmm) cc_final: 0.9127 (ppp) REVERT: E 597 MET cc_start: 0.9756 (tpt) cc_final: 0.9484 (tpp) outliers start: 0 outliers final: 0 residues processed: 40 average time/residue: 0.1883 time to fit residues: 9.6648 Evaluate side-chains 29 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.434 Evaluate side-chains 48 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.326 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 86 LEU cc_start: 0.9717 (mt) cc_final: 0.9477 (mt) REVERT: L 192 MET cc_start: 0.7286 (ptp) cc_final: 0.6538 (ptp) REVERT: L 272 LEU cc_start: 0.8867 (mp) cc_final: 0.8587 (mp) REVERT: L 413 MET cc_start: 0.7651 (mmp) cc_final: 0.7049 (tpp) outliers start: 0 outliers final: 0 residues processed: 48 average time/residue: 0.2063 time to fit residues: 11.5755 Evaluate side-chains 29 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.324 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.003 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0021 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.004 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0024 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 630 random chunks: chunk 452 optimal weight: 9.9990 chunk 147 optimal weight: 0.0050 chunk 595 optimal weight: 2.9990 chunk 472 optimal weight: 0.9980 chunk 250 optimal weight: 6.9990 chunk 565 optimal weight: 7.9990 chunk 356 optimal weight: 2.9990 chunk 562 optimal weight: 0.0470 chunk 299 optimal weight: 2.9990 chunk 607 optimal weight: 0.1980 chunk 168 optimal weight: 20.0000 overall best weight: 0.8494 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN A 356 GLN Total number of N/Q/H flips: 2 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 147 ASN Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2621 r_free = 0.2621 target = 0.024968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2355 r_free = 0.2355 target = 0.018779 restraints weight = 69001.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2389 r_free = 0.2389 target = 0.019625 restraints weight = 44889.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2417 r_free = 0.2417 target = 0.020254 restraints weight = 32516.893| |-----------------------------------------------------------------------------| r_work (final): 0.2381 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.032991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2673 r_free = 0.2673 target = 0.024775 restraints weight = 48824.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 19)----------------| | r_work = 0.2697 r_free = 0.2697 target = 0.025512 restraints weight = 35574.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2718 r_free = 0.2718 target = 0.026094 restraints weight = 27961.449| |-----------------------------------------------------------------------------| r_work (final): 0.2649 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2699 r_free = 0.2699 target = 0.046591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2617 r_free = 0.2617 target = 0.040540 restraints weight = 245.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2620 r_free = 0.2620 target = 0.040907 restraints weight = 216.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2621 r_free = 0.2621 target = 0.041117 restraints weight = 196.245| |-----------------------------------------------------------------------------| r_work (final): 0.2549 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2490 r_free = 0.2490 target = 0.037522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2479 r_free = 0.2479 target = 0.035127 restraints weight = 968.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2483 r_free = 0.2483 target = 0.035561 restraints weight = 466.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2482 r_free = 0.2482 target = 0.035932 restraints weight = 379.218| |-----------------------------------------------------------------------------| r_work (final): 0.2464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8698 moved from start: 0.2666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 53184 Z= 0.202 Angle : 0.670 9.339 72420 Z= 0.339 Chirality : 0.045 0.235 7902 Planarity : 0.006 0.085 9312 Dihedral : 7.305 61.928 8448 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.22 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.10), residues: 6276 helix: 1.16 (0.13), residues: 1620 sheet: -0.42 (0.14), residues: 1086 loop : -0.97 (0.10), residues: 3570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C 87 HIS 0.021 0.002 HIS K 211 PHE 0.036 0.002 PHE K 315 TYR 0.034 0.003 TYR E 200 ARG 0.015 0.001 ARG C 207 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10460 Ramachandran restraints generated. 5230 Oldfield, 0 Emsley, 5230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10460 Ramachandran restraints generated. 5230 Oldfield, 0 Emsley, 5230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 308 MET cc_start: 0.9376 (mmp) cc_final: 0.8602 (mmm) REVERT: A 521 MET cc_start: 0.9550 (tmm) cc_final: 0.9115 (ppp) REVERT: A 597 MET cc_start: 0.9770 (tpt) cc_final: 0.9488 (tpp) outliers start: 0 outliers final: 0 residues processed: 31 average time/residue: 0.1846 time to fit residues: 7.4863 Evaluate side-chains 24 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.436 Evaluate side-chains 37 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 37 time to evaluate : 0.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 87 ASP cc_start: 0.9513 (t0) cc_final: 0.9231 (t0) REVERT: B 413 MET cc_start: 0.7605 (mmp) cc_final: 0.6849 (tpp) outliers start: 0 outliers final: 0 residues processed: 37 average time/residue: 0.1619 time to fit residues: 7.3921 Evaluate side-chains 28 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.328 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0017 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0023 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 630 random chunks: chunk 172 optimal weight: 0.8980 chunk 511 optimal weight: 7.9990 chunk 72 optimal weight: 40.0000 chunk 184 optimal weight: 0.0670 chunk 274 optimal weight: 9.9990 chunk 81 optimal weight: 10.0000 chunk 225 optimal weight: 30.0000 chunk 60 optimal weight: 20.0000 chunk 90 optimal weight: 0.8980 chunk 521 optimal weight: 6.9990 chunk 485 optimal weight: 0.6980 overall best weight: 1.9120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN ** A 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 147 ASN ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 369 GLN Total number of N/Q/H flips: 2 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2612 r_free = 0.2612 target = 0.024640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2344 r_free = 0.2344 target = 0.018522 restraints weight = 69923.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2380 r_free = 0.2380 target = 0.019332 restraints weight = 45754.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 18)----------------| | r_work = 0.2406 r_free = 0.2406 target = 0.019947 restraints weight = 33448.421| |-----------------------------------------------------------------------------| r_work (final): 0.2382 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.032522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2614 r_free = 0.2614 target = 0.023926 restraints weight = 48367.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 16)----------------| | r_work = 0.2639 r_free = 0.2639 target = 0.024721 restraints weight = 35222.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 16)----------------| | r_work = 0.2660 r_free = 0.2660 target = 0.025311 restraints weight = 27712.661| |-----------------------------------------------------------------------------| r_work (final): 0.2629 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2713 r_free = 0.2713 target = 0.046861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2615 r_free = 0.2615 target = 0.039883 restraints weight = 350.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2616 r_free = 0.2616 target = 0.040380 restraints weight = 274.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2624 r_free = 0.2624 target = 0.040921 restraints weight = 234.198| |-----------------------------------------------------------------------------| r_work (final): 0.2547 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2492 r_free = 0.2492 target = 0.037533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2492 r_free = 0.2492 target = 0.035018 restraints weight = 982.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2494 r_free = 0.2494 target = 0.035496 restraints weight = 465.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2492 r_free = 0.2492 target = 0.035850 restraints weight = 375.270| |-----------------------------------------------------------------------------| r_work (final): 0.2465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 moved from start: 0.2837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.162 53184 Z= 0.325 Angle : 0.777 28.743 72420 Z= 0.381 Chirality : 0.045 0.252 7902 Planarity : 0.007 0.105 9312 Dihedral : 7.238 60.635 8448 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 15.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.22 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.10), residues: 6276 helix: 1.06 (0.13), residues: 1620 sheet: -0.42 (0.14), residues: 1086 loop : -1.00 (0.10), residues: 3570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C 87 HIS 0.020 0.002 HIS C 211 PHE 0.025 0.003 PHE C 99 TYR 0.036 0.003 TYR I 200 ARG 0.015 0.001 ARG I 459 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10460 Ramachandran restraints generated. 5230 Oldfield, 0 Emsley, 5230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10460 Ramachandran restraints generated. 5230 Oldfield, 0 Emsley, 5230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 308 MET cc_start: 0.9382 (mmp) cc_final: 0.8900 (mmm) REVERT: A 521 MET cc_start: 0.9548 (tmm) cc_final: 0.9115 (ppp) REVERT: A 597 MET cc_start: 0.9777 (tpt) cc_final: 0.9502 (tpp) outliers start: 0 outliers final: 0 residues processed: 30 average time/residue: 0.1458 time to fit residues: 6.0729 Evaluate side-chains 27 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.436 Evaluate side-chains 36 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.326 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 87 ASP cc_start: 0.9479 (t0) cc_final: 0.9126 (t0) REVERT: B 339 TYR cc_start: 0.9889 (m-80) cc_final: 0.9640 (m-80) REVERT: B 413 MET cc_start: 0.7759 (mmp) cc_final: 0.7100 (tpp) outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.1757 time to fit residues: 7.7138 Evaluate side-chains 28 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.327 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0017 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0024 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 704, in refine_xyz self.minimization_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 801, in minimization_ncs ncs_groups = ncs_groups) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 400, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 133, in refine refine_sites = True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 434, in __init__ ignore_line_search_failed_maxfev=True)) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 459, in compute_functional_and_gradients x=self.x) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 248, in target_and_gradients grad = g_data) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 112, in restraints_target_and_grads compute_gradients = True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 70.9837 > 50: distance: 0 - 1: 5.077 distance: 1 - 2: 33.704 distance: 1 - 4: 15.984 distance: 2 - 3: 57.560 distance: 2 - 12: 56.161 distance: 4 - 5: 26.978 distance: 5 - 6: 44.706 distance: 6 - 8: 6.185 distance: 7 - 9: 17.015 distance: 8 - 10: 18.085 distance: 9 - 10: 18.003 distance: 10 - 11: 55.886 distance: 13 - 14: 24.812 distance: 13 - 16: 7.667 distance: 14 - 15: 24.435 distance: 14 - 23: 15.490 distance: 16 - 17: 39.238 distance: 18 - 20: 21.980 distance: 20 - 22: 19.852 distance: 23 - 24: 44.506 distance: 24 - 25: 11.313 distance: 25 - 26: 50.358 distance: 25 - 27: 38.388 distance: 27 - 28: 18.704 distance: 28 - 29: 37.712 distance: 29 - 30: 16.978 distance: 29 - 39: 50.404 distance: 32 - 33: 36.817 distance: 33 - 35: 34.790 distance: 35 - 37: 28.625 distance: 36 - 37: 28.282 distance: 37 - 38: 44.474 distance: 39 - 40: 42.034 distance: 40 - 41: 41.889 distance: 40 - 43: 13.015 distance: 41 - 42: 42.577 distance: 41 - 46: 12.387 distance: 43 - 44: 39.112 distance: 43 - 45: 41.197 distance: 46 - 47: 35.534 distance: 47 - 48: 45.963 distance: 47 - 50: 34.296 distance: 48 - 49: 38.874 distance: 48 - 54: 40.132 distance: 50 - 51: 43.434 distance: 51 - 52: 12.386 distance: 51 - 53: 19.144 distance: 54 - 55: 57.274 distance: 55 - 58: 58.458 distance: 56 - 57: 39.139 distance: 56 - 66: 56.972 distance: 58 - 59: 18.056 distance: 59 - 60: 52.380 distance: 60 - 62: 35.549 distance: 61 - 63: 50.806 distance: 62 - 64: 61.995 distance: 63 - 64: 50.551 distance: 64 - 65: 40.337 distance: 66 - 67: 41.041 distance: 67 - 68: 40.424 distance: 67 - 70: 41.202 distance: 68 - 77: 40.255 distance: 70 - 71: 46.389 distance: 71 - 72: 42.174 distance: 72 - 73: 40.176 distance: 74 - 75: 56.882 distance: 74 - 76: 56.646 distance: 77 - 78: 55.268 distance: 78 - 79: 23.631 distance: 78 - 81: 10.342 distance: 79 - 80: 39.125 distance: 79 - 84: 39.944 distance: 81 - 82: 10.551 distance: 81 - 83: 11.539 distance: 84 - 85: 15.777 distance: 85 - 86: 15.480 distance: 85 - 88: 30.169 distance: 86 - 87: 40.900 distance: 86 - 91: 46.739 distance: 88 - 89: 19.978 distance: 88 - 90: 20.771 distance: 91 - 92: 37.038