Starting phenix.real_space_refine on Tue Nov 19 08:57:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kdv_22830/11_2024/7kdv_22830.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kdv_22830/11_2024/7kdv_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kdv_22830/11_2024/7kdv_22830.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kdv_22830/11_2024/7kdv_22830.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kdv_22830/11_2024/7kdv_22830.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kdv_22830/11_2024/7kdv_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): 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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: 28.29, per 1000 atoms: 0.55 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: 13.32 Conformation dependent library (CDL) restraints added in 6.4 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: 6.96 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: 23.89 Time building geometry restraints manager: 15.48 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: 0.00 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.730 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: 0.070 Extract box with map and model: 2.130 Check model and map are aligned: 0.360 Set scattering table: 0.460 Process input model: 111.380 Find NCS groups from input model: 2.680 Set up NCS constraints: 0.350 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:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 121.810 ------------------------------------------------------------------------------- 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 : 0.577 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: 0.2633 time to fit residues: 18.6514 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 : 0.590 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 : 0.419 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: 0.2370 time to fit residues: 18.5718 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 : 0.448 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 : 0.005 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 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: 0.0027 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 ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 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 : 0.538 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: 0.8926 (mt) cc_final: 0.8651 (mt) REVERT: E 308 MET cc_start: 0.7883 (mmp) cc_final: 0.7276 (mmm) outliers start: 0 outliers final: 0 residues processed: 40 average time/residue: 0.2201 time to fit residues: 11.2756 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 : 0.551 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 : 0.420 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 87 ASP cc_start: 0.8505 (t0) cc_final: 0.8278 (t0) REVERT: L 371 MET cc_start: 0.8669 (mmp) cc_final: 0.8259 (mmm) outliers start: 0 outliers final: 0 residues processed: 48 average time/residue: 0.2532 time to fit residues: 14.2878 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 : 0.405 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 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: 0.0035 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 317 optimal weight: 5.9990 chunk 177 optimal weight: 10.0000 chunk 476 optimal weight: 3.9990 chunk 389 optimal weight: 0.0370 chunk 157 optimal weight: 5.9990 chunk 573 optimal weight: 0.0870 chunk 619 optimal weight: 5.9990 chunk 510 optimal weight: 0.2980 chunk 568 optimal weight: 8.9990 chunk 195 optimal weight: 2.9990 chunk 459 optimal weight: 0.6980 overall best weight: 0.8238 ------------------------------------------------------------------------------- NQH flips ********* 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... Flipped N/Q/H residues before XYZ refinement: ** L 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 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 ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.2625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 53184 Z= 0.227 Angle : 0.708 9.407 72420 Z= 0.356 Chirality : 0.046 0.276 7902 Planarity : 0.008 0.166 9312 Dihedral : 7.519 64.976 8448 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % 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: -0.51 (0.10), residues: 6276 helix: 1.10 (0.13), residues: 1614 sheet: -0.39 (0.14), residues: 1062 loop : -1.01 (0.10), residues: 3600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP A 87 HIS 0.022 0.002 HIS K 211 PHE 0.027 0.003 PHE E 315 TYR 0.036 0.003 TYR E 200 ARG 0.015 0.001 ARG A 207 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10168 Ramachandran restraints generated. 5084 Oldfield, 0 Emsley, 5084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10168 Ramachandran restraints generated. 5084 Oldfield, 0 Emsley, 5084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 70 LEU cc_start: 0.8975 (mt) cc_final: 0.8734 (mt) REVERT: I 308 MET cc_start: 0.7515 (mmp) cc_final: 0.6976 (mmm) outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.2233 time to fit residues: 9.6584 Evaluate side-chains 25 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.589 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 : 0.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 67 ASP cc_start: 0.8385 (m-30) cc_final: 0.8183 (m-30) REVERT: L 87 ASP cc_start: 0.8488 (t0) cc_final: 0.8265 (t0) REVERT: L 371 MET cc_start: 0.8687 (mmp) cc_final: 0.8214 (mmm) REVERT: L 413 MET cc_start: 0.5952 (tpp) cc_final: 0.5676 (tpp) outliers start: 0 outliers final: 0 residues processed: 38 average time/residue: 0.2116 time to fit residues: 9.8329 Evaluate side-chains 25 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.388 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: 0.0022 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: 0.0030 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 566 optimal weight: 0.4980 chunk 430 optimal weight: 0.4980 chunk 297 optimal weight: 30.0000 chunk 63 optimal weight: 20.0000 chunk 273 optimal weight: 8.9990 chunk 384 optimal weight: 10.0000 chunk 575 optimal weight: 0.6980 chunk 608 optimal weight: 8.9990 chunk 300 optimal weight: 0.4980 chunk 545 optimal weight: 8.9990 chunk 164 optimal weight: 0.0070 overall best weight: 0.4398 ------------------------------------------------------------------------------- NQH flips ********* 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... Flipped N/Q/H residues before XYZ refinement: ** L 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 147 ASN ** L 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.2791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.162 53184 Z= 0.266 Angle : 0.708 9.407 72420 Z= 0.356 Chirality : 0.046 0.276 7902 Planarity : 0.008 0.166 9312 Dihedral : 7.519 64.976 8448 Min Nonbonded Distance : 1.120 Molprobity Statistics. All-atom Clashscore : 24.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -0.51 (0.10), residues: 6276 helix: 1.10 (0.13), residues: 1614 sheet: -0.39 (0.14), residues: 1062 loop : -1.01 (0.10), residues: 3600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP E 87 HIS 0.022 0.002 HIS K 211 PHE 0.027 0.003 PHE I 315 TYR 0.036 0.003 TYR C 200 ARG 0.015 0.001 ARG C 207 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10168 Ramachandran restraints generated. 5084 Oldfield, 0 Emsley, 5084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10168 Ramachandran restraints generated. 5084 Oldfield, 0 Emsley, 5084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 73 MET cc_start: 0.7805 (mtm) cc_final: 0.7285 (mtp) REVERT: E 306 LEU cc_start: 0.7936 (mt) cc_final: 0.7716 (mt) REVERT: E 308 MET cc_start: 0.7783 (mmp) cc_final: 0.7274 (mmm) outliers start: 0 outliers final: 0 residues processed: 28 average time/residue: 0.1721 time to fit residues: 6.8714 Evaluate side-chains 23 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.495 Evaluate side-chains 34 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 371 MET cc_start: 0.8688 (mmp) cc_final: 0.8215 (mmm) REVERT: L 413 MET cc_start: 0.6270 (tpp) cc_final: 0.5678 (tpp) outliers start: 0 outliers final: 0 residues processed: 34 average time/residue: 0.2100 time to fit residues: 8.8473 Evaluate side-chains 25 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.463 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 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 : 0.007 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0030 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-5513/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-5513/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/phenix/phenix/programs/real_space_refine.py", line 213, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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-5513/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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-5513/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 800, in minimization_ncs ncs_groups = ncs_groups) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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-5513/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-5513/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-5513/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-5513/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-5513/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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-5513/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-5513/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-5513/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-5513/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-5513/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-5513/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: 71.6783 > 50: distance: 0 - 1: 40.247 distance: 1 - 2: 28.879 distance: 1 - 4: 20.980 distance: 2 - 3: 19.084 distance: 2 - 11: 47.243 distance: 3 - 36: 28.757 distance: 4 - 5: 19.772 distance: 5 - 6: 14.976 distance: 5 - 7: 24.564 distance: 6 - 8: 17.171 distance: 7 - 9: 13.804 distance: 8 - 10: 32.534 distance: 9 - 10: 21.013 distance: 11 - 12: 56.050 distance: 12 - 13: 43.333 distance: 12 - 15: 44.682 distance: 13 - 14: 41.025 distance: 13 - 19: 47.613 distance: 14 - 41: 26.706 distance: 15 - 16: 44.004 distance: 15 - 17: 43.381 distance: 16 - 18: 23.491 distance: 19 - 20: 44.558 distance: 20 - 21: 49.399 distance: 20 - 23: 45.821 distance: 21 - 22: 26.778 distance: 21 - 28: 28.583 distance: 22 - 51: 38.763 distance: 23 - 24: 69.398 distance: 24 - 25: 51.885 distance: 25 - 26: 41.720 distance: 25 - 27: 40.271 distance: 28 - 29: 39.362 distance: 29 - 30: 31.704 distance: 29 - 32: 54.067 distance: 30 - 31: 34.111 distance: 30 - 36: 69.920 distance: 31 - 60: 41.237 distance: 32 - 33: 41.352 distance: 33 - 34: 18.560 distance: 33 - 35: 27.454 distance: 36 - 37: 38.570 distance: 37 - 38: 49.126 distance: 37 - 40: 15.576 distance: 38 - 39: 39.925 distance: 38 - 41: 38.691 distance: 41 - 42: 42.689 distance: 42 - 43: 53.172 distance: 42 - 45: 20.559 distance: 43 - 44: 45.405 distance: 43 - 51: 35.006 distance: 45 - 46: 15.549 distance: 46 - 47: 8.257 distance: 46 - 48: 42.506 distance: 47 - 49: 42.179 distance: 48 - 50: 28.248 distance: 49 - 50: 43.120 distance: 51 - 52: 32.216 distance: 52 - 53: 54.213 distance: 52 - 55: 33.447 distance: 53 - 54: 12.209 distance: 53 - 60: 69.548 distance: 55 - 56: 24.168 distance: 56 - 57: 26.484 distance: 57 - 58: 17.724 distance: 57 - 59: 5.416 distance: 60 - 61: 23.602 distance: 61 - 62: 53.330 distance: 61 - 64: 23.267 distance: 62 - 63: 68.583 distance: 62 - 68: 38.703 distance: 64 - 65: 41.566 distance: 65 - 66: 52.803 distance: 65 - 67: 41.503 distance: 68 - 69: 52.161 distance: 69 - 70: 39.163 distance: 70 - 71: 44.218 distance: 70 - 72: 58.700 distance: 72 - 73: 33.435 distance: 73 - 74: 24.521 distance: 73 - 76: 34.242 distance: 74 - 75: 38.408 distance: 76 - 77: 4.651 distance: 77 - 78: 6.369